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A

abortTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStore aborts and closes the transaction, delegate to internal ObjectStoreWriter.
abortTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter aborts and closes the transaction
abortTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter aborts and closes the transaction
abortTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Aborts a transaction.
abstract_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
abstract_constraint() - Method in class org.intermine.sql.query.SqlParser
 
abstract_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
abstract_constraint_list(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
abstract_constraint_list_notand(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
abstract_constraint_list_notor(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
abstract_table() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
abstract_table() - Method in class org.intermine.sql.query.SqlParser
 
abstract_table(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
abstract_value() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
abstract_value() - Method in class org.intermine.sql.query.SqlParser
 
abstract_value(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
AbstractConstraint - Class in org.intermine.sql.query
An abstract representation of an item that can be present in the WHERE or HAVING sections of an SQL query.
AbstractConstraint() - Constructor for class org.intermine.sql.query.AbstractConstraint
 
AbstractHelper - Class in org.intermine.api.query.range
A class that can be extended to easily create RangeHelpers for a particular type.
AbstractHelper() - Constructor for class org.intermine.api.query.range.AbstractHelper
 
AbstractListService - Class in org.intermine.webservice.server.lists
Base class for list services.
AbstractListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AbstractListService
 
AbstractQueryService - Class in org.intermine.webservice.server.query
A base class for query services.
AbstractQueryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.AbstractQueryService
Constructor.
AbstractTable - Class in org.intermine.sql.query
An abstract representation of an item that can be present in the FROM section of an SQL query.
AbstractTable() - Constructor for class org.intermine.sql.query.AbstractTable
 
AbstractTableComparator() - Constructor for class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator
Constructor.
AbstractTracker - Class in org.intermine.api.tracker
Abstract interface for creating trackers objects.
AbstractTracker(Queue<Track>, String) - Constructor for class org.intermine.api.tracker.AbstractTracker
Construct a Tracker setting the tracks queue and the table name
AbstractValue - Class in org.intermine.sql.query
An abstract representation of an item that can be present in the SELECT, GROUP BY, or ORDER BY sections of an SQL query, as well as in a constraint.
AbstractValue() - Constructor for class org.intermine.sql.query.AbstractValue
 
accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either
How you go about accessing the values.
accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either.Left
 
accept(EitherVisitor<A, B, T>) - Method in class org.intermine.webservice.server.core.Either.Right
 
AcceptanceTestTask - Class in org.intermine.task
A Task to run acceptance tests, configurable from a file.
AcceptanceTestTask() - Constructor for class org.intermine.task.AcceptanceTestTask
 
acceptInvitation(SharingInvite, Profile) - Method in class org.intermine.api.bag.SharedBagManager
Accept this invitation.
act(Emailer) - Method in interface org.intermine.web.context.MailAction
Inject an emailer, and do something.
action - Variable in class org.intermine.api.search.TaggingEvent
 
ACTUAL - org.intermine.web.logic.widget.GraphWidgetActionType
 
add(E) - Method in class org.intermine.util.ConsistentSet
Add an object to the set.
add(E) - Method in class org.intermine.util.PseudoSet
add(Integer) - Method in class org.intermine.util.IntPresentSet
Adds an int to the set.
add(Object) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
Add an InlineTableResultElement or an empty String
add(String) - Method in class org.intermine.sql.precompute.BestQuery
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryFallback
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryLogger
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.BestQueryStorer
Allows a Query to be added to this tracker.
add(String) - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Allows a Query to be added to this tracker.
add(Map.Entry<K, V>, boolean) - Method in interface org.intermine.webservice.server.jbrowse.MapListener
 
add(Map<K, V>, boolean) - Method in interface org.intermine.webservice.server.jbrowse.MapListener
 
add(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Allows a Candidate to be added to this tracker.
add(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Add a precomputed table to the underlying database.
add(PrecomputedTable, Collection<String>) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Add a precomputed table to the underlying database.
add(AbstractConstraint) - Method in class org.intermine.sql.query.ConstraintSet
Add an AbstractConstraint to this ConstraintSet.
add(AbstractValue) - Method in class org.intermine.sql.query.Function
Adds an operand to this Function object.
add(Constant) - Method in class org.intermine.sql.query.InListConstraint
Add constants to the list.
add(Query) - Method in class org.intermine.sql.precompute.BestQuery
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryFallback
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryLogger
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.BestQueryStorer
Allows a Query to be added to this tracker.
add(Query) - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Allows a Query to be added to this tracker.
ADD - Static variable in class org.intermine.objectstore.query.QueryExpression
Addition of two numeric fields
ADD_HEADER_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The parameter for requesting column headers
addAll(Collection<? extends E>) - Method in class org.intermine.util.ConsistentSet
Add a whole Collection of objects to the set.
addAll(Collection<? extends E>) - Method in class org.intermine.util.PseudoSet
addAll(Collection<? extends Constant>) - Method in class org.intermine.sql.query.InListConstraint
Adds a Collection of Constants to the list.
addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Adds a collection of elements to an ObjectStoreBag, delegate to internal ObjectStoreWriter.
addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds a collection of elements to an ObjectStoreBag.
addAllToBag(ObjectStoreBag, Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Adds a collection of elements to an ObjectStoreBag.
addAllToBagWithConnection(Connection, ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds elements to the given bag.
addAnchor(String) - Method in class org.intermine.web.struts.ForwardParameters
Add an anchor to the path.
addAndConstraint(Query, Constraint) - Static method in class org.intermine.objectstore.query.QueryHelper
Add a constraint to be ANDed with those present in a Query.
addAspectSource(AspectSource) - Method in class org.intermine.web.logic.aspects.Aspect
Add a AspectSource.
addAttribute(Attribute) - Method in class org.intermine.xml.full.Item
Add an attribute.
addAttributes(Attribute) - Method in class org.intermine.model.fulldata.Item
 
addBag(ObjectStoreBag) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Adds a bag to this combination
addBagCombination(ObjectStoreBagCombination) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
 
addBagDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
Add a bag displayer for this Type
addBagValues() - Method in class org.intermine.api.profile.InterMineBag
Save the key field values associated to the bag into bagvalues table
addBagValues(Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag
Save the values given in input into bagvalues table
addBatches - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
addCacheLine(String, String, int) - Method in class org.intermine.sql.precompute.OptimiserCache
Adds a new OptimiserCacheLine object to the cache.
addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.And
Adds a node to the collection of children.
addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.Operator
Adds a node to the collection of children.
addChild(LogicExpression.Node) - Method in class org.intermine.pathquery.LogicExpression.Or
Adds a node to the collection of children.
addCollection(ReferenceList) - Method in class org.intermine.xml.full.Item
Add a collection.
addCollectionElement(Object, String, Object) - Static method in class org.intermine.metadata.TypeUtil
Adds an element to a public or protected collection of an Object given the field name.
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.PermanentToken
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.SavedBag
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.SavedQuery
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.Tag
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.TemplateSummary
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.api.userprofile.UserProfile
 
addCollectionElement(String, InterMineObject) - Method in class org.intermine.model.fulldata.Item
 
addCollections(ReferenceList) - Method in class org.intermine.model.fulldata.Item
 
addCollectionToCurrentNode(Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds a new list, representing a collection to the current node (map)
addColumn(Connection, String, String, DatabaseUtil.Type) - Static method in class org.intermine.sql.DatabaseUtil
Add a column to an existing database table, if it does not already exist.
addColumn(Database, String, String, DatabaseUtil.Type) - Static method in class org.intermine.sql.DatabaseUtil
Add a column in the table specified in input.
AddColumnAction - Class in org.intermine.web.struts
AddColumnAction adds new column to existing WebTable that should be displayed.
AddColumnAction() - Constructor for class org.intermine.web.struts.AddColumnAction
 
addColumns(List<Path>) - Method in class org.intermine.api.results.WebResults
 
addColumns(List<Path>) - Method in interface org.intermine.api.results.WebTable
Adds columns that should be displayed to the table.
addConstraint(Constraint) - Method in class org.intermine.objectstore.query.ConstraintSet
Add a Constraint to the set
addConstraint(PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Adds a PathConstraint to this query.
addConstraint(PathConstraint, String) - Method in class org.intermine.pathquery.PathQuery
Adds a PathConstraints to this query, associated with a given constraint code.
addConstraints(Collection<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery
Adds a collection of constraints to this query.
addConstraints(PathConstraint...) - Method in class org.intermine.pathquery.PathQuery
Adds a group of constraints to this query.
ADDED - org.intermine.api.search.TaggingEvent.TagChange
 
addElement(StringBuilder, String, String) - Method in class org.intermine.webservice.server.output.XMLFormatter
Add an element with some content.
addExecution(TemplateTrack) - Method in class org.intermine.api.tracker.TemplatesExecutionMap
Add a new template track into the map
addFailedTemplate(String, String) - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Record that a template failed.
addFieldConfig(FieldConfig) - Method in class org.intermine.web.logic.config.Type
Add a FieldConfig for this Type
addFieldToMap(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds the attributes contained in the cell to the map given.
addFileSet(FileSet) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the data fileset
addFileSet(FileSet) - Method in class org.intermine.task.FileConverterTask
Set the data fileset
addFileSet(FileSet) - Method in class org.intermine.task.FileDirectDataLoaderTask
Add a FileSet to read from.
addFileSet(FileSet) - Method in class org.intermine.task.FullXmlConverterTask
Set the data fileset
addFrom(FromElement) - Method in interface org.intermine.objectstore.query.HasFromList
Adds a FromElement to the FROM clause of this Query
addFrom(FromElement) - Method in class org.intermine.objectstore.query.Query
Adds a FromElement to the FROM clause of this Query
addFrom(FromElement) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Adds an element to the FROM list.
addFrom(FromElement, String) - Method in class org.intermine.objectstore.query.Query
Adds a FromElement to the FROM clause of this Query
addFrom(FromElement, String) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Adds an element to the FROM list, including an alias.
addFrom(AbstractTable) - Method in class org.intermine.sql.query.Query
Adds a table to the from list of this query.
addGlobalRepository() - Method in class org.intermine.api.search.SearchRepository
Add a global repository
addGroupBy(AbstractValue) - Method in class org.intermine.sql.query.Query
Adds a field to the GROUP BY clause of this query.
addHaving(AbstractConstraint) - Method in class org.intermine.sql.query.Query
Adds a constraint to the HAVING clause of this query.
addHeaderConfigLink(HeaderConfigLink) - Method in class org.intermine.web.logic.config.Type
Add a header configuration, used from WebConfig
addHeaderConfigTitle(HeaderConfigTitle) - Method in class org.intermine.web.logic.config.Type
Add a header configuration, used from WebConfig
addIdsToBag(Collection<Integer>, String) - Method in class org.intermine.api.profile.InterMineBag
Add the given ids to the bag, this updates the bag contents in the database.
addIdsToList(Collection<? extends String>, InterMineBag, String, String, Set<String>, Collection<String>) - Method in class org.intermine.webservice.server.lists.ListUploadService
Adds objects to the a bag for the matches against a set of identifiers.
addIdToBag(Integer, String) - Method in class org.intermine.api.profile.InterMineBag
Add the given id to the bag, this updates the bag contents in the database.
addIndex(String, String, Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Adds an index to the given table on the given field.
addInlineList(InlineListConfig) - Method in class org.intermine.web.logic.config.Type
Add an InlineList for this object, used from WebConfig
addIssue(String, String, String, List) - Method in class org.intermine.api.bag.BagQueryResult
Add an issue to this result.
AdditionalConverter - Class in org.intermine.api.bag
Represents an additional converter config
AdditionalConverter(String, String, String, String, String) - Constructor for class org.intermine.api.bag.AdditionalConverter
Create a new AdditionalConverter object.
additionsFiles - Variable in class org.intermine.task.ModelMergerTask
 
addJsonProperty(StringBuffer, String, Object) - Method in class org.intermine.pathquery.PathQuery
Add a JSON property when serialising
addKey(Map<String, List<FieldDescriptor>>, String, FieldDescriptor) - Static method in class org.intermine.api.config.ClassKeyHelper
Add a key to set of keys for a given class.
addListener(MapListener<String, Object>) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
addLongDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
Add a long displayer for this Type
addMatch(String, Integer) - Method in class org.intermine.api.bag.BagQueryResult
Add a new match from an input string to an InterMineObject id.
addModel(String, Model) - Static method in class org.intermine.metadata.Model
Adds model to known models.
addModel(Model) - Method in class org.intermine.pathquery.PathQueryHandler
 
addNonCoveredFrom(Set<T>, Set<T>, Set<T>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Adds all required FROM items to the FROM list of the new query.
addObserver(WebSearchWatcher) - Method in class org.intermine.api.profile.StorableBag
 
addObserver(WebSearchWatcher) - Method in interface org.intermine.api.search.WebSearchable
Add this observer to the list of interested parties.
addObserver(WebSearchWatcher) - Method in class org.intermine.api.template.ApiTemplate
 
addOrderBy(String, OrderDirection) - Method in class org.intermine.pathquery.PathQuery
Adds an element to the order by list of this query.
addOrderBy(OrderElement) - Method in class org.intermine.pathquery.PathQuery
Adds an element to the order by list of this query.
addOrderBy(AbstractValue) - Method in class org.intermine.sql.query.Query
Adds a field to the ORDER BY clause of this query.
addOrderBys(Collection<OrderElement>) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the order by list of this query.
addOrderBys(OrderElement...) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the order by list of this query.
addOrderBySpaceSeparated(String) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the order by list, given a space-separated list.
addOutputAttribute(String, String) - Method in class org.intermine.webservice.server.widget.WidgetService
Wrapper around addOutputInfo that makes sure we don't add empty values.
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.GraphService
 
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.TableWidgetService
 
addOutputConfig(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetService
Add metadata about the widget we are using.
addOutputFilter(WidgetConfig, String, InterMineBag, String) - Method in class org.intermine.webservice.server.widget.WidgetService
Add information about the filters as attributes to the result.
addOutputIdsInfo(String, String) - Method in class org.intermine.webservice.server.widget.WidgetService
Add metadata about the IDs we are processing.
addOutputInfo(String, String) - Method in class org.intermine.webservice.server.core.JSONService
Add a key value pair to put in the header of json results.
addOutputListInfo(InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService
Add metadata about the list we are processing.
addOutputResult(Widget) - Method in class org.intermine.webservice.server.widget.WidgetService
Send results to the outside world.
addParam(String, String) - Method in class org.intermine.web.logic.config.Displayer
Add a stored parameter to this Displayer.
addParameter(String, String) - Method in class org.intermine.web.struts.ForwardParameters
Add a parameter to the path.
addPermanentTokens(PermanentToken) - Method in class org.intermine.api.userprofile.UserProfile
 
addProblem(String) - Method in class org.intermine.metadata.Model
Add a problem to the model that doesn't prevent it from being created for backwards compatibility but should be checked when creating a new model.
addRange(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
addReference(Query, QueryClass, String, String) - Method in class org.intermine.web.logic.widget.WidgetLdr
Add a contains constraint to Query (q) built with the query class and attribute given in input
addReference(Reference) - Method in class org.intermine.xml.full.Item
Add a reference.
addReferenceConstraint(Model, Query, QueryClass, String, QueryClass, boolean) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Add a contains constraint to Query (q) from qcStart from qcEnd via reference refName.
addReferencedCellToJsonMap(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds the information from a cell representing a reference to the map given.
addReferences(Reference) - Method in class org.intermine.model.fulldata.Item
 
addReferenceToCurrentNode(Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Adds an intermediate reference to the current node.
addRefId(String) - Method in class org.intermine.xml.full.ReferenceList
Add a value to the list of references.
addRenamedBag(String, String) - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Record that a bag was renamed.
addReportDisplayer(ReportDisplayerConfig) - Method in class org.intermine.web.logic.config.WebConfig
Add config for a report page displayer.
addRequest(ResultsBatches, int, boolean, boolean) - Static method in class org.intermine.objectstore.query.PrefetchManager
Adds a request to the Set of pending requests, and wakes up a Thread to handle it.
addResultElementToTableRow(Object, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Add a result element (RE or "" String)
addResultElementToTableRow(Object, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
Add a result element (RE or "" String), used for type safety as overriden on BagUploadConfirm
addResultEntries(Collection<Map.Entry<String, Object>>) - Method in class org.intermine.webservice.server.core.JSONService
 
addResultEntries(Collection<Map.Entry<String, Object>>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a bunch of entries.
addResultEntry(String, Object, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a single entry.
addResultEntry(Map.Entry<String, Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a single entry.
addResultItem(List<? extends Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a list of objects as a JSON array.
addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.MemoryOutput
Add result item to memory.
addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.Output
Adds data to output.
addResultItem(List<String>) - Method in class org.intermine.webservice.server.output.StreamedOutput
Forwards data to associated writer
addResultItem(Map<String, ? extends Object>, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a map of names and values as a JSON object.
addResultValue(Boolean, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a bool as a JSON value.
addResultValue(CharSequence, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a char-sequence as a JSON value.
addResultValue(Number, boolean) - Method in class org.intermine.webservice.server.core.JSONService
Output a number as a JSON value.
addRole(String) - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
Add a role to this permission.
addRow(int, int) - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Adds a row to the batch.
addRow(Object, String[], Object[]) - Method in class org.intermine.sql.writebatch.TableBatch
Adds a row to the batch.
addRow(String...) - Method in class org.intermine.metadata.TextTable
Adds a single row to the table.
addRow(Connection, String, Object, String[], Object[]) - Method in class org.intermine.sql.writebatch.Batch
Adds a row to the batch for a given table.
addRow(Connection, String, String, String, int, int) - Method in class org.intermine.sql.writebatch.Batch
Adds a row to the batch for a given indirection table.
addSavedBags(SavedBag) - Method in class org.intermine.api.userprofile.UserProfile
 
addSavedQuerys(SavedQuery) - Method in class org.intermine.api.userprofile.UserProfile
 
addSavedTemplateQuerys(SavedTemplateQuery) - Method in class org.intermine.api.userprofile.UserProfile
 
addSelect(SelectValue) - Method in class org.intermine.sql.query.Query
Adds a field to the select list of this query.
addSelectedToBag(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Adds the selected object ids to the given bag.
addSubtab(String, String) - Method in class org.intermine.web.logic.results.WebState
Set the subtab for a particular tab
addSummaries(TemplateSummary) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
addSummaryConstraint(SummaryConstraint) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Add a constraint to that applies to this path.
addTableExportConfig(TableExportConfig) - Method in class org.intermine.web.logic.config.WebConfig
Add an TableExportConfig to the Map of TableExportConfig objects using tableExportConfig.getId() as the Map key.
addTableToDatabase(PrecomputedTable, Collection<String>, boolean) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Add a PrecomputedTable to the database.
addTag(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Adds tag and assures that there is only one tag for this combination of tag name, tagged Object and type.
addTag(String, String, String, Profile) - Method in class org.intermine.api.profile.TagManager
Add a new tag.
addTag(String, WebSearchable, Profile) - Method in class org.intermine.api.profile.TagManager
Associate a websearchable obj with a certain tag.
addTag(String, ClassDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Associate a class with a certain tag.
addTag(String, ReferenceDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Associate a reference with a certain tag.
addTags(Tag) - Method in class org.intermine.api.userprofile.UserProfile
 
addTagsToBag(Collection<String>, InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Add tags to a bag.
addTime(long) - Method in class org.intermine.objectstore.intermine.ExtraQueryTime
Adds statistics for an executed query to this object.
addTitleParts(HashMap<String, List<HeaderConfigTitle.TitlePart>>) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Add title parts to this header config.
addToBag(ObjectStoreBag, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Adds an element to an ObjectStoreBag, delegate to internal ObjectStoreWriter.
addToBag(ObjectStoreBag, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds an element to an ObjectStoreBag.
addToBag(ObjectStoreBag, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Adds an element to an ObjectStoreBag.
AddToBagAction - Class in org.intermine.web.struts
Action to save a single object o an existing bag.
AddToBagAction() - Constructor for class org.intermine.web.struts.AddToBagAction
 
addToBagFromQuery(ObjectStoreBag, Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Adds elements to an ObjectStoreBag, delegate to internal ObjectStoreWriter.
addToBagFromQuery(ObjectStoreBag, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds elements to an ObjectStoreBag from the results of a Query.
addToBagFromQuery(ObjectStoreBag, Query) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Adds elements to an ObjectStoreBag from the results of a Query.
addToBagFromQuery(Query) - Method in class org.intermine.api.profile.InterMineBag
Add elements to the bag from a query, this is able to operate entirely in the database without needing to read objects into memory.
addToBagFromQueryWithConnection(Connection, ObjectStoreBag, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Adds elements to a bag from the results of a query.
addToCollection(Integer, Class<?>, String, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Add an object to another object's collection, delegate to internal ObjectStoreWriter.
addToCollection(Integer, Class<?>, String, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Place an object in a many-to-many collection of another object.
addToCollection(Integer, Class<?>, String, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Place an object in a many-to-many collection of another object.
addToCollection(String, String) - Method in class org.intermine.xml.full.Item
Add a reference to a collection of this item.
addToCollection(String, Item) - Method in class org.intermine.xml.full.Item
Add the identifier of the given Item to a collection.
addToCollectionWithConnection(Connection, Integer, Class<?>, String, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs addToCollection with given connection
addToConstraintLogic(LogicExpression, String) - Static method in class org.intermine.api.query.MainHelper
Add a constraint code to a logic expression, ANDed with any constraints already in the expression, e.g.
addToFrom(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
addToGroupBy(QueryNode) - Method in class org.intermine.objectstore.query.Query
Add a QueryNode to the GROUP BY clause of this Query
addToHolder(Object) - Method in class org.intermine.util.CacheHoldingArrayList
Adds an object to the holder.
addToLastBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Adds a statement to the lastBatch.
addToLastBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Adds a statement to the lastBatch.
addToList(List<Constraint>, Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Adds all the constraints present in the argument into the given List.
addToListMap(Map<K, List<V>>, K, V) - Static method in class org.intermine.metadata.Util
Add a value to a Map from keys to Set of values, creating the value list as needed.
addToOrderBy(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
addToOrderBy(QueryOrderable) - Method in class org.intermine.objectstore.query.Query
Add a QueryOrderable to the ORDER BY clause of this Query
addToOrderBy(QueryOrderable, String) - Method in class org.intermine.objectstore.query.Query
Add a QueryOrderable to the ORDER BY clause of this Query
addToPostDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Adds a statement to the postDeleteBatch.
addToPostDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Adds a statement to the postDeleteBatch.
addToPreDeleteBatch(String) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Adds a statement to the preDeleteBatch.
addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.Query
Add a QuerySelectable to the SELECT clause of this Query
addToSelect(QuerySelectable) - Method in interface org.intermine.objectstore.query.Queryable
Adds an element to the SELECT list.
addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Adds an element to the SELECT list.
addToSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Adds an element to the SELECT list.
addToSelect(QuerySelectable) - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect
Adds an element to the SELECT list.
addToSelect(QuerySelectable, String) - Method in class org.intermine.objectstore.query.Query
Add a QuerySelectable to the SELECT clause of this Query
addToSetMap(Map<K, Set<V>>, K, Collection<V>) - Static method in class org.intermine.metadata.Util
Add values to a Map from keys to Set of values, creating the value list as needed.
addToSetMap(Map<K, Set<V>>, K, V) - Static method in class org.intermine.metadata.Util
Add a value to a Map from keys to Set of values, creating the value list as needed.
addToSortOrder(String, String) - Method in class org.intermine.dwr.AjaxServices
Add a Node from the sort order
addToUnion(Query) - Method in class org.intermine.sql.query.Query
Adds another Query to the UNION set of this query.
addToView(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Add a path to the results view.
addToWhere(String) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
addType(Type) - Method in class org.intermine.web.logic.config.WebConfig
Add a type to the WebConfig Map.
addUniqueItemId(String, String) - Method in class org.intermine.dataconversion.DataConverter
List of unique identifiers and their refIds.
addUnresolved(Collection<String>) - Method in class org.intermine.api.bag.BagQueryResult
Set the Map of unresolved input strings.
addUserToShareBag(String, String) - Method in class org.intermine.dwr.AjaxServices
Share the bag given in input with the user which userName is input and send email
addView(String) - Method in class org.intermine.pathquery.PathQuery
Add a single element to the view list.
addViews(String...) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the view list.
addViews(Collection<String>) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the view list.
addViewSpaceSeparated(String) - Method in class org.intermine.pathquery.PathQuery
Adds a group of elements to the view list, given a space-separated list.
addWhere(AbstractConstraint) - Method in class org.intermine.sql.query.Query
Adds a constraint to the where clause for this query.
addWidget(WidgetConfig) - Method in class org.intermine.web.logic.config.Type
Add a widget to the Type
addWidget(WidgetConfig) - Method in class org.intermine.web.logic.config.WebConfig
 
aDescendsFromB(String, String) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Test whether a class named "a" descends from a class named "b".
adjustPValues(ErrorCorrection.Strategy, Map<String, BigDecimal>, Double, int) - Static method in class org.intermine.web.logic.widget.ErrorCorrection
 
af - Variable in class org.intermine.web.struts.ForwardParameters
Original ActionForward.
aIsaB(String, String) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Test whether a class named "A" is, or descends from, a class named "B".
ajaxCollapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - collapse a model browser node.
ajaxEditConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - edit an existing constraint.
ajaxEditJoinStyle(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a constraint's join style settings for a path, and forward to queryBuilderConstraint, for use by ajax.
ajaxEditTemplateConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - edit a template constraint.
ajaxExpand(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - expand a model browser node.
ajaxNewConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - ahow the panel for adding a new constraint to the query.
ajaxRenderPaths(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
AJAX request - render query paths.
AjaxServices - Class in org.intermine.dwr
This class contains the methods called through DWR Ajax
AjaxServices() - Constructor for class org.intermine.dwr.AjaxServices
 
ajaxShowDisplayer(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Show a displayer in response to an AJAX request.
ajaxTemplateCount(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Count number of results for a template for inline templates
ajaxVerbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
 
AKA - Static variable in class org.intermine.api.profile.UserPreferences
What we should call the user.
alias - Variable in class org.intermine.sql.query.AbstractTable
 
alias - Variable in class org.intermine.sql.query.SelectValue
 
alias - Variable in class org.intermine.task.DropPrecomputedTablesTask
 
alias - Variable in class org.intermine.task.RunIqlQueryTask
 
alias - Variable in class org.intermine.task.SummariseObjectStoreTask
 
alias - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
alias(Object, String) - Method in class org.intermine.objectstore.query.Query
Set an alias for an element in the Query.
alias(String) - Method in class org.intermine.dataconversion.DataConverter
Uniquely alias a className
ALIAS - Static variable in class org.intermine.api.profile.UserPreferences
The alias of this user.
ALIAS - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
ALL - Static variable in class org.intermine.api.search.Scope
User or global scope for bags, templates, etc.
ALL_BAGS - Static variable in class org.intermine.api.search.SearchTarget
The search target for all bags
ALL_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
ALL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
The search target for all templates
ALLBUTINTERSECT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing an all but intersect operation
allDigits(String) - Static method in class org.intermine.metadata.StringUtil
Return true if all characters in a given String are digits.
allPkClassesEmptyForClass - Variable in class org.intermine.dataloader.HintingFetcher
 
allSources - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
ALT_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput
The name of the new list (synonym)
alterComparisonAnd(int, int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take a couple of integers as if they are values returned by compare, and assume that they are two loose (and possibly different) descriptions of the relation between the same two AbstractConstraints, and return a value that is a more strict description.
alterComparisonAORB(int, int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take a couple of integers as if they are values returned by compare, for this compared to A, and this compared to B, and return the value that compare should return for this compared to (A OR B).
alterComparisonNotObj(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it is a value returned by compare, and return the value that compare would have returned if second constraint (obj) had been NOTed.
alterComparisonNotThis(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it is a value returned by compare, and return the value that compare would have returned if first constraint (this) had been NOTed.
alterComparisonSwitch(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it is a value returned by compare, and return the value that compare would have returned if this and obj had been switched.
ALWAYS_EXPLAIN_TABLES - Static variable in class org.intermine.sql.precompute.BestQueryExplainer
 
AlwaysMap<K,​V> - Class in org.intermine.util
This is a dumb implementation of a Map.
AlwaysMap(V) - Constructor for class org.intermine.util.AlwaysMap
Construct an AlwaysMap.
AlwaysSet<E> - Class in org.intermine.util
A Set that always returns true for the contains method.
amendTo(String) - Method in class org.intermine.api.profile.InvalidBag
Fix this bag by changing its type.
analyse(Database, boolean) - Static method in class org.intermine.sql.DatabaseUtil
Analyse given database, perform vacuum full analyse if full parameter true.
analyse(Database, ClassDescriptor, boolean) - Static method in class org.intermine.sql.DatabaseUtil
Analyse database table for a given class and all associated indirection tables.
AnalyseDbTask - Class in org.intermine.task
Task to run ANALYSE on a table or whole database.
AnalyseDbTask() - Constructor for class org.intermine.task.AnalyseDbTask
 
anchor - Variable in class org.intermine.web.struts.ForwardParameters
Anchor name.
and(EitherVisitor<A, B, R>) - Method in class org.intermine.webservice.server.core.EitherVisitor
Compose this visitor with another visitor which handles the either after this one has had a go at it, presumably for side-effects like logging and what-not.
AND - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the AND operation
and_constraint_set() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
and_constraint_set() - Method in class org.intermine.sql.query.SqlParser
 
and_constraint_set(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
AND_CONSTRAINT_SET - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
AND_CONSTRAINT_SET - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
AND_EXPR - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
andExpr() - Method in class org.intermine.pathquery.LogicParser
 
AnonProfile - Class in org.intermine.api.util
A null-object for profiles for use with the web services.
AnonProfile() - Constructor for class org.intermine.api.util.AnonProfile
Constructor
api - Variable in class org.intermine.webservice.server.core.WebServiceServlet
 
API - Interface in org.intermine.api
The interface of the API, abstracted for testing purposes.
ApiJavaController - Class in org.intermine.web.struts
 
ApiJavaController() - Constructor for class org.intermine.web.struts.ApiJavaController
 
apiKey - Variable in class org.intermine.api.userprofile.UserProfile
 
ApiPerlController - Class in org.intermine.web.struts
 
ApiPerlController() - Constructor for class org.intermine.web.struts.ApiPerlController
 
ApiTemplate - Class in org.intermine.api.template
This class extends TemplateQuery to provide the features needed by the API - Lucene indexing and database serialisation.
ApiTemplate(String, String, String, PathQuery) - Constructor for class org.intermine.api.template.ApiTemplate
 
ApiTemplate(TemplateQuery) - Constructor for class org.intermine.api.template.ApiTemplate
Construct a new API template that has all the same properties as the TemplateQuery passed into the constructor.
apiTemplateMapToJson(InterMineAPI, Map<String, ApiTemplate>, Profile) - Static method in class org.intermine.api.template.TemplateHelper
Helper routine for serialising a map of templates to JSON.
apiTemplateMapToXml(Map<String, ApiTemplate>, int) - Static method in class org.intermine.api.template.TemplateHelper
Serialse a map of templates to XML.
append(boolean) - Method in class org.intermine.model.StringConstructor
Appends a boolean onto the end of this object.
append(double) - Method in class org.intermine.model.StringConstructor
Appends a double onto the end of this object.
append(float) - Method in class org.intermine.model.StringConstructor
Appends a float onto the end of this object.
append(int) - Method in class org.intermine.model.StringConstructor
Appends an int onto the end of this object.
append(long) - Method in class org.intermine.model.StringConstructor
Appends a long onto the end of this object.
append(Object) - Method in class org.intermine.model.StringConstructor
Appends an Object onto the end of this object.
append(String) - Method in class org.intermine.model.StringConstructor
Appends a String onto the end of this object.
append(String) - Method in class org.intermine.pathquery.Path
Return new Path that has this Path as its prefix and has fieldName as the last element.
apply(Map<String, BigDecimal>, PopulationInfo, Map<String, PopulationInfo>, Double) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Apply the correction coefficient to the pValuesTerm given in input
apply(Constraint) - Method in class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
Perform test for NOT NULL constraint on node
apply(Constraint) - Method in interface org.intermine.objectstore.query.ConstraintTraverseAction
The apply() method is called by ConstraintHelper.traverseConstraints() for each Constraint and sub-Constraint.
ArrayFormatter - Class in org.intermine.webservice.server.jbrowse.util
Not good practice, but this is how JBrowse wants results, so when in Rome.
ArrayFormatter() - Constructor for class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
ASC - org.intermine.pathquery.OrderDirection
ascending
asList() - Method in class org.intermine.api.search.SearchResult
A list of between two and three items containing the information in this result.
asList() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Return this Collection as a List.
asList() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Return this Collection as a List.
asList() - Method in class org.intermine.objectstore.query.Results
Return this Collection as a List.
Aspect - Class in org.intermine.web.logic.aspects
Configuration for a single data set.
Aspect() - Constructor for class org.intermine.web.logic.aspects.Aspect
 
AspectBinding - Class in org.intermine.web.logic.aspects
Routines for unmarshaling Aspect objects from XML.
AspectController - Class in org.intermine.web.struts
Contoller for a single data set tile embedded in a page.
AspectController() - Constructor for class org.intermine.web.struts.AspectController
 
ASPECTS - Static variable in class org.intermine.web.logic.Constants
Servlet context attribute - map from aspect set name to Aspect object.
AspectSource - Class in org.intermine.web.logic.aspects
Describes a source of data contributing to some data set.
AspectSource() - Constructor for class org.intermine.web.logic.aspects.AspectSource
 
AspectTagUtil - Class in org.intermine.api.tag
Util class for working with aspect tags.
assignMapping(Integer, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Puts a mapping into idMap.
assureSize(int) - Method in class org.intermine.util.SensibleByteArrayOutputStream
Resizes the buffer to ensure it is as large as newSize.
ASTERISK - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
ASTERISK - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
ASYMMETRIC_SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical asymmetric substraction.
AsymmetricOperationInput - Class in org.intermine.webservice.server.lists
A list input class for operations that have a left and a right side.
AsymmetricOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.AsymmetricOperationInput
Constructor.
asymmetricSubtract(Model, Collection<InterMineBag>, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
 
AT_LEAST - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the known number of rows has a minimum which exceed the estimate.
AT_MOST - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the known number of rows has a maximum, and the estimate exceeds it.
AT_SIGN - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
AT_SIGN - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
atom() - Method in class org.intermine.pathquery.LogicParser
 
ATTR_MARKER_RE - Static variable in class org.intermine.api.LinkRedirectManager
 
Attribute - Class in org.intermine.model.fulldata
 
Attribute - Class in org.intermine.xml.full
Representation of an Attribute in an object
Attribute() - Constructor for class org.intermine.model.fulldata.Attribute
 
Attribute() - Constructor for class org.intermine.xml.full.Attribute
Constructor
Attribute(String, String) - Constructor for class org.intermine.xml.full.Attribute
Construnctor
ATTRIBUTE_TYPES - Static variable in class org.intermine.pathquery.PathQueryHandler
This is a list of String type descriptions that are attribute types
AttributeDescriptor - Class in org.intermine.metadata
Describes an attribute of a class - i.e.
AttributeDescriptor(String, String, String) - Constructor for class org.intermine.metadata.AttributeDescriptor
Construct, name and type cannot be null.
AttributeLinkURL - Class in org.intermine.web.util
Simple class that parses provided url.
AttributeLinkURL(String) - Constructor for class org.intermine.web.util.AttributeLinkURL
Constructor.
attributeOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
attributeOptions - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
attributes - Variable in class org.intermine.model.fulldata.Item
 
attributes - Variable in class org.intermine.webservice.server.query.result.QueryResultService
 
attributeValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
AuthenticatedListService - Class in org.intermine.webservice.server.lists
A Class that insists on being authenticated.
AuthenticatedListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AuthenticatedListService
Constructor.
AuthenticationException(String) - Constructor for exception org.intermine.api.profile.ProfileManager.AuthenticationException
Constructor
Authenticator - Class in org.intermine.web.struts.oauth2
The action that bounces the user off to their respective authentication provider when they want to use them to log-in with OAuth2.
Authenticator() - Constructor for class org.intermine.web.struts.oauth2.Authenticator
 
AuthenticatorService - Class in org.intermine.webservice.server.oauth2
This service just generates the appropriate link to the oauth2 provider Similar to the Authenticator class used by struts.
AuthenticatorService(InterMineAPI) - Constructor for class org.intermine.webservice.server.oauth2.AuthenticatorService
Constructor
AuthenticatorServlet - Class in org.intermine.webservice.server.oauth2
A Servlet for routing requests to the oauth2 AuthenticatorService.
AuthenticatorServlet() - Constructor for class org.intermine.webservice.server.oauth2.AuthenticatorServlet
 
AUTO_COMPLETER - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute, autocompletion.
AUTOCOMPLETE_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the autocomplete RAMIndexes.
AutoCompleter - Class in org.intermine.web.autocompletion
Autocompleter class for initializing and using the autocompletion
AutoCompleter(ObjectStore) - Constructor for class org.intermine.web.autocompletion.AutoCompleter
Autocompleter build index constructor.
AvailableColumnsController - Class in org.intermine.web.struts
Controller for availableColumns.tile.
AvailableColumnsController() - Constructor for class org.intermine.web.struts.AvailableColumnsController
 
AvailableListsService - Class in org.intermine.webservice.server.lists
A service to report what lists a user has access to, and some details of those lists.
AvailableListsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.AvailableListsService
Constructor
AvailableListsServlet - Class in org.intermine.webservice.server.lists
 
AvailableListsServlet() - Constructor for class org.intermine.webservice.server.lists.AvailableListsServlet
 
AvailableServicesServlet - Class in org.intermine.webservice.server
Report whether a requested service is implementented on this mine.
AvailableServicesServlet() - Constructor for class org.intermine.webservice.server.AvailableServicesServlet
 
AvailableTemplatesService - Class in org.intermine.webservice.server.template
Fetch the names of public template queries for use with the Templates web service.
AvailableTemplatesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.AvailableTemplatesService
Constructor.
AvailableWidgetsService - Class in org.intermine.webservice.server.widget
A service for listing the available widgets.
AvailableWidgetsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.AvailableWidgetsService
Constructor
AvailableWidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet handling requests for information about which widgets are available.
AvailableWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.AvailableWidgetsServlet
 
AVERAGE - Static variable in class org.intermine.objectstore.query.QueryFunction
Average value of a number of rows
AVG - Static variable in class org.intermine.sql.query.Function
AVG(v) aggregate function - takes one operand.

B

backgroundFlush(Connection, Set<String>) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server, but does not guarantee that the operation is finished when this method returns.
backgroundFlush(Connection, Set<String>, boolean) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server, but does not guarantee that the operation is finished when this method returns.
BadQueryException - Exception in org.intermine.api.query
 
BadQueryException(String, Exception) - Constructor for exception org.intermine.api.query.BadQueryException
 
BadRequestException - Exception in org.intermine.webservice.server.exceptions
The BadRequestException is thrown by service when there is a problem with the request.
BadRequestException(String) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException
400 - BAD REQUEST
BadRequestException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException
404 - BAD REQUEST
BadRequestException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.BadRequestException
404 - BAD REQUEST
BadTemplateException - Exception in org.intermine.api.profile
Exception thrown when template has invalid name.
BadTemplateException() - Constructor for exception org.intermine.api.profile.BadTemplateException
Constructor
BadTemplateException(String) - Constructor for exception org.intermine.api.profile.BadTemplateException
Constructor with message.
bag - Variable in class org.intermine.objectstore.query.BagConstraint
 
bag - Variable in class org.intermine.web.logic.widget.Widget
 
bag - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
BAG - Static variable in class org.intermine.api.tag.TagTypes
Bag.
bag_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
BAG_CONSTRAINT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
BAG_INVITES - Static variable in class org.intermine.api.bag.SharedBagManager
The name of the table to persist offers to share a bag with others.
BAG_NAME_PREFIX - Static variable in class org.intermine.web.logic.bag.BagHelper
When generating new bag names, this is used as a prefix.
BAG_QUERY_MAX_BATCH_SIZE - Static variable in class org.intermine.webservice.server.lists.ListUploadService
The maximum number of ids to query for each batch.
BAG_VALUE - org.intermine.template.TemplateValue.ValueType
e.g.
BAG_VALUES - Static variable in class org.intermine.api.profile.InterMineBag
name of bag values table
BagBuildController - Class in org.intermine.web.struts
Controller Action for buildBag.jsp
BagBuildController() - Constructor for class org.intermine.web.struts.BagBuildController
 
BagConstraint - Class in org.intermine.objectstore.query
Constrain a QueryClass or QueryEvaluable to be within a bag.
BagConstraint(QueryNode, ConstraintOp, Collection<?>) - Constructor for class org.intermine.objectstore.query.BagConstraint
Construct a BagConstraint from a Collection.
BagConstraint(QueryNode, ConstraintOp, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.BagConstraint
Construct a BagConstraint from an ObjectStoreBag.
bagConstraintTables - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
bagConstraintToString(SqlGenerator.State, StringBuffer, BagConstraint, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a BagConstraint object into a String suitable for putting on an SQL query.
BagConversionHelper - Class in org.intermine.web.logic.bag
Utility methods used when converting lists (bags) between types.
BagConverter - Class in org.intermine.web.logic.bag
 
BagConverter(InterMineAPI, WebConfig) - Constructor for class org.intermine.web.logic.bag.BagConverter
 
BagDetailsAction - Class in org.intermine.web.struts
Action that builds a PagedCollection to view a bag.
BagDetailsAction() - Constructor for class org.intermine.web.struts.BagDetailsAction
 
BagDetailsController - Class in org.intermine.web.struts
 
BagDetailsController() - Constructor for class org.intermine.web.struts.BagDetailsController
 
BagDoesNotExistException - Exception in org.intermine.api.profile
Exception thrown when bag is not found.
BagDoesNotExistException() - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor
BagDoesNotExistException(String) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor with message.
BagDoesNotExistException(String, Throwable) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor with message and throwable
BagDoesNotExistException(Throwable) - Constructor for exception org.intermine.api.profile.BagDoesNotExistException
Constructor with throwable
BagHelper - Class in org.intermine.web.logic.bag
Helper methods for bags.
BAGID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the bagid column in the osbag table.
bagManager - Variable in class org.intermine.api.InterMineAPI
 
bagManager - Variable in class org.intermine.api.query.QueryExecutor
 
bagManager - Variable in class org.intermine.webservice.server.core.JSONService
 
bagManager - Variable in class org.intermine.webservice.server.lists.ListInput
 
bagManager - Variable in class org.intermine.webservice.server.query.QueryToListService
 
BagManager - Class in org.intermine.api.bag
A BagManager provides access to all global and/or user bags and methods to fetch them by type, etc.
BagManager(Profile, Model) - Constructor for class org.intermine.api.bag.BagManager
The BagManager references the super user profile to fetch global bags.
BagManager.ByTagOrder - Class in org.intermine.api.bag
Compare lists based on their im:order:n tag
BagManager.CaseInsensitiveComparator - Class in org.intermine.api.bag
Lower-case key comparator
bagName - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
bagName - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
BagNotFound - Exception in org.intermine.api.query
 
BagNotFound(String) - Constructor for exception org.intermine.api.query.BagNotFound
 
BagNotFound(String, Throwable) - Constructor for exception org.intermine.api.query.BagNotFound
 
bagOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
BagOperation - Class in org.intermine.api.bag.operations
 
BagOperation(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.BagOperation
 
BagOperationException - Exception in org.intermine.api.bag.operations
 
BagOperationException() - Constructor for exception org.intermine.api.bag.operations.BagOperationException
Constructor
BagOperationException(String) - Constructor for exception org.intermine.api.bag.operations.BagOperationException
 
BagOperationException(String, Throwable) - Constructor for exception org.intermine.api.bag.operations.BagOperationException
 
BagOperationException(Throwable) - Constructor for exception org.intermine.api.bag.operations.BagOperationException
 
BagOperations - Class in org.intermine.api.bag
Perform logical operations on bags - combine bags to create new InterMineBags
BagProducer - Interface in org.intermine.api.bag.operations
Functional interface for BagOperations, so we can be all forward looking.
BagQuery - Class in org.intermine.api.bag
A class encapsulating a query used to create a bag from a collection of input identifiers.
BagQuery(BagQueryConfig, Model, String, String, String, boolean) - Constructor for class org.intermine.api.bag.BagQuery
Create a new BagQuery object.
BagQuery(BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, String) - Constructor for class org.intermine.api.bag.BagQuery
Create a new BagQuery object for the default query - search for all key fields of the given class.
bagQueryConfig - Variable in class org.intermine.api.InterMineAPI
 
BagQueryConfig - Class in org.intermine.api.bag
Configuration for BagQuery objects.
BagQueryConfig(Map<String, List<BagQuery>>, Map<String, List<BagQuery>>, Map<String, Set<AdditionalConverter>>) - Constructor for class org.intermine.api.bag.BagQueryConfig
Create a new BagQueryConfig object.
BagQueryHandler - Class in org.intermine.api.bag
Handler for bag-query.xml files.
BagQueryHandler(Model) - Constructor for class org.intermine.api.bag.BagQueryHandler
Create a new BagQueryHandler object.
BagQueryHelper - Class in org.intermine.api.bag
 
BagQueryResult - Class in org.intermine.api.bag
Class to hold the results of querying for a bag of objects.
BagQueryResult() - Constructor for class org.intermine.api.bag.BagQueryResult
 
BagQueryResult.IssueResult - Class in org.intermine.api.bag
Simple struct to hold three pieces of information together.
bagQueryRunner - Variable in class org.intermine.api.InterMineAPI
 
bagQueryRunner - Variable in class org.intermine.api.query.QueryExecutor
 
BagQueryRunner - Class in org.intermine.api.bag
For a given list of input strings search for objects using default and configured queries for a particular type.
BagQueryRunner(ObjectStore, Map<String, List<FieldDescriptor>>, BagQueryConfig, TemplateManager) - Constructor for class org.intermine.api.bag.BagQueryRunner
Construct with configured bag queries and a map of type -> key fields.
BagQueryUpgrade - Class in org.intermine.api.bag
 
BagQueryUpgrade(BagQueryRunner, InterMineBag) - Constructor for class org.intermine.api.bag.BagQueryUpgrade
 
BagResultCategoryKeyFormatter - Class in org.intermine.webservice.server.idresolution
Format a bag query result, grouping by category of issue.
BagResultCategoryKeyFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.BagResultCategoryKeyFormatter
 
BagResultFormatter - Interface in org.intermine.webservice.server.idresolution
 
BagResultOutputKeyFormatter - Class in org.intermine.webservice.server.idresolution
Format a bag result grouping by matched object.
BagResultOutputKeyFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.BagResultOutputKeyFormatter
 
bags_for() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
BAGS_FOR - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
BagSet - Class in org.intermine.api.profile
A class containing valiud and invalid bags.
BagSet(Map<String, InterMineBag>, Map<String, InvalidBag>) - Constructor for class org.intermine.api.profile.BagSet
Constructor
BagState - Enum in org.intermine.api.profile
Enumeration for describing the state of a bag: current not current (= the upgrading process has not been executed yet) upgrading (= the upgrading process is upgrading it) to upgrade (= the upgrading process has not been able to upgrade it because there are some conflicts that the user has to solve manually ))
bagTablesInDatabase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
bagTablesToRemove - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
BagUpgradeAction - Class in org.intermine.web.struts
An action that prepare a BagQueryResult and save it into the session.
BagUpgradeAction() - Constructor for class org.intermine.web.struts.BagUpgradeAction
 
BagUploadConfirmAction - Class in org.intermine.web.struts
Action class for saving a bag from the bagUploadConfirm page into the user profile.
BagUploadConfirmAction() - Constructor for class org.intermine.web.struts.BagUploadConfirmAction
 
BagUploadConfirmController - Class in org.intermine.web.struts
Controller for the bagUploadConfirm; retrieve an IDResolutionService job id
BagUploadConfirmController() - Constructor for class org.intermine.web.struts.BagUploadConfirmController
 
BagUploadConfirmForm - Class in org.intermine.web.struts
Form for the bagUploadConfirm page.
BagUploadConfirmForm() - Constructor for class org.intermine.web.struts.BagUploadConfirmForm
Constructor
BagUploadConfirmInlineResultsTable - Class in org.intermine.web.logic.results
An inline table of ResultElements used ob BagUploadConfirm At the moment, we use this custom class to create a custom type of table row that will be extended with identifier and rowspan attributes needed on list upload confirmation step
BagUploadConfirmInlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Construct a new InlineResultsTable object
BagUploadConfirmInlineResultsTableRow - Class in org.intermine.web.logic.results
Used on BagUploadConfirmIssueController (List upload confirm step) to add an identifier the user was trying to resolve with the number of rows in the ResultsTable corresponding to the said identifier.
BagUploadConfirmInlineResultsTableRow() - Constructor for class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
 
BagUploadConfirmIssueController - Class in org.intermine.web.struts
Controller for the bagUploadConfirmIssue tile.
BagUploadConfirmIssueController() - Constructor for class org.intermine.web.struts.BagUploadConfirmIssueController
 
BAGVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the value column in the osbag table.
bagValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
BagValue - Class in org.intermine.api.profile
A class representing a value stored in an InterMineBag.
BagValue(String, String) - Constructor for class org.intermine.api.profile.BagValue
Constructor
Base64PublicKeyDecoder - Class in org.intermine.web.security
A public key decoder that reads public keys encoded as base64 strings.
Base64PublicKeyDecoder() - Constructor for class org.intermine.web.security.Base64PublicKeyDecoder
Construct a new decoder.
BaseDisclosureTag - Class in org.intermine.web.tags.disclosure
Base tag handler from which are all disclosure tag handlers derived.
BaseDisclosureTag() - Constructor for class org.intermine.web.tags.disclosure.BaseDisclosureTag
 
BaseEquivalentObjectFetcher - Class in org.intermine.dataloader
Class providing methods to look up equivalent objects by primary key in a production objectstore.
BaseEquivalentObjectFetcher(Model, IntToIntMap, ObjectStore) - Constructor for class org.intermine.dataloader.BaseEquivalentObjectFetcher
Constructor for this EquivalentObjectFetcher.
BASIC_FORMATS - Static variable in enum org.intermine.webservice.server.Format
The basic formats: HTML, TEXT, XML, JSON
batch - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
Batch - Class in org.intermine.sql.writebatch
A class representing a collection of writes to an SQL database.
Batch(BatchWriter) - Constructor for class org.intermine.sql.writebatch.Batch
Constructs an empty Batch, with no tables.
BATCH_SIZE - Static variable in class org.intermine.api.config.Constants
Batch size for the underlying objectstore
BATCH_SIZE - Static variable in class org.intermine.webservice.server.query.result.QueryResultService
Batch size to use
batchCommit(Connection) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server, then commits and re-opens the transaction, but does not guarantee that the operation is finished when this method returns.
batchCommitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
batchCommitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
batchCommitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter commits and closes the transaction and then opens a new one, without guaranteeing that the operation is finished before this method returns.
batchCommitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Commits a transaction and opens a new one, without guaranteeing the operation is finished before this method returns.
batches - Variable in class org.intermine.objectstore.query.ResultsBatches
 
batchesCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
BatchingFetcher - Class in org.intermine.dataloader
Class providing EquivalentObjectFetcher functionality that batches fetches to improve performance.
BatchingFetcher(BaseEquivalentObjectFetcher, DataTracker, Source) - Constructor for class org.intermine.dataloader.BatchingFetcher
Constructor
batchQueried - Variable in class org.intermine.dataloader.BatchingFetcher
 
batchSize - Variable in class org.intermine.objectstore.query.ResultsBatches
 
BatchWriter - Interface in org.intermine.sql.writebatch
An interface representing an object that can flush a TableBatch to an SQL server Connection.
BatchWriterPostgresCopyImpl - Class in org.intermine.sql.writebatch
An implementation of the BatchWriter interface that uses PostgreSQL-specific COPY commands.
BatchWriterPostgresCopyImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
BatchWriterPreparedStatementImpl - Class in org.intermine.sql.writebatch
An implementation of the BatchWriter interface that uses JDBC PreparedStatement addBatch() and executeBatch() methods.
BatchWriterPreparedStatementImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
 
BatchWriterSimpleImpl - Class in org.intermine.sql.writebatch
An implementation of the BatchWriter interface that uses simple JDBC addBatch() and executeBatch() methods.
BatchWriterSimpleImpl() - Constructor for class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
BeginAction - Class in org.intermine.web.struts
Prepare templates and news to be rendered on home page
BeginAction() - Constructor for class org.intermine.web.struts.BeginAction
 
beginTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStore begins a transaction, delegate to internal ObjectStoreWriter.
beginTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter begins a transaction
beginTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter begins a transaction
beginTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Begins a transaction.
BENJAMINI_HOCHBERG - org.intermine.web.logic.widget.ErrorCorrection.Strategy
The Benjamini Hochberg error correction strategy
beof - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
bestCandidate - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
BestQuery - Class in org.intermine.sql.precompute
This object is an abstract superclass for a Best Query tracker.
BestQuery() - Constructor for class org.intermine.sql.precompute.BestQuery
 
BestQueryException - Exception in org.intermine.sql.precompute
An Exception that may be thrown by an BestQuery.
BestQueryException() - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException
BestQueryException(String) - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException with the specified detail message.
BestQueryException(String, Throwable) - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException with the specified detail message and nested throwable.
BestQueryException(Throwable) - Constructor for exception org.intermine.sql.precompute.BestQueryException
Constructs an BestQueryException with the specified nested throwable.
BestQueryExplainer - Class in org.intermine.sql.precompute
Gets the database to explain each Query added and keeps hold of the best one so far.
BestQueryExplainer() - Constructor for class org.intermine.sql.precompute.BestQueryExplainer
Constructs an empty BestQueryExplainer for testing purposes
BestQueryExplainer(Connection, long) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer
Constructs a BestQueryExplainer that will use the given Connection to explain Queries.
BestQueryExplainer.Candidate - Class in org.intermine.sql.precompute
A class representing a candidate optimised query.
BestQueryExplainerVerbose - Class in org.intermine.sql.precompute
Gets the database to explain each Query added and keeps hold of the best one, logging all actions for the benefit of the IqlShell user.
BestQueryExplainerVerbose(Connection, long) - Constructor for class org.intermine.sql.precompute.BestQueryExplainerVerbose
Constructs an empty BestQueryExplainerVerbose.
BestQueryFallback - Class in org.intermine.sql.precompute
Gets the database to explain each Query added and keeps hold of the best one so far.
BestQueryFallback(Query, String) - Constructor for class org.intermine.sql.precompute.BestQueryFallback
Constructs a BestQueryFallback
BestQueryLogger - Class in org.intermine.sql.precompute
Logs each query added.
BestQueryLogger(boolean) - Constructor for class org.intermine.sql.precompute.BestQueryLogger
Constructs a BestQueryLogger
BestQueryStorer - Class in org.intermine.sql.precompute
Stores each query added.
BestQueryStorer() - Constructor for class org.intermine.sql.precompute.BestQueryStorer
Constructs a BestQueryStorer
bestQueryString - Variable in class org.intermine.sql.precompute.BestQueryLogger
 
betterThan(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns true if the argument is slower than this, or if the argument is null.
BG_PROPERTIES - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the bluegenes properties.
BG_PROPS - Static variable in class org.intermine.webservice.server.bg.BGPropertiesServlet
 
BGPropertiesCreationService - Class in org.intermine.webservice.server.bg
Create a new bluegenes property.
BGPropertiesCreationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.bg.BGPropertiesCreationService
Constructor
BGPropertiesDelationService - Class in org.intermine.webservice.server.bg
Delete an existing bluegenes property.
BGPropertiesDelationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.bg.BGPropertiesDelationService
Constructor
BGPropertiesService - Class in org.intermine.webservice.server.bg
Return all the existing bluegenes property or a specific one
BGPropertiesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.bg.BGPropertiesService
Constructor
BGPropertiesServlet - Class in org.intermine.webservice.server.bg
Runs BGProperties related web service.
BGPropertiesServlet() - Constructor for class org.intermine.webservice.server.bg.BGPropertiesServlet
 
BGPropertiesUpdateService - Class in org.intermine.webservice.server.bg
Update an existing bluegenes property.
BGPropertiesUpdateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.bg.BGPropertiesUpdateService
Constructor
BIG_BATCH_SIZE - Static variable in class org.intermine.api.results.WebResults
The batch size to use when we need to iterate through the whole result set.
BIG_BATCH_SIZE - Static variable in class org.intermine.web.struts.SaveBagAction
The batch size to use when we need to iterate through the whole result set.
bigint - org.intermine.sql.DatabaseUtil.Type
big int
BioEntityMarkupService - Class in org.intermine.webservice.server.fair
Serve bioentity markup to be added to the report page
BioEntityMarkupService(InterMineAPI) - Constructor for class org.intermine.webservice.server.fair.BioEntityMarkupService
Constructor
BODY - org.intermine.web.struts.oauth2.MessageFormat
This provider expects parameters in the BODY
BONFERRONI - org.intermine.web.logic.widget.ErrorCorrection.Strategy
The Bonferroni error correction strategy
BOOLEAN_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
Common keys
BOOLEAN_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
boolean_type - org.intermine.sql.DatabaseUtil.Type
boolean
BOTH_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being both false.
BOTH_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being both true.
bracketedExpr() - Method in class org.intermine.pathquery.LogicParser
 
BrandingService - Class in org.intermine.webservice.server.branding
Serve branding information so that a client can provide a branded visual experience.
BrandingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.branding.BrandingService
 
broken - Variable in class org.intermine.dataloader.DataTracker
 
bufferToHexString(byte[]) - Static method in class org.intermine.metadata.StringUtil
Convert a byte buffer to a hexadecimal string.
BuildBagAction - Class in org.intermine.web.struts
An action that makes a bag from text.
BuildBagAction() - Constructor for class org.intermine.web.struts.BuildBagAction
 
BuildBagForm - Class in org.intermine.web.struts
Form bean to represent the inputs needed to create a bag from user input.
BuildBagForm() - Constructor for class org.intermine.web.struts.BuildBagForm
 
BuildDbTask - Class in org.intermine.task
Generates and inserts SQL given database name, schema and temporary directory
BuildDbTask() - Constructor for class org.intermine.task.BuildDbTask
 
Builder() - Constructor for class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
buildFromComponent(SqlGenerator.State, Query, DatabaseSchema, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds the FROM list for the SQL query.
buildGroupBy(Query, DatabaseSchema, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a String representing the GROUP BY component of the Sql query.
buildIndex(ObjectStore) - Method in class org.intermine.web.autocompletion.AutoCompleter
Build the index from the database blob
buildKeyStore() - Method in class org.intermine.web.security.KeyStoreBuilder
Build the key store.
buildObject(ResultSet, String, ObjectStoreInterMineImpl, Class<?>, Set<String>) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Builds an object from separate fields in flat mode.
buildOrderBy(SqlGenerator.State, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a String representing the ORDER BY component of the Sql query.
buildQueryValue(PathConstraint) - Method in class org.intermine.web.logic.widget.WidgetLdr
Return a QueryValue instance using the path contraint given in input
buildSelectComponent(SqlGenerator.State, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a String representing the SELECT component of the Sql query.
buildTokenTypeASTClassMap() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
buildTokenTypeASTClassMap() - Method in class org.intermine.pathquery.LogicParser
 
buildTokenTypeASTClassMap() - Method in class org.intermine.sql.query.SqlParser
 
buildTree(String) - Method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper.NodeBuilder
Recurse through the model and build a tree of metadata nodes based on this
buildWhereClause(SqlGenerator.State, Query, Constraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds the WHERE clause for the SQL query.
ByTagOrder() - Constructor for class org.intermine.api.bag.BagManager.ByTagOrder
 

C

cache - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
CACHE_LARGEST_OBJECT - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
CacheHoldingArrayList<E> - Class in org.intermine.util
This is an extension of the the ArrayList class, designed to be used by systems that return Lists of data, with extra data that should not be flushed out of a cache until the List is garbage collected.
CacheHoldingArrayList() - Constructor for class org.intermine.util.CacheHoldingArrayList
Empty constructor
CacheHoldingArrayList(int) - Constructor for class org.intermine.util.CacheHoldingArrayList
Constructs a new instance with the given initial capacity.
CacheHoldingArrayList(Collection<E>) - Constructor for class org.intermine.util.CacheHoldingArrayList
Constructs a new instance from another Collection.
cacheLines - Variable in class org.intermine.sql.precompute.OptimiserCache
A Map that holds a mapping from unoptimised query string (with LIMIT and OFFSET stripped off) to a Set of OptimiserCacheLine objects.
cacheLinks(MultiKey, Collection<PartnerLink>) - Method in class org.intermine.api.mines.FriendlyMineManager
 
CacheMap<K,​V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
CacheMap() - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the default initial capacity (16) and the default load factor (0.75).
CacheMap(int) - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the given initial capacity and the default load factor, which is 0.75.
CacheMap(int, float) - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the given initial capacity and the given load factor.
CacheMap(String) - Constructor for class org.intermine.util.CacheMap
Constructs a new, empty CacheMap with the default initial capacity (16) and the default load factor (0.75), and a name.
CacheMap(Map<K, V>) - Constructor for class org.intermine.util.CacheMap
Constructs a new CacheMap with the same mappings as the specified Map.
cacheMisses - Variable in class org.intermine.dataloader.BatchingFetcher
 
cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Places an entry into the objectstore getObjectById cache.
cacheObjectById(Integer, InterMineObject) - Method in interface org.intermine.objectstore.ObjectStore
Places an entry into the objectstore getObjectById cache.
cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Places an entry into the objectstore getObjectById cache.
cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Places an entry into the objectstore getObjectById cache.
calculate(EnrichmentInput, Double, String, boolean, CorrectionCoefficient) - Static method in class org.intermine.web.logic.widget.EnrichmentCalculation
Perform an enrichment calculation based on input from some source and return results that include a p-value and count for each attribute that was observed in the sample.
call(A) - Method in class org.intermine.webservice.server.core.F
The body of the function
call(A) - Method in interface org.intermine.webservice.server.core.Function
Take an A and return a B.
call(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
 
call(Either<A, B>) - Method in class org.intermine.webservice.server.core.EitherVisitor
 
call(T) - Method in interface org.intermine.webservice.server.core.Predicate
Apply some test to some kind of thing.
call(X) - Method in class org.intermine.webservice.server.core.F.Constant
Call this function, returning the value supplied to the constructor.
Callback - Class in org.intermine.web.struts.oauth2
The controller that handles the requests made after the user has visited their authorisation provider to log-in.
Callback() - Constructor for class org.intermine.web.struts.oauth2.Callback
 
CALLBACK_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The callback to be supplied for jsonp calls
CallbackService - Class in org.intermine.webservice.server.oauth2
The service handles the requests made after the user has visited their authorisation provider to log-in.
CallbackService(InterMineAPI) - Constructor for class org.intermine.webservice.server.oauth2.CallbackService
Constructor
CallbackServlet - Class in org.intermine.webservice.server.oauth2
A Servlet for routing requests to the oauth2 CallbackService.
CallbackServlet() - Constructor for class org.intermine.webservice.server.oauth2.CallbackServlet
 
canAssignObjectToType(Class<?>, InterMineObject) - Static method in class org.intermine.api.util.PathUtil
Return true if given type (of a constraint) can be assigned to the InterMineObject - i.e.
cancelRequest(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method cancels any Statement running in a given request ID, and blacklists that ID.
Candidate(String) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Constructor.
Candidate(Query) - Constructor for class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Constructor.
candidates - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
candidateTables - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
canDoPkNow(PrimaryKey, ClassDescriptor, Map<PrimaryKey, ClassDescriptor>) - Method in class org.intermine.dataloader.BatchingFetcher
Returns whether this primary key can be fetched now.
canExport(List<Class<?>>) - Method in interface org.intermine.web.logic.export.Exporter
This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.
canExport(List<Class<?>>) - Method in class org.intermine.web.logic.export.ExporterImpl
This method finds out if result row composed from instances of these classes can be exported with actual implementation of exporter.
canExport(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
 
canExport(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
Check if this TableExporter can export the given PagedTable.
canExport(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
Return true if the specified class or a subclass is found in a column of the paged table (or is the parent class of a field displayed in the table).
canHaveCollection(String) - Method in class org.intermine.xml.full.Item
Return true if and only if the argument names a possible collection for this Item.
canHaveReference(String) - Method in class org.intermine.xml.full.Item
Return true if and only if the argument names a possible reference for this Item.
canonicaliseIndexes(Collection<String>) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
Takes a collection of index strings, and removes redundant entries.
canServe(Format) - Method in class org.intermine.webservice.server.lists.AvailableListsService
 
canServe(Format) - Method in class org.intermine.webservice.server.lists.JaccardIndexService
 
canServe(Format) - Method in class org.intermine.webservice.server.lists.ListMakerService
 
canServe(Format) - Method in class org.intermine.webservice.server.model.ModelService
 
canServe(Format) - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.CodeService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRemovalService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryToListService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.QueryUploadService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.result.TableRowService
 
canServe(Format) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.SystemTemplatesService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateRemovalService
 
canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateUploadService
 
canServe(Format) - Method in class org.intermine.webservice.server.VersionService
 
canServe(Format) - Method in class org.intermine.webservice.server.WebService
Check whether the format is acceptable.
canServe(Format) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
capitalise(String) - Static method in class org.intermine.metadata.StringUtil
Returns a capitalised version of the given String
CaseInsensitiveComparator() - Constructor for class org.intermine.api.bag.BagManager.CaseInsensitiveComparator
 
castBagsToCommonType(Collection<InterMineBag>, String, Set<String>, Profile, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
Given a common type, return a collection of bags cast to that type.
CATEGORIES - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute, List of category names.
categoriseBasedOnTags(FieldDescriptor, String, DisplayField, Map<String, DisplayField>, TagManager, String, Map<String, Map<String, DisplayField>>, boolean) - Static method in class org.intermine.web.struts.ReportController
For a given FieldDescriptor, look up its 'aspect:' tags and place it in the correct map within placementRefsAndCollections.
category - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
CEIL - Static variable in class org.intermine.objectstore.query.QueryFunction
Smallest integer value greater than input.
ChangeEvent - Interface in org.intermine.api.search
Events that represent changes in something.
ChangePasswordAction - Class in org.intermine.web.struts
 
ChangePasswordAction() - Constructor for class org.intermine.web.struts.ChangePasswordAction
 
ChangePasswordForm - Class in org.intermine.web.struts
Form bean to represent the inputs needed to change a password from user input.
ChangePasswordForm() - Constructor for class org.intermine.web.struts.ChangePasswordForm
 
ChangePasswordService - Class in org.intermine.webservice.server.user
Class for changing the password of an existing user
ChangePasswordService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.ChangePasswordService
Constructor
changePasswordWithToken(String, String) - Method in class org.intermine.api.profile.ProfileManager
Changes the password of a profile if the given token is valid.
changePath(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Change the currently active metadata Node
changeSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Increments the sequence numbers for the given set of database components.
ChangeTableAction - Class in org.intermine.web.struts
Implementation of DispatchAction.
ChangeTableAction() - Constructor for class org.intermine.web.struts.ChangeTableAction
 
ChangeTableSizeAction - Class in org.intermine.web.struts
Changes the size of the results displayed.
ChangeTableSizeAction() - Constructor for class org.intermine.web.struts.ChangeTableSizeAction
 
ChangeTableSizeForm - Class in org.intermine.web.struts
Form bean for changing the page size.
ChangeTableSizeForm() - Constructor for class org.intermine.web.struts.ChangeTableSizeForm
Constructor
changeViewPathDescription(String, String) - Method in class org.intermine.dwr.AjaxServices
Set the description of a view path.
characters(char[], int, int) - Method in class org.intermine.api.bag.BagQueryHandler
characters(char[], int, int) - Method in class org.intermine.api.bag.InvitationHandler
characters(char[], int, int) - Method in class org.intermine.api.profile.PreferencesHandler
characters(char[], int, int) - Method in class org.intermine.pathquery.PathQueryHandler
characters(char[], int, int) - Method in class org.intermine.webservice.server.ServiceListingHandler
 
charAt(int) - Method in class org.intermine.model.StringConstructor
charAt(int) - Method in class org.intermine.objectstore.query.ClobAccess
Return a character from the specified index.
charAt(int) - Method in class org.intermine.objectstore.query.PendingClob
Return a character from the specified index.
CHART - org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
There is the chart type, that produces data suitable for visual display.
check(Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.precompute.OptimiserMappingChecker
Checks a partial mapping.
check(Map<T, T>) - Method in interface org.intermine.util.MappingUtilChecker
Checks a partial mapping.
checkAttribute(String) - Method in class org.intermine.xml.full.Item
Return true if the name parameter is an attribute of the class for this Item or if the Model or the className of this Item haven't been set.
checkCollection(String) - Method in class org.intermine.xml.full.Item
Throw a RuntimeException if the name parameter isn't an collection in the class set by setClassName() in the Model set by setModel().
checkComparisonEquals(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it was created by compare, and return true if this implies that the left constraint is EQUAL to the right constraint, in a loose sense.
checkComparisonImplies(int) - Static method in class org.intermine.sql.query.AbstractConstraint
Take an integer as if it was created by compare, and return true if this implies that the left constraint IMPLIES the right constraint, in a loose sense.
CheckForIsNotNullConstraint - Class in org.intermine.objectstore.intermine
For use with ConstraintHelper.traverseConstraints().
CheckForIsNotNullConstraint(QueryNode) - Constructor for class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
Construct with the QueryNode to test for NOT NULL constraint.
checkImplementations(String) - Method in class org.intermine.xml.full.Item
Throw RuntimeException if the given implementations don't match the model.
checkLists(Map<String, InterMineBag>, List<String>) - Method in class org.intermine.webservice.server.lists.ListInput
Make sure that any lists names exist.
checkPassword(String, String) - Static method in class org.intermine.util.PasswordHasher
Checks to see if a password matches an optionally hashed password entry.
checkPathFormat(String) - Static method in class org.intermine.pathquery.PathQuery
Verifies the format of a path for a query.
checkReference(String) - Method in class org.intermine.xml.full.Item
Throw a RuntimeException if the name parameter isn't an reference in the class set by setClassName() in the Model set by setModel().
checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Checks a number against the sequence number, and throws an exception if they do not match.
checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Checks a number against the sequence number, and throws an exception if they do not match.
checkStartLimit(int, int, Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Checks the start and limit to see whether they are inside the hard limits for this ObjectStore
CLASS - Static variable in class org.intermine.api.tag.TagTypes
A Class/ClassDescriptor.
CLASS_KEYS - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the class_keys.properties file.
ClassAttributes - Class in org.intermine.api.searchengine
container class to cache class attributes
ClassAttributes(String, Set<AttributeDescriptor>) - Constructor for class org.intermine.api.searchengine.ClassAttributes
constructor
ClassChooserController - Class in org.intermine.web.struts
Gets list of help text blurbs for each class, and passes them on to the display page.
ClassChooserController() - Constructor for class org.intermine.web.struts.ClassChooserController
 
ClassConstraint - Class in org.intermine.objectstore.query
Constrain whether a QueryClass is equal/not equal to another QueryClass or an example of an object belonging to a QueryClass.
ClassConstraint(QueryClass, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ClassConstraint
Construct ClassConstraint
ClassConstraint(QueryClass, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ClassConstraint
Construct ClassConstraint
classConstraintToString(SqlGenerator.State, StringBuffer, ClassConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a ClassConstraint object into a String suitable for putting in an SQL query.
ClassDescriptor - Class in org.intermine.metadata
Describe a business model class.
ClassDescriptor(String, String, boolean, Collection<AttributeDescriptor>, Collection<ReferenceDescriptor>, Collection<CollectionDescriptor>, String) - Constructor for class org.intermine.metadata.ClassDescriptor
Construct a ClassDescriptor.
ClassKeyHelper - Class in org.intermine.api.config
Methods to read and manage keys for classes.
classKeys - Variable in class org.intermine.api.InterMineAPI
 
ClassKeys - Interface in org.intermine.api.types
Type alias for classkeys - simplifies matters and prevents mistakes.
ClassKeyServlet - Class in org.intermine.webservice.server
A Servlet for routing requests to the ClassKeyService.
ClassKeyServlet() - Constructor for class org.intermine.webservice.server.ClassKeyServlet
 
ClassKeysNotFoundException - Exception in org.intermine.api.bag
Exception thrown when given attempting to create a bag for a type that isn't in the model, this can happen when reading bags from a userprofile database and the data model has changed.
ClassKeysNotFoundException(String) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
Constructs an IncompatibleBagTypesException with the specified detail message.
ClassKeysNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.
ClassKeysNotFoundException(Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
Constructs an IncompatibleBagTypesException with the specified nested throwable.
ClassKeysService - Class in org.intermine.webservice.server
A service to fetch a JSON representation of class keys for all classes in the model.
ClassKeysService(InterMineAPI) - Constructor for class org.intermine.webservice.server.ClassKeysService
Construct with the InterMineAPI.
className - Variable in class org.intermine.model.fulldata.Item
 
className - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
className - Variable in class org.intermine.web.struts.QueryClassSelectForm
 
ClassNameURIIdentifierMapper - Class in org.intermine.web.uri
Class to map the class name defined in the core.xml with the identifier used to generate the InterMineLUI (e.g.
classNotExists(Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns true if there were no instances of the given class in the database.
ClassResourceOpener - Class in org.intermine.web.logic
Objects that open resources relative to a classpath.
ClassResourceOpener(Class<?>) - Constructor for class org.intermine.web.logic.ClassResourceOpener
Constructor.
classToType(Class<?>) - Static method in class org.intermine.objectstore.query.UnknownTypeValue
Converts a Class into an approximate type.
cld - Variable in class org.intermine.metadata.FieldDescriptor
 
clean() - Method in class org.intermine.dataloader.ObjectDescription
Marks the ObjectDescription as clean - that is all the data has been flushed to the backing database.
cleanTags(TagManager) - Static method in class org.intermine.web.struts.InitialiserPlugin
Remove class tags from the user profile that refer to classes that non longer exist
cleanUp() - Method in class org.intermine.webservice.server.WebService
Subclasses may put clean-up code here, to be run after the request has been executed.
clear() - Method in class org.intermine.api.profile.UserPreferences
 
clear() - Method in class org.intermine.dataloader.DataTracker
Clears the data tracker of all entries.
clear() - Static method in class org.intermine.sql.precompute.OptimiserCache
used only for testing
clear() - Method in class org.intermine.sql.writebatch.Batch
Clears the batch without writing it to the database.
clear() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Clears the batch.
clear() - Method in interface org.intermine.sql.writebatch.Table
Clears the batch.
clear() - Method in class org.intermine.sql.writebatch.TableBatch
Clears the batch.
clear() - Method in class org.intermine.util.AlwaysMap
clear() - Method in class org.intermine.util.IdentityMap
clear() - Method in class org.intermine.util.IntPresentSet
Removes all ints from the object.
clear() - Method in class org.intermine.util.IntToIntMap
Removes all mappings from the object.
clear() - Method in class org.intermine.util.PseudoSet
clear() - Method in class org.intermine.util.ReferenceMap
clearConstraints() - Method in class org.intermine.pathquery.PathQuery
Clears the entire set of constraints from this query, and resets the constraint logic.
clearConstraints() - Method in class org.intermine.template.TemplateQuery
Clears the entire set of constraints from this query, and resets the constraint logic.
clearDescriptions() - Method in class org.intermine.pathquery.PathQuery
Removes all path descriptions from this query.
clearObj(Integer) - Method in class org.intermine.dataloader.DataTracker
Clears the cache for a particular object, in preparation for writing all the data for that object.
clearOrderBy() - Method in class org.intermine.objectstore.query.Query
Clears the ORDER BY clause of this Query
clearOrderBy() - Method in class org.intermine.pathquery.PathQuery
Clears the entire order by list.
clearOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery
Clears all outer join status data from this query.
clearProblem() - Method in class org.intermine.sql.writebatch.Batch
Clears the problem with the Batch.
clearSelect() - Method in class org.intermine.objectstore.query.Query
Clears the SELECT list
clearSelectIds() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Clear the table selection
clearView() - Method in class org.intermine.pathquery.PathQuery
Clears the entire view list.
clob - Variable in class org.intermine.objectstore.query.ClobAccess
 
Clob - Class in org.intermine.objectstore.query
Object representing a large String that has been stored in the database.
Clob(int) - Constructor for class org.intermine.objectstore.query.Clob
Constructs a new Clob.
CLOB_PAGE_SIZE - Static variable in class org.intermine.objectstore.query.Clob
Page size for clob data
CLOB_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the table that stores Clobs.
ClobAccess - Class in org.intermine.objectstore.query
Class used to read a Clob from the ObjectStore.
ClobAccess() - Constructor for class org.intermine.objectstore.query.ClobAccess
Protected constructor for use by PendingClob only.
ClobAccess(ObjectStore, Clob) - Constructor for class org.intermine.objectstore.query.ClobAccess
Construct a ClobAccess object from an ObjectStore and a Clob.
ClobAccess.ClobAccessSubclassFactory - Class in org.intermine.objectstore.query
Class to provide fast access to the constructor of plugin subclasses of ClobAccess.
ClobAccessSubclassFactory() - Constructor for class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory
 
CLOBID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the clobid column in the clob table.
CLOBPAGE_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the page number column in the clob table.
CLOBVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the value column in the clob table.
clone() - Method in class org.intermine.api.profile.InterMineBag
Create copy of bag.
clone() - Method in class org.intermine.api.template.ApiTemplate
Clone this ApiQuery
clone() - Method in class org.intermine.pathquery.PathQuery
Returns a deep copy of this object.
clone() - Method in class org.intermine.template.TemplateQuery
Clone this TemplateQuery.
cloneAttributeDescriptors(Set<AttributeDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Clone a set of AttributeDescriptors.
cloneClassDescriptor(ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Construct a ClassDescriptor that takes on all the properties of cld without attaching to a particular Model.
cloneCollectionDescriptors(Set<CollectionDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Clone a set of CollectionDescriptors.
cloneQuery(Query) - Static method in class org.intermine.objectstore.query.QueryCloner
Clones a query object.
cloneReferenceDescriptors(Set<ReferenceDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Clone a set of ReferenceDescriptors.
cloneWithoutEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Return a clone of this template query with all editable constraints removed - i.e.
close() - Method in class org.intermine.api.bag.BagManager
Close the TagManager
close() - Method in class org.intermine.api.profile.ProfileManager
Close this ProfileManager
close() - Method in class org.intermine.api.profile.TagManager
Close this TagManager.
close() - Method in class org.intermine.api.tracker.TrackerDelegate
Release the db connection when done.
close() - Method in class org.intermine.dataconversion.DataConverter
Perform any necessary clean-up after processing
close() - Method in class org.intermine.dataconversion.DirectoryConverter
Perform any necessary clean-up after post-conversion
close() - Method in interface org.intermine.dataconversion.ItemWriter
Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.
close() - Method in class org.intermine.dataconversion.MockItemWriter
Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.
close() - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Flushes any store queue, closes transactions, and generally makes sure that every Item passed to the store() method is committed to the destination.
close() - Method in class org.intermine.dataloader.DataTracker
Closes this DataTracker, releasing both connections to the database.
close() - Method in class org.intermine.dataloader.DirectDataLoader
Close the DirectDataLoader, must be called to make sure final batch of data is stored.
close() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Closes the connection associated with this ObjectStoreWriter
close() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Closes the connection associated with this ObjectStoreWriter
close() - Method in class org.intermine.dataloader.XmlDataLoader
Perform any necessary clean-up and close the integration writer
close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
 
close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
 
close() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Closes this ObjectStore's DB log connection.
close() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Closes this ObjectStore's DB log connection.
close() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Closes the connection associated with this ObjectStoreWriter
close() - Method in class org.intermine.sql.logging.DatabaseWriter
Close this Writer
close(Connection) - Method in class org.intermine.sql.writebatch.Batch
Closes this BatchWriter.
close(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Close method - prints out summary data.
close(Source) - Method in class org.intermine.dataloader.BatchingFetcher
Close method - prints out summary data.
close(Source) - Method in class org.intermine.dataloader.HintingFetcher
Close method - prints out summary data.
close(Source) - Method in class org.intermine.dataloader.ParallelBatchingFetcher
Close method - prints out summary data.
CLOSE_PAREN - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
CLOSE_PAREN - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
CLOSE_PAREN - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
closeSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
cls - Variable in class org.intermine.objectstore.query.ContainsConstraint
 
cls - Variable in class org.intermine.objectstore.query.SubqueryConstraint
 
clsName - Variable in class org.intermine.task.AnalyseDbTask
 
clsName - Variable in class org.intermine.task.DirectoryConverterTask
 
clsName - Variable in class org.intermine.task.FileConverterTask
 
clsName - Variable in class org.intermine.task.PostProcessorTask
 
COALESCE - Static variable in class org.intermine.sql.query.Function
COALESCE operator - used by the precomputed tables' orderby fields.
CodeService - Class in org.intermine.webservice.server.query
A service for generating code based on a query.
CodeService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.CodeService
Constructor.
CodeServlet - Class in org.intermine.webservice.server.query
A servlet for routing requests to the code service.
CodeServlet() - Constructor for class org.intermine.webservice.server.query.CodeServlet
 
CodeTranslator - Class in org.intermine.webservice.server
Translates strings between codes used in ConstraintOp class and abbreviations or full code names of operations.
collapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
COLLECTION - Static variable in class org.intermine.api.tag.TagTypes
Collection.
collection_from_question_mark() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
collection_path_expression() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
collection_select_list() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
COLLECTION_SELECT_LIST - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
collection_select_value() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
COLLECTION_SELECT_VALUE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
CollectionDescriptor - Class in org.intermine.metadata
Describes a field that references a collection of other objects.
CollectionDescriptor(String, String, String) - Constructor for class org.intermine.metadata.CollectionDescriptor
Construct a CollectionDescriptor.
CollectionDetailsAction - Class in org.intermine.web.struts
Action that creates a table of collection elements for display.
CollectionDetailsAction() - Constructor for class org.intermine.web.struts.CollectionDetailsAction
 
collections - Variable in class org.intermine.model.fulldata.Item
 
CollectionTableAction - Class in org.intermine.web.struts
Action that creates a table of collection elements for display in a table widget.
CollectionTableAction() - Constructor for class org.intermine.web.struts.CollectionTableAction
 
collectionToSQLString(Collection<? extends SQLStringable>, String) - Static method in class org.intermine.sql.query.Query
Converts a collection of objects that implement the getSQLString method into a String, with the given comma string between each element.
collectionToSQLString(Collection<? extends SQLStringable>, Collection<String>, String) - Static method in class org.intermine.sql.query.Query
Converts a collection of objects that implement the getSQLString method into a String, with the given comma string between each element.
CollectionUtil - Class in org.intermine.util
Utilities for Collections.
colonsToDots(String) - Static method in class org.intermine.metadata.StringUtil
Converts all the colons in a String into dots.
COLONTYPE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
COLONTYPE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
Column - Class in org.intermine.api.results
Configuration information for a column in a table
Column(String, int, Class) - Constructor for class org.intermine.api.results.Column
Constructor that takes a String name.
Column(Path, int, Class) - Constructor for class org.intermine.api.results.Column
Constructor that takes a Path object.
Column(Path, String, int, Class) - Constructor for class org.intermine.api.results.Column
Constructor that takes a Path object.
COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter
The key for the header columns
columnExists(Connection, String, String) - Static method in class org.intermine.sql.DatabaseUtil
Tests if a column exists in the database
columnFullNames - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
ColumnHeaderStyle - Enum in org.intermine.webservice.server
Enumeration for outer join status.
columnId - Variable in class org.intermine.api.results.Column
 
combineBags() - Method in class org.intermine.api.bag.operations.BagOperation
 
combineBags() - Method in class org.intermine.api.bag.operations.RelativeComplement
 
CombinedIterator<E> - Class in org.intermine.util
An Iterator that combines the contents of various other Iterators.
CombinedIterator(List<Iterator<? extends E>>) - Constructor for class org.intermine.util.CombinedIterator
Constructs a CombinedIterator from a List of Iterators.
combineWith(ProfileMergeIssues) - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Combine this set of merge issues with another set.
COMMA - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
COMMA - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
Command - Class in org.intermine.webservice.server.jbrowse
 
Command(Commands.Action, String, String, Segment, Map<String, String>) - Constructor for class org.intermine.webservice.server.jbrowse.Command
 
CommandRunner - Class in org.intermine.webservice.server.jbrowse
 
CommandRunner(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.CommandRunner
 
Commands - Class in org.intermine.webservice.server.jbrowse
 
Commands.Action - Enum in org.intermine.webservice.server.jbrowse
 
comment - Variable in class org.intermine.template.TemplateQuery
The private comment for this query.
commitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Request that the ObjectStore commits and closes the transaction, delegate to internal ObjectStoreWriter.
commitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Request that the ObjectStoreWriter commits and closes the transaction
commitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Request that the ObjectStoreWriter commits and closes the transaction
commitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Commits a transaction.
COMMON_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
Common keys
CommutativeOperationInput - Class in org.intermine.webservice.server.lists
An input class for operations that are commutative.
CommutativeOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.CommutativeOperationInput
Constructor.
comparable(Class<?>, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
Check whether the two arguments are of comparable types i.e.
compare(Object, Object) - Method in class org.intermine.util.NullFirstComparator
compare(Object, Object) - Method in class org.intermine.xml.full.RendererComparator
Compare two Class objects by name.
compare(String, String) - Method in class org.intermine.api.bag.BagManager.ByTagOrder
 
compare(String, String) - Method in class org.intermine.api.bag.BagManager.CaseInsensitiveComparator
 
compare(InterMineObject, InterMineObject) - Method in class org.intermine.dataloader.SourcePriorityComparator
Compares two objects.
compare(Path, Path) - Method in class org.intermine.pathquery.PathLengthComparator
Compare paths by number elements they contain, shortest paths come first.
compare(AbstractConstraint) - Method in class org.intermine.sql.query.AbstractConstraint
Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractConstraint
Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constraint
Compare this Constraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet
Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.InListConstraint
Compare this InListConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.NotConstraint
Compare this NotConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.SubQueryConstraint
Compare this SubQueryConstraint with another AbstractConstraint, ignoring aliases in member fields and tables.
compare(AbstractTable, AbstractTable) - Method in class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator
Compare two AbstractTables using equalsIgnoreAlias().
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constant
Compare this Constant to another AbstractValue.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Field
Compare this field to another AbstractValue.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Function
Compare the value of this AbstractValue with another.
compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.OrderDescending
Compare the value of this AbstractValue with another.
compare(TemplateQuery, TemplateQuery) - Method in class org.intermine.template.TemplateComparator
Compare two TemplateQuery objects by title, falling back to name if the titles are identical.
compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Compares 2 sets of AbstractConstraints
compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Compares 2 sets of AbstractConstraints
comparesActualToExpected() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
compareSelectLists(List<SelectValue>, List<SelectValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Compares two Lists of SelectValues, and returns true if all the items in the first List are present in the second List, ignoring the SelectValue alias.
compareTo(ClassDescriptor) - Method in class org.intermine.metadata.ClassDescriptor
compareTo(ParallelPrecomputer.Job) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer.Job
compareTo(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTable
Implements Comparable's method, so we can put PrecomputedTable objects into SortedMaps.
compareTo(Row) - Method in class org.intermine.sql.writebatch.Row
compareTo(SummaryPath) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
compareTo(Item) - Method in class org.intermine.xml.full.Item
Compare items first by class, then by identifier, intended for creating ordered output files.
comparison_op() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
comparison_op() - Method in class org.intermine.sql.query.SqlParser
 
comparison_op(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
complete - Variable in class org.intermine.objectstore.query.ResultsInfo
 
complete - Variable in class org.intermine.sql.query.ExplainResult
 
completelyFalse(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns true if this constraint is always false, regardless of row values.
CompletelyFalseException - Exception in org.intermine.objectstore.intermine
Exception thrown if a Constraint is deemed to be completely false.
CompletelyFalseException() - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
CompletelyFalseException(String) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
CompletelyFalseException(String, Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
CompletelyFalseException(Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
Constructor.
completelyTrue(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns true if this constraint is always true, regardless of row values.
compose(F<B, C>) - Method in class org.intermine.webservice.server.core.F
Compose two functions f and g producing a function h such that h(x) = f(g(x)).
composeClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil
Return the Class for the array of Class objects.
composeClass(Set<Class<?>>) - Static method in class org.intermine.util.DynamicUtil
Return the Class for a set of Class objects.
composeDescriptiveClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil
Return the Class for the array of Class objects.
COMPUTE_TOTAL_COUNT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Compute total count parameter name.
con - Variable in class org.intermine.sql.logging.DatabaseWriter
 
con - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
con - Variable in class org.intermine.sql.query.NotConstraint
 
con - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
config - Variable in class org.intermine.web.displayer.ReportDisplayer
 
config - Variable in class org.intermine.web.logic.widget.Widget
 
Config - Class in org.intermine.webservice.server.jbrowse
Provide standard JBrowse configuration files (trackList.json and refSeqs.json) that are required to run a JBrowse instance.
Config(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.Config
Build a new instance with the injected API
configFileName - Variable in class org.intermine.task.SummariseObjectStoreTask
 
ConfigurableMine - Interface in org.intermine.api.mines
A sub-interface of Mine to encapsulate the mutable elements of the interface, and not expose them the the consumer.
ConfigurableWebServiceServlet - Class in org.intermine.webservice.server.core
A servlet that can be configured entirely in XML.
ConfigurableWebServiceServlet() - Constructor for class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
 
ConfigurationException - Exception in org.intermine.api.mines
An error caused when trying to configure something.
ConfigurationException(String) - Constructor for exception org.intermine.api.mines.ConfigurationException
Construct an exception with a message.
configure(Properties) - Method in interface org.intermine.api.mines.ConfigurableMine
Configure this mine with a the properties provided.
configure(Properties) - Method in class org.intermine.api.mines.HttpRequester
 
configure(Properties) - Method in class org.intermine.api.mines.LocalMine
 
configure(Properties) - Method in interface org.intermine.api.mines.MineRequester
Accept configuration provided in the form of properties.
configure(Properties) - Method in class org.intermine.api.mines.RemoteMine
 
configure(Properties) - Method in class org.intermine.sql.Database
Configures a datasource from a Properties object
configureDynamicAttributes(Object) - Method in class org.intermine.task.DynamicAttributeTask
Look at set methods on a target object and lookup values in project properties.
conn - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
conn - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
connection - Variable in class org.intermine.api.tracker.TrackerDelegate
 
connection - Variable in class org.intermine.api.tracker.xml.TrackHandler
 
connectionTakenBy - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
connInUse - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
cons - Variable in class org.intermine.sql.query.ConstraintSet
 
ConsistentSet<E> - Class in org.intermine.util
A Set that allows for its member objects to be changed whilst still belonging to the set.
ConsistentSet() - Constructor for class org.intermine.util.ConsistentSet
Constructor.
constant() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
constant() - Method in class org.intermine.sql.query.SqlParser
 
constant(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
constant(B) - Static method in class org.intermine.webservice.server.core.F
Construct a constant function that discards its input and always returns the same value.
Constant - Class in org.intermine.sql.query
A representation of a constant value in an SQL query.
Constant(String) - Constructor for class org.intermine.sql.query.Constant
Constructor for this Constant object.
Constant(R) - Constructor for class org.intermine.webservice.server.core.F.Constant
Construct a constant function.
CONSTANT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
CONSTANT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
Constants - Class in org.intermine.api.config
A single constant.
Constants - Class in org.intermine.web.logic
Container for ServletContext and Session attribute names used by the webapp
constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
constraint() - Method in class org.intermine.sql.query.SqlParser
 
constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
Constraint - Class in org.intermine.objectstore.query
Abstract reperesentation of a query constraint.
Constraint - Class in org.intermine.sql.query
A representation of a normal constraint, comparing two AbstractValue objects.
Constraint() - Constructor for class org.intermine.objectstore.query.Constraint
 
Constraint(AbstractValue, int, AbstractValue) - Constructor for class org.intermine.sql.query.Constraint
Constructor for a Constraint object.
CONSTRAINT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
CONSTRAINT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
constraint_set() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
constraint_set() - Method in class org.intermine.sql.query.SqlParser
 
constraintAttributes - Variable in class org.intermine.pathquery.PathQueryHandler
 
constraintCode - Variable in class org.intermine.pathquery.PathQueryHandler
 
constraintDescriptions - Variable in class org.intermine.template.TemplateQuery
Descriptions of constraints
ConstraintHelper - Class in org.intermine.objectstore.query
Static methods to create Lists of Constraint objects in a query and Constraints in a query relating to a given QueryClass, plus helper methods for dealing with Constraints.
ConstraintInput - Class in org.intermine.web.logic.template
Simple object that carries constraint values for other processing.
ConstraintInput(String, String, String, ConstraintOp, String, List<String>, String) - Constructor for class org.intermine.web.logic.template.ConstraintInput
ConstraintLoad constructor.
constraintLogic - Variable in class org.intermine.pathquery.PathQueryHandler
 
ConstraintOp - Class in org.intermine.metadata
Operations used in building constraints.
ConstraintOptions - Class in org.intermine.api.query.range
A bundle of options consumed by the AbstractHelper when generating constraint sets for a set of ranges.
ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp) - Constructor for class org.intermine.api.query.range.ConstraintOptions
Construct a new set of constraint options.
ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp, String, String) - Constructor for class org.intermine.api.query.range.ConstraintOptions
Construct a new set of constraint options.
constraintPath - Variable in class org.intermine.pathquery.PathQueryHandler
 
constraints - Variable in class org.intermine.objectstore.query.ConstraintSet
 
Constraints - Class in org.intermine.pathquery
Builds constraints for the PathQuery.
ConstraintSet - Class in org.intermine.objectstore.query
Groups a series of Constraints together.
ConstraintSet - Class in org.intermine.sql.query
A representation of a set of constraints ORed together.
ConstraintSet() - Constructor for class org.intermine.sql.query.ConstraintSet
Constructor for a ConstraintSet object.
ConstraintSet(ConstraintOp) - Constructor for class org.intermine.objectstore.query.ConstraintSet
Construct empty ConstraintSet
constraintSetToString(SqlGenerator.State, StringBuffer, ConstraintSet, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a ConstraintSet object into a String suitable for putting in an SQL query.
constraintSwitchOffAbility - Variable in class org.intermine.template.TemplateQuery
Configuration for switch-off-ability of constraints
constraintToJson(PathConstraint, String) - Method in class org.intermine.pathquery.PathQuery
 
constraintToString(SqlGenerator.State, StringBuffer, Constraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a Constraint object into a String suitable for putting in an SQL query.
constraintToString(Query, Constraint, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a Constraint into a String.
ConstraintTraverseAction - Interface in org.intermine.objectstore.query
ConstraintTraverseActions are passed to the traverseConstraints() method.
ConstraintValueParser - Class in org.intermine.pathquery
Parser for parsing constraint value.
constraintValues - Variable in class org.intermine.pathquery.PathQueryHandler
 
ConstraintWithBag - Interface in org.intermine.objectstore.query
Common interface for BagConstraint and MultipleInBagConstraint defining the getBag() method.
constructQueries(boolean, ObjectStore, String, String) - Static method in class org.intermine.task.PrecomputeTask
Create queries for given path.
constructQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Construct an objectstore query represented by the given path.
ContactAction - Class in org.intermine.web.struts
Action handles submission of user feedback form.
ContactAction() - Constructor for class org.intermine.web.struts.ContactAction
 
ContactForm - Class in org.intermine.web.struts
Form bean representing feedback form.
ContactForm() - Constructor for class org.intermine.web.struts.ContactForm
Creates a new instance of ContactForm
contains(int) - Method in class org.intermine.util.IntPresentSet
Returns whether the given int is present in this set.
contains(Integer) - Method in class org.intermine.util.IntPresentSet
Returns whether the given Integer is present in this set.
contains(Object) - Method in class org.intermine.util.AlwaysSet
contains(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to contain a value.
contains(Collection<?>, Object) - Static method in class org.intermine.web.logic.WebUtil
So we can test set membership in JSPs.
CONTAINS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument contains the second
contains_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
CONTAINS_CONSTRAINT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
containsAll(Collection<?>) - Method in class org.intermine.util.AlwaysSet
containsAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
containsCollections() - Method in class org.intermine.pathquery.Path
Return true if and only if any part of the path is a collection.
ContainsConstraint - Class in org.intermine.objectstore.query
Constrain whether a QueryClass is member of a QueryReference or not.
ContainsConstraint(QueryReference, ConstraintOp) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
Constructor for ContainsConstraint, constrain a reference/collection to be NULL/ NOT NULL
ContainsConstraint(QueryReference, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
Constructor for ContainsConstraint.
ContainsConstraint(QueryReference, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
Constructor for ContainsConstraint.
containsConstraintToString(SqlGenerator.State, StringBuffer, ContainsConstraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a ContainsConstraint object into a String suitable for putting in an SQL query.
containsHeaders(String, StringBuffer) - Method in class org.intermine.web.struts.ContactForm
Check part of the message for injected headers.
containsKey(Object) - Method in class org.intermine.util.AlwaysMap
containsKey(Object) - Method in class org.intermine.util.IdentityMap
containsKey(Object) - Method in class org.intermine.util.ReferenceMap
containsKey(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory
Always returns true because get always returns an Object.
containsKey(Map<?, ?>, Object) - Static method in class org.intermine.web.logic.WebUtil
So we can test map membership in JSPs.
containsReferences() - Method in class org.intermine.pathquery.Path
Return true if and only if any part of the path is a reference.
containsValue(Object) - Method in class org.intermine.util.AlwaysMap
containsValue(Object) - Method in class org.intermine.util.IdentityMap
containsValue(Object) - Method in class org.intermine.util.ReferenceMap
ContentType - Enum in org.intermine.api.mines
An enumeration of the content-types we know about.
ContextNotInitialisedException - Exception in org.intermine.web.context
An error thrown when the InterMineContext object has not been initialised.
ContextNotInitialisedException(String) - Constructor for exception org.intermine.web.context.ContextNotInitialisedException
 
convert(ResultSet, Query, ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Method to convert from SQL results to InterMine object-based results.
convert(List<ResultElement>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ResultElementConverter
Converts data from ResultElement to Objects.
convert(Item) - Static method in class org.intermine.xml.full.ItemHelper
Convert a data model item to an XML one
convert(Attribute) - Static method in class org.intermine.xml.full.ItemHelper
Convert a xml Attribute to a fulldata Attribute that can then be stored with ItemWriter
convert(Item) - Static method in class org.intermine.xml.full.ItemHelper
Convert an XML item to a data model one
convert(Reference) - Static method in class org.intermine.xml.full.ItemHelper
Convert a xml Reference to a fulldata Reference that can then be stored with ItemWriter
convert(ReferenceList) - Static method in class org.intermine.xml.full.ItemHelper
Convert a xml ReferenceList to a fulldata ReferenceList that can then be stored with ItemWriter
ConvertBagController - Class in org.intermine.web.struts
 
ConvertBagController() - Constructor for class org.intermine.web.struts.ConvertBagController
 
ConvertedObjectPair - Class in org.intermine.api.bag
A class to represent the mapping between an object before type conversion and the converted object.
ConvertedObjectPair(InterMineObject, InterMineObject) - Constructor for class org.intermine.api.bag.ConvertedObjectPair
Create a new ConvertedObjectPair.
ConverterTask - Class in org.intermine.task
Task superclass for invoking converters.
ConverterTask() - Constructor for class org.intermine.task.ConverterTask
 
convertToClasses(Set<String>) - Static method in class org.intermine.util.DynamicUtil
Convert a set of interface names to a set of Class objects
copyField(FastPathObject, FastPathObject, Source, Source, FieldDescriptor, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Copies the value of the field given from the source object into the destination object.
correction - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
CorrectionCoefficient - Interface in org.intermine.web.logic.widget
An Interface which defines when/how a correction coefficient can be applied to the results obtained by a enrichment widget
count - Variable in class org.intermine.dataconversion.FullXmlConverter
 
count(Query, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Counts the number of rows the query will produce
count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Counts the number of rows the query will produce
count(PathQuery) - Method in class org.intermine.api.query.QueryExecutor
Take a query and return the results row count.
COUNT - Static variable in class org.intermine.objectstore.query.QueryFunction
Count rows
COUNT - Static variable in class org.intermine.sql.query.Function
COUNT(*) aggregate function - takes no operands.
countOccurances(String, String) - Static method in class org.intermine.metadata.StringUtil
Returns the number of occurances of str in target
CountProcessor - Class in org.intermine.webservice.server.core
A class that processes counts.
CountProcessor() - Constructor for class org.intermine.webservice.server.core.CountProcessor
Constructor
CountTableController - Class in org.intermine.web.struts
Start a count in a separate thread of the number of rows in the PagedTable given by the "resultsTable" request attribute.
CountTableController() - Constructor for class org.intermine.web.struts.CountTableController
 
countWithConnection(Connection, Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Counts the results in a query, given a Connection.
create(Class<? extends FastPathObject>, Class<?>[]) - Static method in class org.intermine.util.DynamicBean
Create a DynamicBean
CreateAccountAction - Class in org.intermine.web.struts
 
CreateAccountAction() - Constructor for class org.intermine.web.struts.CreateAccountAction
 
CreateAccountForm - Class in org.intermine.web.struts
Form bean to represent the inputs to create a new user account
CreateAccountForm() - Constructor for class org.intermine.web.struts.CreateAccountForm
 
createAnonymousProfile() - Method in class org.intermine.api.profile.ProfileManager
Create a profile not tied to an entry in the user db.
createAttributePath(String[], int) - Method in class org.intermine.web.logic.widget.WidgetLdr
Return the path of the attribute at the the position index in the paths given in input without reference to subclass.
createBag(String, String, String, Map) - Method in class org.intermine.api.util.AnonProfile
 
createBag(String, String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.Profile
Create a bag and save it to the userprofile database.
createBagFromPathQuery(PathQuery, String, String, String, Profile, InterMineAPI) - Static method in class org.intermine.web.logic.bag.BagHelper
Create a bag for the given profile and bag name from a PathQuery.
createBagTable(Database, Connection, String, Collection<?>, Class<?>) - Static method in class org.intermine.sql.DatabaseUtil
Create a new table the holds the contents of the given Collection (bag).
createBagValuesTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil
Create the table 'bagvalues' containing the values of the key field objects contained in a bag and an extra values
createBasicLocalProfile(String, String, String) - Method in class org.intermine.api.profile.ProfileManager
Create a new Profile with the given username, password and api-key.
createClassFindingQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Takes a String representation of a query (a path), and creates a query.
createClob() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Creates a new empty Clob that is valid for this ObjectStore.
createClob() - Method in interface org.intermine.objectstore.ObjectStore
Creates a new empty Clob that is valid for this ObjectStore.
createClob() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Creates a new empty Clob that is valid for this ObjectStore.
createClob() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Creates a new empty Clob that is valid for this ObjectStore.
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.AbstractHelper
Extending classes may with to override this method if they need to adjust the main constraint set in some way, such as adding an extra constraint.
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.IntHelper
 
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.StringHelper
 
createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in interface org.intermine.api.query.RangeHelper
 
createConstraintStructure(LogicExpression.Node, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper
Given a LogicExpression.Node, a Map from codes to Constraint objects, and a ConstraintSet to put it all in, construct a tree of ConstraintSets that reflects the expression.
createConstraintStructure(LogicExpression, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper
Given a LogicExpression, a Map from codes to Constraint objects, and a ConstraintSet to put it all in, construct a tree of ConstraintSets that reflects the expression.
createDefaultBagQuery(String, BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, Collection<String>) - Static method in class org.intermine.api.bag.BagQueryHelper
Create a BagQuery that constrains the class key fields of the given type.
createDefaultFeedbackMsg(HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
Create the default feedback messages.
createIndex(Connection, String, IndexStatement, int) - Method in class org.intermine.task.CreateIndexesTask
Create an named index on the specified columns of a table.
createIndex(ObjectStore, Map<String, List<FieldDescriptor>>) - Method in interface org.intermine.api.searchengine.IndexHandler
Main method to create the index Used mostly in post process tasks
createIndex(ObjectStore, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.searchengine.solr.SolrIndexHandler
 
CreateIndexesTask - Class in org.intermine.task
Task to create indexes on a database holding objects conforming to a given model by reading that model's primary key configuration information.
CreateIndexesTask() - Constructor for class org.intermine.task.CreateIndexesTask
 
createItem(String) - Method in class org.intermine.dataconversion.DataConverter
Create item for the given class name.
createKeyStore() - Method in class org.intermine.web.task.KeyStoreTask
Create and return the configured key-store.
createList(Query) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Converts a constraint from a query into a List of Constraint objects.
createList(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Return a List of Constraint objects that relate to the given FromElement.
createNew(String) - Static method in class org.intermine.metadata.TypeUtil
Encapsulate the logic of requesting an object of a class named name where that class has a default no-arguments constructor.
createNewProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager
Create a new profile in db with username and password given in input
createObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader
Create a new object of the given class and give it a unique ID.
createObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil
Create a new object given a class (not an interface).
createObject(String) - Method in class org.intermine.dataloader.DirectDataLoader
Create a new object of the given class name and give it a unique ID.
createObject(Set<? extends Class<?>>) - Static method in class org.intermine.util.DynamicUtil
Create a DynamicBean from a Set of Class objects
createObjectStoreBag() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns a new empty ObjectStoreBag for this ObjectStore, delegate to internal ObjectStoreWriter.
createObjectStoreBag() - Method in interface org.intermine.objectstore.ObjectStore
Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.
createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Creates a new empty ObjectStoreBag object that is valid for this ObjectStore.
createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.
createPasswordChangeToken(String) - Method in class org.intermine.api.profile.ProfileManager
Creates a password change token assigned to the given username that will expire after a day.
createPathConstraint(PathConstraint, String) - Method in class org.intermine.api.profile.PathQueryUpdate
Create a pathconstraint with the same operator and value of path contraint given in input and with the path given in input
createPathQuery() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Returns the pathquery based on the views set in config file and the bag constraint Executed when the user selects any item in the matches column in the enrichment widget.
createPathQueryView(ObjectStore, WidgetConfig) - Method in class org.intermine.web.logic.widget.Widget
Create a pathquery having a view composed by all items set in the view attribute in the config file
createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.HintingFetcher
Generates a query that searches for all objects in the database equivalent to a given example object, considering only one of it's classes.
createPKQuery(InterMineObject, Source, boolean) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.
createPKQuery(InterMineObject, Source, boolean) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
Generates a query that searches for all objects in the database equivalent to a given example object according to the primary keys defined for the given source.
createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Adds a Query to handle a primary key to a Set.
createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.HintingFetcher
Adds a Query to handle a primary key to a Set.
createProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Creates a profile in the userprofile database.
createProfileWithoutBags(Profile) - Method in class org.intermine.api.profile.ProfileManager
Creates a profile in the userprofile database without adding bag.
createQueryFieldByPath(String, Query, boolean) - Method in class org.intermine.web.logic.widget.WidgetLdr
Create a queryField starting from the path given in input and add the contain constraints between all the queryclass composing the path.
createQueryForExampleObject(Model, InterMineObject, Set<String>) - Static method in class org.intermine.objectstore.query.QueryCreator
Generates a query that searches for all objects in the database that have the fieldnames set to the values in the object.
createQueryForId(Integer, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator
Create a query that will retrieve an object from the objectstore, given an ID.
createQueryForIds(Collection<Integer>, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator
Create a query that will retrieve all objects with the given IDs from the objectstore.
createQueryForQueryNodeValues(Query, QueryNode) - Static method in class org.intermine.objectstore.query.QueryCreator
Create a query that will list the options for a particular field or class in a query, given the existing constraints
CreateSearchIndexTask - Class in org.intermine.web.task
Create a keyword search index for a mine.
CreateSearchIndexTask() - Constructor for class org.intermine.web.task.CreateSearchIndexTask
 
createSignature() - Method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
 
createSimpleObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader
Create a 'simple object' which doesn't inherit from InterMineObject and doesn't have an id.
createSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
createSQLStatement(String, String) - Method in class org.intermine.sql.logging.DatabaseWriter
Creates an SQL String suitable for initialising a PreparedStatement
createSuperUser(String, String, String) - Method in class org.intermine.api.profile.ProfileManager
Create a super-user with the given username, password and API-key.
createTempBagTable(Connection, ConstraintWithBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates a temporary bag table for the given BagConstraint.
createTempBagTable(Connection, QueryClassBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates a temporary bag table for the given QueryClassBag.
createTempBagTable(ConstraintWithBag) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates a temporary bag table for the given BagConstraint.
createTempBagTables(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Create temporary tables for use with Query that use bags.
CreateTemplateAction - Class in org.intermine.web.struts
Action to create a new TemplateQuery from current query.
CreateTemplateAction() - Constructor for class org.intermine.web.struts.CreateTemplateAction
 
createToken(Profile, int) - Method in class org.intermine.webservice.server.user.DeletionTokens
Create a new DeletionToken
createTrackerTable(Connection) - Method in class org.intermine.api.tracker.AbstractTracker
Create the table where the tracker saves data
createTrackerTable(Connection) - Method in interface org.intermine.api.tracker.Tracker
Create the table where the tracker saves data
createTrailLabel(InterMineObject, Model) - Static method in class org.intermine.web.struts.ObjectTrailController
Create trail element label.
CREATION - org.intermine.api.tracker.util.ListTrackerEvent
list creation
CreationEvent - Class in org.intermine.api.search
A representation of a notification a web searchable object has been created.
CreationEvent(WebSearchable) - Constructor for class org.intermine.api.search.CreationEvent
Constructor.
CSV - org.intermine.webservice.server.Format
Comma-separated-values
CSVExportForm - Class in org.intermine.web.struts
A form to hold options for CSV and tab separated output.
CSVExportForm() - Constructor for class org.intermine.web.struts.CSVExportForm
 
CSVFormatter - Class in org.intermine.webservice.server.output
Formats data to comma separated data format.
CSVFormatter() - Constructor for class org.intermine.webservice.server.output.CSVFormatter
Construct a CSV formatter.
CSVHttpExporter - Class in org.intermine.web.logic.export.http
Exporter that exports table with results in comma separated format.
CSVHttpExporter() - Constructor for class org.intermine.web.logic.export.http.CSVHttpExporter
Constructor.
CSVRowFormatter - Class in org.intermine.web.logic.export.rowformatters
Row formatter formats line as comma separated strings.
CSVRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.CSVRowFormatter
Constructor.
CURRENT - org.intermine.api.profile.BagState
 
currentArray - Variable in class org.intermine.webservice.server.output.JSONResultsIterator
 
currentIterator - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
 
currentIterator - Variable in class org.intermine.util.CombinedIterator
 
currentMap - Variable in class org.intermine.webservice.server.output.JSONResultsIterator
 
currentNodePath - Variable in class org.intermine.pathquery.PathQueryHandler
 
CurrentQueryAction - Class in org.intermine.web.struts
Action to display the query builder (if there is a current query) or redirect to project.sitePrefix.
CurrentQueryAction() - Constructor for class org.intermine.web.struts.CurrentQueryAction
 
CustomOAuthProvider - Class in org.intermine.web.struts.oauth2
A representation of an OAuth provider which has been configured entirely in web-properties.
CustomOAuthProvider(Properties, String) - Constructor for class org.intermine.web.struts.oauth2.CustomOAuthProvider
Construct a new provider.
CustomPrintWriter - Class in org.intermine.web.logic.export
Customized PrintWriter that terminates end of the lines with defined line separator.
CustomPrintWriter(OutputStream, String) - Constructor for class org.intermine.web.logic.export.CustomPrintWriter
Constructor.

D

database - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
database - Variable in class org.intermine.task.AnalyseDbTask
 
database - Variable in class org.intermine.task.BuildDbTask
 
database - Variable in class org.intermine.task.GrantTask
 
database - Variable in class org.intermine.task.RetrieveMetadataTask
 
database - Variable in class org.intermine.task.StoreMetadataTask
 
Database - Class in org.intermine.sql
Class that represents a physical SQL database
Database() - Constructor for class org.intermine.sql.Database
No argument constructor for testing purposes
Database(Properties) - Constructor for class org.intermine.sql.Database
Constructs a Database object from a set of properties
databaseAltered(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Internal method called by the ObjectStoreWriter, to notify the ObjectStore that some of the data in the database has changed.
databaseAltered(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Internal method called by the ObjectStoreWriter, to notify the ObjectStore that some of the data in the database has changed.
DatabaseConnectionException - Exception in org.intermine.sql
Exception thrown on failing to object a database connection.
DatabaseConnectionException() - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an DatabaseConnectionException
DatabaseConnectionException(String) - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an ObjectStoreException with the specified detail message.
DatabaseConnectionException(String, Throwable) - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an ObjectStoreException with the specified detail message and nested throwable.
DatabaseConnectionException(Throwable) - Constructor for exception org.intermine.sql.DatabaseConnectionException
Constructs an ObjectStoreException with the specified nested throwable.
databaseEmpty() - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns true if the database was empty at the start of the run.
DatabaseFactory - Class in org.intermine.sql
Creates Databases
databases - Static variable in class org.intermine.sql.DatabaseFactory
 
DatabaseSchema - Class in org.intermine.objectstore.intermine
An object that represents the mapping of a Model onto a relational database.
DatabaseSchema(Model, List<ClassDescriptor>, boolean, Set<String>, int) - Constructor for class org.intermine.objectstore.intermine.DatabaseSchema
Returns an instance of DatabaseSchema, for the given Model and and List of truncated classes.
DatabaseSchema.Fields - Class in org.intermine.objectstore.intermine
Inner class to hold information on Attributes and References.
DatabaseUtil - Class in org.intermine.sql
Collection of commonly used Database utilities
DatabaseUtil.Type - Enum in org.intermine.sql
 
DatabaseWriter - Class in org.intermine.sql.logging
Writes tab-separated Strings to a database table
DatabaseWriter() - Constructor for class org.intermine.sql.logging.DatabaseWriter
Construct an empty DatabaseWriter for testing purposes
DatabaseWriter(Connection, String) - Constructor for class org.intermine.sql.logging.DatabaseWriter
Construct a DatabaseWriter
DataChangedException - Exception in org.intermine.objectstore
An Exception that may be thrown by an ObjectStore indicating that a request cannot be serviced because the database has changed since the request was started.
DataChangedException() - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException
DataChangedException(String) - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException with the specified detail message.
DataChangedException(String, Throwable) - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException with the specified detail message and nested throwable.
DataChangedException(Throwable) - Constructor for exception org.intermine.objectstore.DataChangedException
Constructs an DataChangedException with the specified nested throwable.
DataConverter - Class in org.intermine.dataconversion
Abstract parent class of all DataConverters
DataConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.DataConverter
Constructor that should be called by children
DataConverterStoreHook - Interface in org.intermine.dataconversion
A hook that is called immediately before each Item is stored by the DataConverter.
dataDir - Variable in class org.intermine.task.DirectoryConverterTask
 
DataLoader - Class in org.intermine.dataloader
Loads information from a data source into the InterMine database.
DataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.DataLoader
Construct a DataLoader
DataLoaderHelper - Class in org.intermine.dataloader
Class providing utility methods to help with primary key and data source priority configuration
DATAPACKAGE_FILENAME - Static variable in class org.intermine.webservice.server.query.result.FrictionlessDataPackage
 
dataPackageAttributes - Variable in class org.intermine.webservice.server.query.result.FrictionlessDataPackage
 
dataPackageOutput - Variable in class org.intermine.webservice.server.WebService
 
DataService - Class in org.intermine.webservice.server.data
 
DataService(InterMineAPI) - Constructor for class org.intermine.webservice.server.data.DataService
 
DataSetLdr - Interface in org.intermine.web.logic.widget
An Interface which defines a frame in which data can be retrieved, organised and created to then be passed to a JFreeChart for representation
datasource - Variable in class org.intermine.sql.Database
 
dataTracker - Variable in class org.intermine.dataloader.BatchingFetcher
 
dataTracker - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
DataTracker - Class in org.intermine.dataloader
Interface providing access to data tracking.
DataTracker(Database, int, int) - Constructor for class org.intermine.dataloader.DataTracker
Constructor for DataTracker.
DATE_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
dateCreated - Variable in class org.intermine.api.userprofile.PermanentToken
 
dateCreated - Variable in class org.intermine.api.userprofile.SavedBag
 
db - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
DBConverter - Class in org.intermine.dataconversion
A DataConverter that reads from a Database and writes to a ItemWriter
DBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.dataconversion.DBConverter
Constructor
DBConverterTask - Class in org.intermine.task
Task to call DBConverters.
DBConverterTask() - Constructor for class org.intermine.task.DBConverterTask
 
dbIdsStored - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
dbLog(long, long, long, long, long, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Produce an entry in the DB log.
dbLog(long, long, long, long, long, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Produce an entry in the DB log.
decapitalise(String) - Static method in class org.intermine.metadata.StringUtil
Returns a decapitalised version of the given String unless string is an acronym.
declarePrinted() - Method in class org.intermine.webservice.server.output.JSONFormatter
Signal that we have started printing results and that it isn't safe to print headers.
decode(String) - Method in class org.intermine.web.security.Base64PublicKeyDecoder
 
decode(String) - Method in interface org.intermine.web.security.KeyDecoder
Decode the string and make the key.
decodeDbDescription(ObjectStore, String) - Static method in class org.intermine.objectstore.query.ClobAccess
Decodes a String from the database representing a clob object.
decodeLZWString(String) - Static method in class org.intermine.webservice.server.query.QueryRequestParser
Take in a LZW encoded string and return a decoded plain-text string.
DecodingException - Exception in org.intermine.web.security
The error that indicates we cannot decode something.
DecodingException(Throwable) - Constructor for exception org.intermine.web.security.DecodingException
Constructor.
decomposeClass(Class<?>) - Static method in class org.intermine.metadata.Util
Convert a dynamic Class into a Set of Class objects that comprise it.
decomposePath() - Method in class org.intermine.pathquery.Path
Returns a list of paths, each corresponding to one step further along the path.
decompressLZW(List<Integer>) - Static method in class org.intermine.webservice.server.query.QueryRequestParser
Decompress a list of output ks to a string.
DEFAULT - org.intermine.webservice.server.Format
The format for when the user will accept whatever.
DEFAULT - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
The default context - normal operation with no time limit.
DEFAULT_ALGORITHM - Static variable in class org.intermine.web.security.KeySigner
The default algorithm to use
DEFAULT_BATCH_SIZE - Static variable in class org.intermine.api.query.PathQueryExecutor
default batch size
DEFAULT_BATCH_SIZE - Static variable in class org.intermine.objectstore.query.ResultsBatches
This is the default batch size for Results objects
DEFAULT_CALLBACK - Static variable in class org.intermine.webservice.server.WebService
Default jsonp callback
DEFAULT_LIMIT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
10 000 000 default size actually means that web service will return all results
DEFAULT_MAX_VALUES - Static variable in class org.intermine.objectstore.ObjectStoreSummary
The default number of values to make available for UI dropdowns - attributes with more values will not become dropdowns.
DEFAULT_MESSAGE - Static variable in class org.intermine.api.bag.BagQueryHelper
Message associated with default bag query.
DEFAULT_OPERATOR - Static variable in class org.intermine.web.logic.Constants
Session attribut containing the default operator name, either 'and' or 'or'.
DEFAULT_RESULT_SIZE - Static variable in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Default value of size parameter
DEFAULT_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants
Default size of table implemented by PagedTable.
DefaultOAuthProvider - Class in org.intermine.web.struts.oauth2
A representation of an OAuth provider which is one of the default providers provided for end-users.
DefaultOAuthProvider(Properties, OAuthProviderType) - Constructor for class org.intermine.web.struts.oauth2.DefaultOAuthProvider
Construct a new provider.
DelegatedIdentity - Class in org.intermine.web.struts.oauth2
A simple struct class for containing information about a delegated identity.
DelegatedIdentity(String, String, String, String) - Constructor for class org.intermine.web.struts.oauth2.DelegatedIdentity
Construct a new delegated identity.
delete() - Method in class org.intermine.api.bag.SharingInvite
 
delete() - Method in class org.intermine.api.profile.InterMineBag
Delete this bag from the userprofile database, bag should not be used after this method has been called.
delete() - Method in class org.intermine.api.profile.InvalidBag
Delete this bag from the userprofile database, bag should not be used after this method has been called.
delete() - Method in class org.intermine.api.profile.StorableBag
Delete this bag.
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction
Delete some queries
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction
Delete some templates.
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.UserTemplateAction
Delete a template query.
delete(InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Delete an object from this ObjectStore, delegate to internal ObjectStoreWriter.
delete(InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Delete an object from this ObjectStore
delete(InterMineObject) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Delete an object from this ObjectStore
delete(QueryClass, Constraint) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Deletes a set of objects from this ObjectStore.
delete(QueryClass, Constraint) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Deletes a set of objects from this ObjectStore.
delete(QueryClass, Constraint) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Deletes a set of objects from this ObjectStore.
delete(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Delete a precomputed table from the underlying database.
DELETE - org.intermine.webservice.server.core.WebServiceServlet.Method
DELETE
DELETE - Static variable in class org.intermine.api.profile.ModelUpdate
label in modelUpdate.properties file to identify deleted classes or fields
deleteAllBagValues() - Method in class org.intermine.api.profile.InterMineBag
 
deleteAllBagValues() - Method in class org.intermine.api.profile.StorableBag
Remove all the values from the bag-value table.
deleteAllPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager
 
deleteApiKey(String) - Method in class org.intermine.dwr.AjaxServices
Delete a user's API key, thus disabling webservice access.
deleteBag(String) - Method in class org.intermine.api.profile.Profile
Delete a bag from the user account, if user is logged in also deletes from the userprofile database.
deleteBags() - Method in class org.intermine.api.profile.ModelUpdate
Delete all bags having as a type one of the classes deleted
deleteBagValues(List<String>) - Method in class org.intermine.api.profile.InterMineBag
Delete a given set of bag values from the bag value table.
deleteBatches - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
deleteFrom(FromElement) - Method in class org.intermine.objectstore.query.Query
Remove a FromElement from the FROM clause
deleteFromGroupBy(QueryNode) - Method in class org.intermine.objectstore.query.Query
Remove a QueryNode from the GROUP BY clause
deleteFromOrderBy(QueryOrderable) - Method in class org.intermine.objectstore.query.Query
Remove a QueryOrderable from the ORDER BY clause
deleteFromSelect(QuerySelectable) - Method in class org.intermine.objectstore.query.Query
Remove a QuerySelectable from the SELECT clause
deleteGlobalRepository(Profile) - Method in class org.intermine.api.search.GlobalRepository
 
deleteHistory(String) - Method in class org.intermine.api.profile.Profile
Remove an item from the query history.
deleteLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Delete a large object from the database based on a given metadata key.
deleteObjectTags(String, String, String) - Method in class org.intermine.api.profile.TagManager
Deletes all tags assigned to a specified object.
deletePreference(Profile, String) - Method in class org.intermine.api.profile.PreferencesManager
 
DeletePreferencesService - Class in org.intermine.webservice.server.user
A service that deletes a user's preferences.
DeletePreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeletePreferencesService
 
deleteProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Completely remove a profile and all of its associated data from the data-store.
deleteQuery(String) - Method in class org.intermine.api.profile.Profile
Delete a query
deleteRow(int, int) - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Deletes a row from the batch.
deleteRow(String, Object) - Method in class org.intermine.sql.writebatch.TableBatch
Deletes a row from the batch.
deleteRow(Connection, String, String, Object) - Method in class org.intermine.sql.writebatch.Batch
Deletes a row from the batch for a given table.
deleteRow(Connection, String, String, String, int, int) - Method in class org.intermine.sql.writebatch.Batch
Deletes a row from the batch for a given indirection table.
deleteSomeBagValues(List<String>) - Method in class org.intermine.api.profile.StorableBag
Delete a given set of bag values from the bag value table.
deleteTableFromDatabase(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Delete a PrecomputedTable from the database.
deleteTag(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Deletes tag.
deleteTag(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
Deletes a tag object from the database.
deleteTag(String, WebSearchable, Profile) - Method in class org.intermine.api.profile.TagManager
Delete a tag by name from a web-searchable object.
deleteTag(String, ClassDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Delete a tag by name from a class-descriptor.
deleteTag(String, ReferenceDescriptor, Profile) - Method in class org.intermine.api.profile.TagManager
Delete a tag by name from a reference-descriptor.
deleteTag(Tag) - Method in class org.intermine.api.profile.TagManager
Delete a tag object from the database.
deleteTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
Deletes tags object from the database.
deleteTemplate(String, TrackerDelegate, boolean) - Method in class org.intermine.api.profile.Profile
Delete a template and its tags, rename the template tracks adding the prefix "deleted_" to the previous name.
deleteTempTableSize - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
DeleteTokensService - Class in org.intermine.webservice.server.user
Service which ensures that the authenticating user has no tokens.
DeleteTokensService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeleteTokensService
 
deleteUserToShareBag(String, String) - Method in class org.intermine.dwr.AjaxServices
Un-share the bag given in input with the user which userName is input
deleteWithConnection(Connection, InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs a delete, with a connection.
deleteWithConnection(Connection, QueryClass, Constraint) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs a delete, with a connection.
DeletionEvent - Class in org.intermine.api.search
A representation of a notification that a websearchable has been deleted.
DeletionEvent(WebSearchable) - Constructor for class org.intermine.api.search.DeletionEvent
Constructor.
DeletionToken - Class in org.intermine.webservice.server.user
A class representing a deletion token.
DeletionToken(Profile, UUID, Date) - Constructor for class org.intermine.webservice.server.user.DeletionToken
 
DeletionTokenCancellationService - Class in org.intermine.webservice.server.user
A service that cancels the profile deletion process by deleting the token that could be used to complete it.
DeletionTokenCancellationService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.DeletionTokenCancellationService
 
DeletionTokenInfoService - Class in org.intermine.webservice.server.user
A service that retrieves information about a deletion token.
DeletionTokenInfoService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.DeletionTokenInfoService
 
DeletionTokens - Class in org.intermine.webservice.server.user
A class that manages deletion tokens for the lifespan of a webapp.
DELIM - Static variable in class org.intermine.codegen.JavaModelOutput
The string that delimits the sections of the NotXml.
DELIM - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
The string that delimits the sections of the NotXml.
DelimitedFileConfiguration - Class in org.intermine.task
This class specifies how the values in a tab or comma separated file should be used to fill in objects in an ObjectStore.
DelimitedFileConfiguration(Model, InputStream) - Constructor for class org.intermine.task.DelimitedFileConfiguration
Create a new DelimitedFileConfiguration from an InputStream.
densities(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
DENSITIES - org.intermine.webservice.server.jbrowse.Commands.Action
densities
deregisterRequestId(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method deregisters a Thread from a request ID.
deregisterStatement(Statement) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method deregisters a Statement for the request ID of the current thread.
DeregistrationService - Class in org.intermine.webservice.server.user
 
DeregistrationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.DeregistrationService
 
DeregistrationTokenServlet - Class in org.intermine.webservice.server.user
A servlet for routing requests to do with deregistration.
DeregistrationTokenServlet() - Constructor for class org.intermine.webservice.server.user.DeregistrationTokenServlet
 
DESC - org.intermine.pathquery.OrderDirection
descending
description - Variable in class org.intermine.api.userprofile.SavedBag
 
description - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
DESCRIPTION_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The description
DescriptorUtils - Class in org.intermine.metadata
 
deSelectId(Integer) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Remove the object with the given object id from the list of selected objects.
deSelectId(String, String) - Static method in class org.intermine.dwr.AjaxServices
remove an Id from the PagedTable
destDir - Variable in class org.intermine.task.ModelOutputTask
 
destDir - Variable in class org.intermine.task.RetrieveMetadataTask
 
destFile - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask
 
destroy() - Method in class org.intermine.web.filters.ExpiresHeaderFilter
destroy() - Method in class org.intermine.web.filters.HeaderFilter
destroy() - Method in class org.intermine.web.filters.PermanentURLFilter
destroy() - Method in class org.intermine.web.filters.ReleaseEtagFilter
 
destroy() - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Take this filter out of service.
destroy() - Method in class org.intermine.web.struts.InitialiserPlugin
Destroy method called at Servlet destroy.
destroy() - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter
 
destroy() - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
deVerify() - Method in class org.intermine.pathquery.PathQuery
assert that the query is dirty and needs to be re-checked.
DevNullMap<K,​V> - Class in org.intermine.api.util
An implementation of Map that is totally forgetful.
DevNullMap() - Constructor for class org.intermine.api.util.DevNullMap
 
didNotExplain(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Internal method that records that a query was not explained.
didNotExplain(BestQueryExplainer.Candidate) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Internal method that records that a query was not explained.
DirectDataLoader - Class in org.intermine.dataloader
A DataLoader with helper methods for creating and storing objects using an IntegrationWriter.
DirectDataLoader(IntegrationWriter, String, String) - Constructor for class org.intermine.dataloader.DirectDataLoader
Create a new DirectDataLoader using the given IntegrationWriter and source name.
DirectDataLoaderTask - Class in org.intermine.task
This task uses a DirectDataLoader to create objects and store them directly into an ObjectStore using an IntegrationWriter.
DirectDataLoaderTask() - Constructor for class org.intermine.task.DirectDataLoaderTask
 
DirectoryConverter - Class in org.intermine.dataconversion
Parent class for DataConverters that read from directories
DirectoryConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.DirectoryConverter
Constructor
DirectoryConverterTask - Class in org.intermine.task
Initiates retrieval and conversion of data from a source directory.
DirectoryConverterTask() - Constructor for class org.intermine.task.DirectoryConverterTask
 
disableResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
disableSaving() - Method in class org.intermine.api.profile.Profile
Disable saving until enableSaving() is called.
DisclosureBodyTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureBody tag.
DisclosureBodyTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureBodyTag
 
DisclosureDetailsTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureDetails tag.
DisclosureDetailsTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureDetailsTag
 
DisclosureHeadTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureHead tag.
DisclosureHeadTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureHeadTag
 
DisclosureTag - Class in org.intermine.web.tags.disclosure
This class renders disclosure tag.
DisclosureTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureTag
 
DisclosureTitleTag - Class in org.intermine.web.tags.disclosure
This class renders disclosureTitle tag.
DisclosureTitleTag() - Constructor for class org.intermine.web.tags.disclosure.DisclosureTitleTag
 
display(HttpServletRequest, ReportObject) - Method in class org.intermine.web.displayer.ReportDisplayer
To be implemented in subclasses where any specific information to be displayed should be put on the request.
DisplayCollection - Class in org.intermine.web.logic.results
Class to represent a collection field of an object for the webapp
DisplayCollection(Collection<?>, CollectionDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.DisplayCollection
Construct a new DisplayCollection object
DisplayCollection(Collection<?>, CollectionDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>, String) - Constructor for class org.intermine.web.logic.results.DisplayCollection
Construct a DisplayCollection object.
DisplayConstraint - Class in org.intermine.web.logic.query
Representation of a PathQuery constraint for use by JSP pages.
DisplayConstraint(Path, Profile, PathQuery, AutoCompleter, ObjectStoreSummary, BagQueryConfig, Map<String, List<FieldDescriptor>>, BagManager) - Constructor for class org.intermine.web.logic.query.DisplayConstraint
Construct for a new constraint that is being added to a query.
DisplayConstraint.DisplayConstraintOption - Class in org.intermine.web.logic.query
Representation of a constraint operation to populate a dropdown.
DisplayConstraintFactory - Class in org.intermine.web.logic.query
A class that will help you manufacture instances of DisplayConstraint.
DisplayConstraintFactory(InterMineAPI, AutoCompleter) - Constructor for class org.intermine.web.logic.query.DisplayConstraintFactory
Get an object that creates display constraints.
DisplayConstraintHelpMessages - Class in org.intermine.web.logic.query
Class to generate help messages appropriate to a given constraint for display in the QueryBuilder and template form.
DisplayConstraintOption(String, Integer) - Constructor for class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
Construct with the constraint lable and index
Displayer - Class in org.intermine.web.logic.config
Configuration object describing details of a displayer
Displayer() - Constructor for class org.intermine.web.logic.config.Displayer
 
DisplayerManager - Class in org.intermine.web.displayer
Read in and provide access to report page displayers.
DisplayField - Class in org.intermine.web.logic.results
Class to represent a field of an object for the webapp
DisplayField(Collection<?>, FieldDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.DisplayField
Create a new DisplayField object.
DisplayField(Collection<?>, FieldDescriptor, WebConfig, Properties, Map<String, List<FieldDescriptor>>, List<Class<?>>, String) - Constructor for class org.intermine.web.logic.results.DisplayField
Create a new DisplayField object.
DisplayLookupMessageHandler - Class in org.intermine.web.struts
 
DisplayLookupMessageHandler() - Constructor for class org.intermine.web.struts.DisplayLookupMessageHandler
 
DisplayPath - Class in org.intermine.web.logic.querybuilder
A small wrapper around Path with more jsp-accessible data.
DisplayPath(Path) - Constructor for class org.intermine.web.logic.querybuilder.DisplayPath
Constructs a new DisplayPath object from a Path.
DisplayReference - Class in org.intermine.web.logic.results
Class to represent a reference field of an object for display in the webapp
DisplayReference(ProxyReference, ReferenceDescriptor, WebConfig, Map<String, List<FieldDescriptor>>, String) - Constructor for class org.intermine.web.logic.results.DisplayReference
Create a new DisplayReference object.
distinct - Variable in class org.intermine.sql.query.Query
 
DIVIDE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
DIVIDE - Static variable in class org.intermine.objectstore.query.QueryExpression
Division of two numeric fields
DIVIDE - Static variable in class org.intermine.sql.query.Function
DIVIDE function - takes two operands.
DIVIDE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
DivNumberFormat(int) - Constructor for class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
 
doAdditionalConstraintStuff(PathQuery, PathConstraint, XMLStreamWriter) - Method in class org.intermine.pathquery.PathQueryBinding
Adds any extra information for a constraint, like say Template extras.
doAdditionalConstraintStuff(PathQuery, PathConstraint, XMLStreamWriter) - Method in class org.intermine.template.xml.TemplateQueryBinding
Adds any extra information for a constraint, like say Template extras.
doAnalyse(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs an ANALYSE of a table.
doDelete(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doDeletes(String, TableBatch) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the deletes for the given table name and table batch.
DOES_NOT_CONTAIN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument does not contain the second
DOES_NOT_EXIST - Static variable in class org.intermine.metadata.ConstraintOp
Subquery does not exist
DOES_NOT_MATCH - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments do not match
DOES_NOT_OVERLAP - Static variable in class org.intermine.metadata.ConstraintOp
Require that a range does not overlap another range
doesNotContain(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to not contain a value.
doFacetSearch(InterMineAPI, String, Map<String, String>) - Method in interface org.intermine.api.searchengine.KeywordSearchHandler
A method specifically designed to handle facet return webservice
doFacetSearch(InterMineAPI, String, Map<String, String>) - Method in class org.intermine.api.searchengine.solr.SolrKeywordSearchHandler
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.ExpiresHeaderFilter
Add an expires header to matching files to help browsers avoid reloading static files.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.HeaderFilter
Do the filtering.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.PermanentURLFilter
Filters all the intermine requests
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.ReleaseEtagFilter
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Select and set (if specified) the character encoding to be used to interpret request parameters for this request.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter
 
doFinalise() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Finalise this object.
doFinalise() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Overrides Object.finalize - release the connection back to the objectstore.
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.logic.login.OpenIDAuthenticator
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ClassKeyServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.FacetListServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.model.ModelServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.oauth2.AuthenticatorServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.oauth2.CallbackServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.path.PossibleValuesServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.CodeServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.result.QueryResultServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.SchemaServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ServicesListingsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.SummaryServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.LogoutServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.RequestPswResetServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.TokenServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.VersionServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.webproperties.WebPropertiesServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.AvailableWidgetsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.GraphWidgetsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.TableWidgetsServlet
}
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.WidgetsServlet
}
doIndirectionDeletes(String, IndirectionTableBatch) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the delete operations for the given IndirectionTableBatch and name.
doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
Performs all the insert operations for the given IndirectionTableBatch and name.
doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Performs all the insert operations for the given IndirectionTableBatch and name.
doIndirectionInserts(String, IndirectionTableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the insert operations for the given IndirectionTableBatch and name.
doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
Performs all the inserts for the given table name and table batch.
doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
Performs all the inserts for the given table name and table batch.
doInserts(String, TableBatch, List<FlushJob>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the inserts for the given table name and table batch.
doKeywordSearch(InterMineAPI, String, Map<String, String>, List<Integer>, int) - Method in interface org.intermine.api.searchengine.KeywordSearchHandler
Main method to do the search
doKeywordSearch(InterMineAPI, String, Map<String, String>, List<Integer>, int) - Method in class org.intermine.api.searchengine.solr.SolrKeywordSearchHandler
 
doLogin(HttpServletRequest, String, String) - Method in class org.intermine.web.logic.profile.LoginHandler
Log-in a user.
doMarshal(PathQuery, String, String, XMLStreamWriter, int) - Method in class org.intermine.pathquery.PathQueryBinding
Marshal to an XMLStreamWriter.
doMarshal(TemplateQuery, XMLStreamWriter, int) - Method in class org.intermine.template.xml.TemplateQueryBinding
Convert a TemplateQuery to XML and write XML to given writer.
doPk(PrimaryKey, ClassDescriptor, Map<InterMineObject, Set<InterMineObject>>, List<InterMineObject>, Set<Integer>) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches equivalent objects for a particular primary key.
doPks(Map<PrimaryKey, ClassDescriptor>, Map<InterMineObject, Set<InterMineObject>>, Map<ClassDescriptor, List<InterMineObject>>, long) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches data for the given primary keys.
doPks(Map<PrimaryKey, ClassDescriptor>, Map<InterMineObject, Set<InterMineObject>>, Map<ClassDescriptor, List<InterMineObject>>, long) - Method in class org.intermine.dataloader.ParallelBatchingFetcher
Fetches data for the given primary keys.
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.FeedbackServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.model.ModelServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.path.PossibleValuesServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.CodeServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.result.QueryResultServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.ServicesListingsServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.LoginServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.VersionServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.webproperties.WebPropertiesServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.GraphWidgetsServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.TableWidgetsServlet
}
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.widget.WidgetsServlet
}
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.AvailableServicesServlet
}
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
 
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryListAppendServlet
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.query.QueryToListServlet
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.template.TemplateListAppendServlet
doPut(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.PswResetServlet
doQueryGetPagedTable(HttpServletRequest, InterMineBag) - Static method in class org.intermine.web.logic.session.SessionMethods
Execute a query and return a PagedTable to display contents of an InterMineBag
doQueryGetPagedTable(HttpServletRequest, InterMineObject, String, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Execute a query and return a PagedTable to display contents of a Collection, field of a given InterMineObject.
doReplace() - Method in class org.intermine.webservice.server.lists.ListInput
 
doRequest(PrefetchManager.Request) - Static method in class org.intermine.objectstore.query.PrefetchManager
Returns the batch described by the request.
doRequest(ResultsBatches, int, boolean, boolean) - Static method in class org.intermine.objectstore.query.PrefetchManager
Returns when the given request is completed.
doShutdown() - Static method in class org.intermine.web.context.InterMineContext
Send the signal that shutdown is happening - try and release resources.
doSQL(ObjectStore) - Method in class org.intermine.task.ConverterTask
Runs various performance-enhancing SQL statements.
doStaticLogin(HttpServletRequest, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler
Main log-in logic.
doSummarise - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
DOT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
DOT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag
Renders tag.
doTag() - Method in class org.intermine.web.tags.table.NavigationBarTag
According pageSize and currentPage parameter navigation bar computes link to following and previous page.
doTag() - Method in class org.intermine.web.tags.table.TableTag
doTag() - Method in class org.intermine.web.tags.util.TreatStringTag
 
doTrackerFor(Class<?>) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Returns true if the given class is NOT a subclass of any of the classes in trackerMissingClasses.
double_precision - org.intermine.sql.DatabaseUtil.Type
double
doUpgrade() - Method in interface org.intermine.api.bag.IdUpgrader
Return true if upgrade should be performed
doUpgrade() - Method in class org.intermine.api.bag.PkQueryIdUpgrader
Return true if upgrade should be performed.
download(String) - Method in class org.intermine.web.util.HttpClient
 
doWrite() - Method in class org.intermine.dataloader.DataTracker
Performs maintenance of the cache, writing stuff to the backing database.
drainToPrintStream(PrintStream) - Method in class org.intermine.objectstore.query.ClobAccess
Sends the entire contents of the Clob into the given PrintStream.
driver - Variable in class org.intermine.sql.Database
 
dropAffected(Set<String>) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Deletes all precomputed tables that would be affected by changes in any table in a given list of table names.
dropEverything() - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Deletes every single precomputed table.
dropIndex(String, int) - Method in class org.intermine.task.CreateIndexesTask
Drop an index by name, ignoring any resulting errors
dropIndex(WebSearchable) - Method in class org.intermine.api.search.SearchRepository
Drop the index that contains information about the websearchable object passed in.
DropPrecomputedTablesTask - Class in org.intermine.task
A Task that drops all precomputed tables in an ObjectStore.
DropPrecomputedTablesTask() - Constructor for class org.intermine.task.DropPrecomputedTablesTask
 
DummyExplainResult - Class in org.intermine.sql.query
Subclass of ExplainResult not associated with a database.
DummyExplainResult(Query) - Constructor for class org.intermine.sql.query.DummyExplainResult
Constructs an instance of PostgresExplainResult without any data.
DumpDefaultTemplatesTask - Class in org.intermine.web.task
Dump templates and configuration tags.
DumpDefaultTemplatesTask() - Constructor for class org.intermine.web.task.DumpDefaultTemplatesTask
 
DUPLICATE - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the query for the input string found more than one object.
DuplicateMappingException - Exception in org.intermine.api.profile
 
DuplicateMappingException(String, String) - Constructor for exception org.intermine.api.profile.DuplicateMappingException
 
duplicateObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
This is a list of the objects in the destination database that we have written to as a non-skeleton more than once.
duplicateQuotes(String) - Static method in class org.intermine.metadata.StringUtil
Duplicates single quotes in Strings for correct storage in postgres.
DynamicAttributeTask - Class in org.intermine.task
An ant task that provides a method for setting attributes dynamically within a class.
DynamicAttributeTask() - Constructor for class org.intermine.task.DynamicAttributeTask
 
DynamicBean - Class in org.intermine.util
Class which represents a generic bean
DynamicBean() - Constructor for class org.intermine.util.DynamicBean
Construct the interceptor
DynamicUtil - Class in org.intermine.util
Utilities to create DynamicBeans

E

editable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
editableConstraints - Variable in class org.intermine.template.TemplateQuery
List of those Constraints that are editable
editConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a constraint on the query identified by the constraint code.
edited - Variable in class org.intermine.template.TemplateQuery
Whether this is an edited version of another template.
EDITING_TEMPLATE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the status editing template
editJoinStyle(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a the join style settings for a path.
EditPropertiesAction - Class in org.intermine.web.struts
A controller to edit the properties of a running application.
EditPropertiesAction() - Constructor for class org.intermine.web.struts.EditPropertiesAction
 
EditPropertiesForm - Class in org.intermine.web.struts
An overly verbose way of passing parameters back to the controller.
EditPropertiesForm() - Constructor for class org.intermine.web.struts.EditPropertiesForm
 
EditTemplateAction - Class in org.intermine.web.struts
Action to edit a user template query.
EditTemplateAction() - Constructor for class org.intermine.web.struts.EditTemplateAction
 
editTemplateConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Edit a constraint's template settings identified by code in query.
Either<A,​B> - Class in org.intermine.webservice.server.core
Disjoint type union
Either.Left<A,​B> - Class in org.intermine.webservice.server.core
 
Either.Right<A,​B> - Class in org.intermine.webservice.server.core
 
EitherVisitor<A,​B,​T> - Class in org.intermine.webservice.server.core
A mapping function capable of accessing a disjoint sum-type (an Either A B).
EitherVisitor() - Constructor for class org.intermine.webservice.server.core.EitherVisitor
 
email(String, String) - Method in class org.intermine.util.Emailer
Send a message to a user.
email(String, String) - Method in class org.intermine.web.context.NullMailer
 
email(String, String, Object...) - Method in class org.intermine.util.Emailer
Send a message to a user with some data.
email(String, String, Object...) - Method in class org.intermine.web.context.NullMailer
 
email(String, String, String, String, Properties) - Static method in class org.intermine.util.MailUtils
Send an email to an address, supplying the recipient, subject and body.
email(String, String, String, Properties) - Static method in class org.intermine.util.MailUtils
 
EMAIL - Static variable in class org.intermine.api.profile.UserPreferences
This is known to the API as the Profile needs to read this to provide getEmailAddress().
Emailer - Class in org.intermine.util
A class that will send emails to people.
Emailer(Properties) - Constructor for class org.intermine.util.Emailer
Instantiate an emailer.
EmailerFactory - Class in org.intermine.web.context
 
emailPasswordToken(String, String, Properties) - Static method in class org.intermine.util.MailUtils
Send a password change email to an email address
EMPTY - org.intermine.webservice.server.Format
The format for when no value is given
emptyAttributesMap - Variable in class org.intermine.objectstore.ObjectStoreSummary
 
emptyFieldsMap - Variable in class org.intermine.objectstore.ObjectStoreSummary
 
enableSaving() - Method in class org.intermine.api.profile.Profile
Re-enable saving when saveTemplate(), deleteQuery() etc.
enableSaving() - Method in class org.intermine.api.util.AnonProfile
 
EncloseSubqueryBestQuery - Class in org.intermine.sql.precompute
This object is a BestQuery tracker that encloses all added queries into a surrounding query as a subquery, and passes them onto another BestQuery tracker.
EncloseSubqueryBestQuery(BestQuery, String, String) - Constructor for class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Constructor.
encode(Object) - Static method in class org.intermine.webservice.server.LinkGeneratorBase
Encodes object string value to be able to be part of url.
encode(Object) - Static method in class org.intermine.webservice.server.query.result.QueryResultService
URL Encode an object.
ENCODED_DELIM - Static variable in class org.intermine.codegen.JavaModelOutput
The character that denotes an encoded delimiter in the string.
ENCODED_DELIM - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
The character that denotes an encoded delimiter in the string.
encodeString(String) - Static method in class org.intermine.web.util.URLUtil
Encodes string to be URL safe.
encodeURL(String) - Static method in class org.intermine.web.util.URLUtil
Encodes URL.
encoding - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter
The default character encoding to set for requests that pass through this filter.
end - Variable in class org.intermine.objectstore.query.OverlapRange
 
endDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler
 
endElement(String, String, String) - Method in class org.intermine.api.bag.BagQueryHandler
endElement(String, String, String) - Method in class org.intermine.api.bag.InvitationHandler
endElement(String, String, String) - Method in class org.intermine.api.profile.PreferencesHandler
endElement(String, String, String) - Method in class org.intermine.api.profile.TagHandler
endElement(String, String, String) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler
endElement(String, String, String) - Method in class org.intermine.api.xml.InterMineBagHandler
endElement(String, String, String) - Method in class org.intermine.api.xml.SavedQueryHandler
endElement(String, String, String) - Method in class org.intermine.api.xml.SharedBagHandler
endElement(String, String, String) - Method in class org.intermine.pathquery.PathQueryHandler
endElement(String, String, String) - Method in class org.intermine.template.xml.TemplateQueryHandler
endElement(String, String, String) - Method in class org.intermine.webservice.server.ServiceListingHandler
 
endElement(String, String, String) - Method in class org.intermine.xml.full.FullHandler
endIsAttribute() - Method in class org.intermine.pathquery.Path
Return true if and only if the end of the path is an attribute.
endIsCollection() - Method in class org.intermine.pathquery.Path
Return true if and only if the end of the path is a collection.
endIsReference() - Method in class org.intermine.pathquery.Path
Return true if and only if the end of the path is a reference .
endl - Variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
ENDL - Static variable in class org.intermine.codegen.JavaModelOutput
 
ENDL - Static variable in class org.intermine.metadata.ClassDescriptor
 
ENDL - Static variable in class org.intermine.metadata.Model
 
ENDL - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
Endpoint - Class in org.intermine.webservice.server.jbrowse
 
Endpoint(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.Endpoint
 
ENRICHMENT - org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
There is the enrichment type, that calculates relationship enrichment
EnrichmentCalculation - Class in org.intermine.web.logic.widget
Calculate enrichment of an attribute applied to members of a sample that is a subset of a larger population.
EnrichmentInput - Interface in org.intermine.web.logic.widget
Define methods to access data an enrichment calculation needs to be provided with.
EnrichmentInputWidgetLdr - Class in org.intermine.web.logic.widget
Executes queries and summarises data for a specific EnrichmentWidgetLdr ready for calculation.
EnrichmentInputWidgetLdr(ObjectStore, EnrichmentWidgetImplLdr) - Constructor for class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
Construct with an EnrichmentWidgetLdr that contains queries needed for specific widget tests.
EnrichmentJSONProcessor - Class in org.intermine.webservice.server.widget
 
EnrichmentOptions - Interface in org.intermine.web.logic.widget
The type of options that enrichment widgets expect to receive.
EnrichmentResultProcessor - Interface in org.intermine.webservice.server.widget
The type of objects that can process enrichment results for serialisation to the outside world.
EnrichmentResults - Class in org.intermine.web.logic.widget
A container for results from an Enrichment analysis.
EnrichmentResults(Map<String, BigDecimal>, Map<String, Integer>, Map<String, String>, int, Map<String, PopulationInfo>, int) - Constructor for class org.intermine.web.logic.widget.EnrichmentResults
Construct with pre-populated maps from enriched attributes to p-values, counts and labels.
EnrichmentWidget - Class in org.intermine.web.logic.widget
 
EnrichmentWidget(EnrichmentWidgetConfig, InterMineBag, InterMineBag, ObjectStore, EnrichmentOptions, String, String) - Constructor for class org.intermine.web.logic.widget.EnrichmentWidget
 
EnrichmentWidgetConfig - Class in org.intermine.web.logic.widget.config
A description of an enrichment calculation.
EnrichmentWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
EnrichmentWidgetForm - Class in org.intermine.web.struts
 
EnrichmentWidgetForm() - Constructor for class org.intermine.web.struts.EnrichmentWidgetForm
Constructor
EnrichmentWidgetImplLdr - Class in org.intermine.web.logic.widget
Implement methods to access data an enrichment calculation needs to be provided with.
EnrichmentWidgetImplLdr(InterMineBag, InterMineBag, ObjectStore, EnrichmentWidgetConfig, String, boolean, CorrectionCoefficient, String, String) - Constructor for class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
Construct an Enrichment widget loader, which performs the queries needed for enrichment statistics.
EnrichmentWidgetResultService - Class in org.intermine.webservice.server.widget
Web service that returns the result of an enrichment calculation over a list of objects.
EnrichmentWidgetResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
EnrichmentXMLProcessor - Class in org.intermine.webservice.server.widget
A widget result processor for enrichment results that produces output as XML.
ensureBagIsDeleted(Profile, String) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
After this method returns, the will be no bag with the given name in the given profile.
entrySet() - Method in class org.intermine.api.profile.UserPreferences
 
entrySet() - Method in class org.intermine.api.util.DevNullMap
 
entrySet() - Method in class org.intermine.util.AlwaysMap
entrySet() - Method in class org.intermine.util.IdentityMap
entrySet() - Method in class org.intermine.util.ReferenceMap
eof - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
EOF - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
EOF - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
EOF - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
eq(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be equal to a value.
EQ - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
EQ - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that left is equal to right.
EQ - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
EQUAL - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes one constraint as being equal to another constraint.
EQUAL - Static variable in class org.intermine.sql.query.AbstractValue
Describes two AbstractValues as being equal.
equals(Object) - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
equals(Object) - Method in class org.intermine.api.bag.SharingInvite
 
equals(Object) - Method in class org.intermine.api.beans.ObjectDetails
 
equals(Object) - Method in class org.intermine.api.beans.PartnerLink
 
equals(Object) - Method in class org.intermine.api.idresolution.ResolutionJob
 
equals(Object) - Method in class org.intermine.api.mines.ObjectRequest
 
equals(Object) - Method in class org.intermine.api.mines.RemoteMine
 
equals(Object) - Method in class org.intermine.api.profile.BagValue
Two bag values are identical if they have the same value and extra value.
equals(Object) - Method in class org.intermine.api.profile.SavedQuery
Test receiver for equality with passed object.
equals(Object) - Method in class org.intermine.api.results.Column
equals(Object) - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
equals(Object) - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
equals(Object) - Method in class org.intermine.api.results.ResultElement
equals(Object) - Method in class org.intermine.api.template.ApiTemplate
 
equals(Object) - Method in class org.intermine.api.userprofile.PermanentToken
 
equals(Object) - Method in class org.intermine.api.userprofile.SavedBag
 
equals(Object) - Method in class org.intermine.api.userprofile.SavedQuery
 
equals(Object) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
equals(Object) - Method in class org.intermine.api.userprofile.Tag
 
equals(Object) - Method in class org.intermine.api.userprofile.TemplateSummary
 
equals(Object) - Method in class org.intermine.api.userprofile.UserProfile
 
equals(Object) - Method in class org.intermine.metadata.AttributeDescriptor
equals(Object) - Method in class org.intermine.metadata.ClassDescriptor
equals(Object) - Method in class org.intermine.metadata.CollectionDescriptor
equals(Object) - Method in class org.intermine.metadata.Model
equals(Object) - Method in class org.intermine.metadata.PrimaryKey
equals(Object) - Method in class org.intermine.metadata.ReferenceDescriptor
equals(Object) - Method in class org.intermine.metadata.StringUtil.LineWrappedString
equals(Object) - Method in class org.intermine.model.fulldata.Item
 
equals(Object) - Method in class org.intermine.objectstore.query.BagConstraint
equals(Object) - Method in class org.intermine.objectstore.query.ClassConstraint
Tests whether two ClassConstraints are equal.
equals(Object) - Method in class org.intermine.objectstore.query.Clob
Override Object#equals.
equals(Object) - Method in class org.intermine.objectstore.query.ConstraintSet
Test whether two ConstraintSets are equal, overrides Object.equals().
equals(Object) - Method in class org.intermine.objectstore.query.ContainsConstraint
Test whether two ContainsConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.objectstore.query.iql.IqlQuery
equals(Object) - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBag
Override Object#equals.
equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
equals(Object) - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
equals(Object) - Method in class org.intermine.objectstore.query.OverlapConstraint
equals(Object) - Method in class org.intermine.objectstore.query.PathExpressionField
equals(Object) - Method in class org.intermine.objectstore.query.QueryCast
equals(Object) - Method in class org.intermine.objectstore.query.QueryField
Returns true if this is equal to the given object.
equals(Object) - Method in class org.intermine.objectstore.query.QueryValue
Overrides Object.
equals(Object) - Method in class org.intermine.objectstore.query.Results
 
equals(Object) - Method in class org.intermine.objectstore.query.ResultsInfo
equals(Object) - Method in class org.intermine.objectstore.query.SimpleConstraint
Test whether two SimpleConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.objectstore.query.SubqueryConstraint
Test whether two SubqueryConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
Test whether two SubqueryConstraints are equal, overrides Object.equals()
equals(Object) - Method in class org.intermine.pathquery.LogicExpression
equals(Object) - Method in class org.intermine.pathquery.Node
equals(Object) - Method in class org.intermine.pathquery.OrderElement
equals(Object) - Method in class org.intermine.pathquery.Path
equals(Object) - Method in class org.intermine.pathquery.PathQuery
 
equals(Object) - Method in class org.intermine.sql.precompute.PrecomputedTable
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.AbstractConstraint
Overrides Object.equals();
equals(Object) - Method in class org.intermine.sql.query.AbstractTable
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.AbstractValue
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Constant
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.ExplainResult
equals(Object) - Method in class org.intermine.sql.query.Field
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Function
Overrides Object.equals.
equals(Object) - Method in class org.intermine.sql.query.OrderDescending
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Query
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.SelectValue
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.SubQuery
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.query.Table
Overrides Object.equals().
equals(Object) - Method in class org.intermine.sql.writebatch.Row
equals(Object) - Method in class org.intermine.template.TemplateQuery
 
equals(Object) - Method in class org.intermine.util.AlwaysMap
equals(Object) - Method in class org.intermine.util.IdentityMap
equals(Object) - Method in class org.intermine.util.ReferenceMap
equals(Object) - Method in class org.intermine.web.logic.config.Displayer
equals(Object) - Method in class org.intermine.web.logic.config.FieldConfig
equals(Object) - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
 
equals(Object) - Method in class org.intermine.web.logic.config.TableExportConfig
equals(Object) - Method in class org.intermine.web.logic.config.Type
equals(Object) - Method in class org.intermine.web.logic.config.WebConfig
equals(Object) - Method in class org.intermine.web.logic.template.ConstraintInput
 
equals(Object) - Method in class org.intermine.web.logic.TreeNode
equals(Object) - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
equals(Object) - Method in class org.intermine.webservice.server.core.Either
 
equals(Object) - Method in class org.intermine.webservice.server.jbrowse.Command
 
equals(Object) - Method in class org.intermine.webservice.server.jbrowse.Segment
 
equals(Object) - Method in class org.intermine.webservice.server.JWTBuilder
 
equals(Object) - Method in class org.intermine.xml.full.Attribute
equals(Object) - Method in class org.intermine.xml.full.Item
equals(Object) - Method in class org.intermine.xml.full.Reference
equals(Object) - Method in class org.intermine.xml.full.ReferenceList
equals(Object, Object) - Static method in class org.intermine.metadata.Util
Compare two objects, using their .equals method, but comparing null to null as equal.
EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are equal, regardless of case for strings
equalsExactly(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be exactly equal to a value.
equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.AbstractTable
Compare this AbstractTable to another, ignoring little details like aliases.
equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.SubQuery
Compare this SubQuery to another AbstractTable, ignoring alias.
equalsIgnoreAlias(AbstractTable) - Method in class org.intermine.sql.query.Table
Compare this Table to another AbstractTable, ignoring alias.
equalsNoUnion(Object) - Method in class org.intermine.sql.query.Query
Returns true if this Query is equivalent to obj, disregarding other queries in the UNION.
equalsOnlyAlias(AbstractTable) - Method in class org.intermine.sql.query.AbstractTable
Compare this AbstractTable to another, only comparing the alias.
equalsTableOnlyAlias(AbstractValue) - Method in class org.intermine.sql.query.Field
Compare this Field to another AbstractValue, including only the table alias.
equalToLoop(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be equal to a loopPath.
EquivalentObjectFetcher - Interface in org.intermine.dataloader
Interface providing methods to look up equivalent objects by primary key in a production objectstore.
EquivalentObjectHints - Class in org.intermine.dataloader
Object for holding hint data for the getEquivalentObjects method in IntegrationWriters.
EquivalentObjectHints(ObjectStore) - Constructor for class org.intermine.dataloader.EquivalentObjectHints
Constructor.
equivalents - Variable in class org.intermine.dataloader.BatchingFetcher
 
error(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
}
ERROR - org.intermine.api.idresolution.Job.JobStatus
job failed
ERROR_INTRO - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter
The string that begins an error line.
ERROR_INTRO - Static variable in class org.intermine.webservice.server.output.PlainFormatter
The string that begins an error line.
ERROR_UPGRADER - Static variable in interface org.intermine.api.bag.IdUpgrader
An upgrader that always fails.
ErrorCorrection - Class in org.intermine.web.logic.widget
See online help docs for detailed description of what error correction is and why we need it.
ErrorCorrection.Strategy - Enum in org.intermine.web.logic.widget
 
ErrorMessagesController - Class in org.intermine.web.struts
Take the messages stored in the session which are not using ActionMessages or ActionErrors and put them in the request
ErrorMessagesController() - Constructor for class org.intermine.web.struts.ErrorMessagesController
 
ERRORS - Static variable in class org.intermine.web.logic.Constants
Session attribute that temporarily holds a Vector of errors that will be displayed by the errorMessages.jsp on the next page viewed by the user and then removed (allows errors after redirect).
escapeAttribute(Object) - Method in class org.intermine.webservice.server.output.XMLFormatter
 
escapeBackslash(String) - Static method in class org.intermine.metadata.StringUtil
Escape single backslash with single forwardslash for correct storage in postgres.
ESCAPED_STRING - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
escapeElementContent(String) - Method in class org.intermine.webservice.server.output.XMLFormatter
Escape the content of an element.
escapeReservedWord(String) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts words into escaped form.
escapeWithBackslashes(String) - Static method in class org.intermine.metadata.StringUtil
Escapes single quotes and backslashes, with backslashes.
estimate(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in interface org.intermine.objectstore.ObjectStore
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Explain a Query (give estimate for execution time and number of rows).
estimate(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Explain a Query (give estimate for execution time and number of rows).
ESTIMATE - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the result of getRows() is a pure estimate that is not contradicted by the min or max
estimatedRows - Variable in class org.intermine.sql.query.ExplainResult
 
estimateWithConnection(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Runs an EXPLAIN for the given query.
everOptimise() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns whether optimisation should be permitted.
everOptimise() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns whether optimisation should be permitted.
evictFromCache(Profile) - Method in class org.intermine.api.profile.ProfileManager
Remove a profile from the cache
EvictOrphansTask - Class in org.intermine.web.task
A task for removing tags that don't point to anything.
EvictOrphansTask() - Constructor for class org.intermine.web.task.EvictOrphansTask
 
EXACT_MATCH - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are exactly equal
EXCEPT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing an EXCEPT operation
EXCLUDES - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being mutually exclusive.
execute() - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
execute() - Method in class org.intermine.dataloader.XmlDataLoaderTask
execute() - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
execute() - Method in class org.intermine.task.AcceptanceTestTask
 
execute() - Method in class org.intermine.task.AnalyseDbTask
execute() - Method in class org.intermine.task.BuildDbTask
execute() - Method in class org.intermine.task.CreateIndexesTask
execute() - Method in class org.intermine.task.DBConverterTask
Run the task
execute() - Method in class org.intermine.task.DirectDataLoaderTask
 
execute() - Method in class org.intermine.task.DirectoryConverterTask
Run the task.
execute() - Method in class org.intermine.task.DropPrecomputedTablesTask
execute() - Method in class org.intermine.task.FileConverterTask
Run the task
execute() - Method in class org.intermine.task.FullXmlConverterTask
execute() - Method in class org.intermine.task.GenerateUpdateTriggersTask
execute() - Method in class org.intermine.task.GrantTask
execute() - Method in class org.intermine.task.ModelMergerTask
execute() - Method in class org.intermine.task.ModelOutputTask
execute() - Method in class org.intermine.task.PostProcessorTask
Run the task
execute() - Method in class org.intermine.task.PrecomputeTask
execute() - Method in class org.intermine.task.RetrieveMetadataTask
execute() - Method in class org.intermine.task.RunIqlQueryTask
execute() - Method in class org.intermine.task.StaticMethodTask
 
execute() - Method in class org.intermine.task.StoreMetadataTask
execute() - Method in class org.intermine.task.SummariseObjectStoreTask
execute() - Method in class org.intermine.web.task.CreateSearchIndexTask
 
execute() - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Write templates and tags to a file.
execute() - Method in class org.intermine.web.task.EvictOrphansTask
 
execute() - Method in class org.intermine.web.task.IssueTokenTask
 
execute() - Method in class org.intermine.web.task.LoadBagValuesTask
Execute the task - load bagvalues table.
execute() - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Load templates from an xml file into a userprofile account.
execute() - Method in class org.intermine.web.task.ModelUpdateTask
Update savedquery, savedtemplatequery and savedbag in the userprofile through ModelUpdate object
execute() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
execute() - Method in class org.intermine.web.task.ProfileReadTask
Execute the task - read the profiles.
execute() - Method in class org.intermine.web.task.ProfileWriteTask
Execute the task - write the profiles as XML.
execute() - Method in class org.intermine.web.task.TemplateTrackReadTask
Execute the task - read the profiles.
execute() - Method in class org.intermine.web.task.TemplateTrackWriteTask
Execute the task - write the template tracks as XML.
execute() - Method in class org.intermine.web.task.UpdateListTablesTask
Execute the task.
execute() - Method in class org.intermine.web.task.UpdateTrackTableTask
Execute the task - read the profiles.
execute() - Method in class org.intermine.web.task.VerifyTokenTask
 
execute() - Method in class org.intermine.webservice.server.bg.BGPropertiesCreationService
 
execute() - Method in class org.intermine.webservice.server.bg.BGPropertiesDelationService
 
execute() - Method in class org.intermine.webservice.server.bg.BGPropertiesService
 
execute() - Method in class org.intermine.webservice.server.bg.BGPropertiesUpdateService
 
execute() - Method in class org.intermine.webservice.server.branding.BrandingService
 
execute() - Method in class org.intermine.webservice.server.ClassKeysService
 
execute() - Method in class org.intermine.webservice.server.clob.SequenceService
 
execute() - Method in class org.intermine.webservice.server.data.DataService
 
execute() - Method in class org.intermine.webservice.server.FacetListService
 
execute() - Method in class org.intermine.webservice.server.FacetService
 
execute() - Method in class org.intermine.webservice.server.fair.BioEntityMarkupService
 
execute() - Method in class org.intermine.webservice.server.fair.HomePageMarkupService
 
execute() - Method in class org.intermine.webservice.server.fair.PermanentURLService
 
execute() - Method in class org.intermine.webservice.server.FeedbackService
 
execute() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService
 
execute() - Method in class org.intermine.webservice.server.idresolution.JobRemovalService
 
execute() - Method in class org.intermine.webservice.server.idresolution.JobResultsService
 
execute() - Method in class org.intermine.webservice.server.idresolution.JobStatusService
 
execute() - Method in class org.intermine.webservice.server.idresolution.ListResolutionService
 
execute() - Method in class org.intermine.webservice.server.jbrowse.Config
 
execute() - Method in class org.intermine.webservice.server.jbrowse.Endpoint
 
execute() - Method in class org.intermine.webservice.server.jbrowse.Names
 
execute() - Method in class org.intermine.webservice.server.lists.AvailableListsService
 
execute() - Method in class org.intermine.webservice.server.lists.JaccardIndexService
 
execute() - Method in class org.intermine.webservice.server.lists.ListDeletionService
 
execute() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
execute() - Method in class org.intermine.webservice.server.lists.ListRenameService
 
execute() - Method in class org.intermine.webservice.server.lists.ListShareCreationService
Runs service.
execute() - Method in class org.intermine.webservice.server.lists.ListShareDeletionService
 
execute() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDeletionService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
 
execute() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService
 
execute() - Method in class org.intermine.webservice.server.lists.ListTagAddingService
 
execute() - Method in class org.intermine.webservice.server.lists.ListTagService
 
execute() - Method in class org.intermine.webservice.server.lists.ListUpdateService
 
execute() - Method in class org.intermine.webservice.server.lists.ListUpgradingService
 
execute() - Method in class org.intermine.webservice.server.model.ModelService
Runs service.
execute() - Method in class org.intermine.webservice.server.oauth2.AuthenticatorService
 
execute() - Method in class org.intermine.webservice.server.oauth2.CallbackService
 
execute() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
execute() - Method in class org.intermine.webservice.server.query.CodeService
 
execute() - Method in class org.intermine.webservice.server.query.QueryRemovalService
 
execute() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
execute() - Method in class org.intermine.webservice.server.query.QueryStoreService
 
execute() - Method in class org.intermine.webservice.server.query.QueryToListService
 
execute() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
execute() - Method in class org.intermine.webservice.server.query.result.QueryResultService
Executes service specific logic.
execute() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
execute() - Method in class org.intermine.webservice.server.SchemaListService
 
execute() - Method in class org.intermine.webservice.server.search.QuickSearch
 
execute() - Method in class org.intermine.webservice.server.SessionService
 
execute() - Method in class org.intermine.webservice.server.SummaryService
 
execute() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
execute() - Method in class org.intermine.webservice.server.template.result.TemplateResultService
Executes service specific logic.
execute() - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
execute() - Method in class org.intermine.webservice.server.template.SystemTemplatesService
 
execute() - Method in class org.intermine.webservice.server.template.TemplateRemovalService
 
execute() - Method in class org.intermine.webservice.server.template.TemplateTagAddingService
 
execute() - Method in class org.intermine.webservice.server.template.TemplateTagService
 
execute() - Method in class org.intermine.webservice.server.template.TemplateUploadService
 
execute() - Method in class org.intermine.webservice.server.user.ChangePasswordService
 
execute() - Method in class org.intermine.webservice.server.user.DeletePreferencesService
 
execute() - Method in class org.intermine.webservice.server.user.DeleteTokensService
 
execute() - Method in class org.intermine.webservice.server.user.DeletionTokenCancellationService
 
execute() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService
 
execute() - Method in class org.intermine.webservice.server.user.DeregistrationService
 
execute() - Method in class org.intermine.webservice.server.user.LoginService
 
execute() - Method in class org.intermine.webservice.server.user.LogoutService
 
execute() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
 
execute() - Method in class org.intermine.webservice.server.user.NewUserService
 
execute() - Method in class org.intermine.webservice.server.user.PermaTokenDeletionService
 
execute() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService
 
execute() - Method in class org.intermine.webservice.server.user.PswResetService
 
execute() - Method in class org.intermine.webservice.server.user.ReadPreferencesService
 
execute() - Method in class org.intermine.webservice.server.user.RequestPswResetService
 
execute() - Method in class org.intermine.webservice.server.user.SetPreferencesService
 
execute() - Method in class org.intermine.webservice.server.user.TokenService
 
execute() - Method in class org.intermine.webservice.server.user.TokensService
 
execute() - Method in class org.intermine.webservice.server.user.WhoAmIService
 
execute() - Method in class org.intermine.webservice.server.VersionService
 
execute() - Method in class org.intermine.webservice.server.webproperties.WebPropertiesService
 
execute() - Method in class org.intermine.webservice.server.WebService
Runs service.
execute() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
 
execute() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
Executes service specific logic.
execute() - Method in class org.intermine.webservice.server.widget.GraphService
 
execute() - Method in class org.intermine.webservice.server.widget.TableWidgetService
 
execute(Exception, ExceptionConfig, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InterMineExceptionHandler
Handle the exception.
execute(Connection, String) - Method in class org.intermine.task.CreateIndexesTask
Execute an sql statement.
execute(HttpServletRequest, ReportObject) - Method in class org.intermine.web.displayer.ReportDisplayer
Execute is called for each report page with the object to be displayed.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AddColumnAction
Executes action.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AddToBagAction
Save a single object to an existing bag.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AvailableColumnsController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagBuildController
Set up environment for the buildBag page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagDetailsAction
Set up session attributes for the bag details page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUpgradeAction
Action for creating BagQueryResult for a specific bag not yet current
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmAction
Action to save a bag from the bagUploadConfirm page into the user profile.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BeginAction
Either display the query builder or redirect to project.sitePrefix.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BuildBagAction
Action for creating a bag of InterMineObjects or Strings from identifiers in text field.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangePasswordAction
Method called when user has finished filling out the 'change password' form
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableSizeAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CollectionDetailsAction
Create PagedTable for this collection, register it with an identifier and redirect to results.do?table=identifier
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CollectionTableAction
Create PagedTable for this collection, register it with an identifier
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ContactAction
Method called when user has submitted valid feedback form
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CreateAccountAction
Method called when user has finished updating a constraint.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CreateTemplateAction
Take the current query and TemplateBuildState from the session and create a TemplateQuery.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CurrentQueryAction
Either display the query builder or redirect to project.sitePrefix.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.EditPropertiesAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.EditTemplateAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportQueryAction
Method called to export a saved Query.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportTagsAction
Export user's tags.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FileDownloadAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FindInListAction
Method called when user has submitted the search form.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.GetAttributeAsFileAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.GotoWebSearchableAction
Method called when user has submitted search form.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HeartbeatAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ImportQueriesAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ImportTagsAction
Import user's tags.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InvitationAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LabelsSummaryAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoginAction
Method called for login in
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LogoutAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyBagAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyBagDetailsAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction
Forward to the correct method based on the button pressed.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifySuperUserAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction
Forward to the correct method based on the button pressed.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.oauth2.Authenticator
Method called for login in
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.oauth2.Callback
Method called for login in
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PasswordResetAction
Method called when the form is submitted.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PollQueryAction
Handle request from client.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PortalQueryAction
Link-ins from other sites end up here (after some redirection).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderConstraintAction
Method called when user has finished updating a constraint.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewAction
Run the query and forward to the results page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryClassSelectAction
Add a QueryClass of a specified type to the current query.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportController
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.RequestPasswordAction
Method called when user has finished updating a constraint
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ResultsAction
Called before results table is rendered.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.RunQueryAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveFromIdsToBagAction
 
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveQueryAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SummariseTemplatesAction
Summarises every public template, and then forwards to the mymine template page.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TableExportAction
Method called to export a PagedTable object.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateAction
Build a query based on the template and the input from the user.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesExportAction
Build a query based on the template and the input from the user.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesImportAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TriageBagAction
Forward to the correct method based on the button pressed
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.WebserviceCodeGenAction
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ApiJavaController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ApiPerlController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.AspectController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagDetailsController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmController
Set up the bagUploadConfirm page.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.BagUploadConfirmIssueController
Initialise attributes for the bagUploadConfirmIssue.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ClassChooserController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ConvertBagController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.CountTableController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ErrorMessagesController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ExportOptionsController
Set up the exportOptions tile.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.FavouritesController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.HtmlHeadController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InlineTagEditorController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.KeywordSearchResultsController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ListTagsController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoginController
Set up the form for login.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.MyMineController
Set up attributes for the myMine page.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ObjectTrailController
Looks at the "trail" request parameter and extracts the object ids from it, then looks up the actual objects and creates a list of TrailItems.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ObjectViewController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.PasswordResetController
Set up the form.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderConstraintController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderSummaryController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportAspectController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportDisplayerController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportInListController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ReportTemplateController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SharingBagUsersController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SubMenuController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TableController
Set up table tile.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateController
Finds the correct template to display in the following ways: First, looks for a "name" request parameter and uses that for a the lookup.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateListController
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplateProblemsController
Called before template problem page is rendered.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TemplatesController
Set up attributes for the templates page.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.UsersController
 
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.WebSearchableListController
Set up the attributes for webSearchableList.tile
execute(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore
execute(Query) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore
execute(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore
execute(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Execute a Query on this ObjectStore, asking for a certain range of rows to be returned.
execute(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor
Executes object store query and returns results as iterator over rows.
execute(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Create and ObjectStore query from a PathQuery and execute it, returning results in a format appropriate for displaying a web table.
execute(PathQuery, int, int) - Method in class org.intermine.api.query.PathQueryExecutor
Executes object store query and returns results as iterator over rows.
execute(PathQuery, Map<String, BagQueryResult>) - Method in class org.intermine.api.query.WebResultsExecutor
Create and ObjectStore query from a PathQuery and execute it, returning results in a format appropriate for displaying a web table.
executeSingleton(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in interface org.intermine.objectstore.ObjectStore
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSingleton(Query, int, boolean, boolean, boolean) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Execute a Query on this ObjectStore, returning a SingletonResults
executeSqlInParallel(String) - Method in class org.intermine.sql.Database
Executes an SQL statement on the database in a separate thread.
executeWithConnection(Connection, Query, int, int, boolean, boolean, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Performs the actual execute, given a Connection.
executeWithConnection(Connection, Query, int, int, boolean, boolean, Map<Object, Integer>, Set<PrecomputedTable>, OptimiserCache) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Performs the actual execute, given a Connection.
EXECUTION - org.intermine.api.tracker.util.ListTrackerEvent
execution
executor - Variable in class org.intermine.webservice.server.query.result.QueryResultService
 
existingBagName - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
existingBagName - Variable in class org.intermine.web.struts.SaveBagForm
 
exists() - Method in class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
Check whether a NOT NULL constraint was found.
EXISTS - Static variable in class org.intermine.metadata.ConstraintOp
Subquery exists
expand(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
expandPath(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Given a path return a set of paths replacing a path with a '+' preceding a class name with an additional path for every subclass of that class.
EXPECTED - org.intermine.web.logic.widget.GraphWidgetActionType
 
EXPIRE_INTERVAL - Static variable in class org.intermine.sql.precompute.OptimiserCache
Number of events to happen before an expiration run.
ExpiresHeaderFilter - Class in org.intermine.web.filters
A Filter that modifies response headers of outgoing pages.
ExpiresHeaderFilter() - Constructor for class org.intermine.web.filters.ExpiresHeaderFilter
 
explain - Variable in class org.intermine.objectstore.query.Results
 
explain - Variable in class org.intermine.sql.query.Query
 
explain(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Explain a query and return estimates of execution time and row count.
explainResult - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
ExplainResult - Class in org.intermine.sql.query
Represents a result from an EXPLAIN request to a database.
ExplainResult() - Constructor for class org.intermine.sql.query.ExplainResult
 
export(Iterator<? extends List<ResultElement>>) - Method in interface org.intermine.web.logic.export.Exporter
Perform the export with the exporter's defaults in the absence of path collection changes.
export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.web.logic.export.ExporterImpl
 
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in interface org.intermine.web.logic.export.Exporter
Do export.
export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ExporterImpl
Do export.
export(List<List<String>>) - Method in class org.intermine.web.logic.export.string.StringTableExporter
Perform export.
export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction
Load a template from template name passed as parameter.
export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryAction
Export the selected queries
export(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyTemplateAction
Export the selected templates.
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
Perform export.
export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
Method called to export a PagedTable object
ExportController - Class in org.intermine.web.struts
Controller to initialise for the export.tile
ExportController() - Constructor for class org.intermine.web.struts.ExportController
 
exportDataPackage(PathQuery, HttpServletRequest, PathQueryExecutor, String) - Method in class org.intermine.webservice.server.query.result.FrictionlessDataPackage
 
Exporter - Interface in org.intermine.web.logic.export
Simple exporter interface.
ExporterImpl - Class in org.intermine.web.logic.export
Simple exporter exporting data as tab separated, comma separated and so.
ExporterImpl(OutputStream, RowFormatter) - Constructor for class org.intermine.web.logic.export.ExporterImpl
Constructor.
ExporterImpl(OutputStream, RowFormatter, String, List<String>) - Constructor for class org.intermine.web.logic.export.ExporterImpl
Constructor.
ExportException - Exception in org.intermine.web.logic.export
Exception thrown if the there is a problem while exporting (eg.
ExportException(String) - Constructor for exception org.intermine.web.logic.export.ExportException
Create a new ExportException.
ExportException(String, Exception) - Constructor for exception org.intermine.web.logic.export.ExportException
Create a new ExportException.
exportField(InterMineObject, String, ObjectStore, HttpServletResponse) - Method in interface org.intermine.web.logic.export.FieldExporter
Example FieldExporter that splits the a String field at the first comma and outputs each bit on a new line.
ExportHelper - Class in org.intermine.web.logic.export
Helper methods for exporters.
ExportOptionsController - Class in org.intermine.web.struts
Controller for exportOptions.tile
ExportOptionsController() - Constructor for class org.intermine.web.struts.ExportOptionsController
 
ExportQueryAction - Class in org.intermine.web.struts
Export the current query in XML format.
ExportQueryAction() - Constructor for class org.intermine.web.struts.ExportQueryAction
 
ExportResultsIterator - Class in org.intermine.api.results
An Iterator that produces data in a format suitable for exporting.
ExportResultsIterator(PathQuery, Query, Results, Map<String, QuerySelectable>) - Constructor for class org.intermine.api.results.ExportResultsIterator
Constructor for ExportResultsIterator.
ExportTagsAction - Class in org.intermine.web.struts
Export tags.
ExportTagsAction() - Constructor for class org.intermine.web.struts.ExportTagsAction
 
expr() - Method in class org.intermine.pathquery.LogicParser
 
EXTRA_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
extra value parameter
EXTRA_VALUE_CONSTRAINT - Static variable in class org.intermine.api.config.Constants
Constrain by an extra value
extraAttribute - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
extraFieldValue - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
ExtraQueryTime - Class in org.intermine.objectstore.intermine
An object that holds information about extra queries run during the ResultsConverter operation.
ExtraQueryTime() - Constructor for class org.intermine.objectstore.intermine.ExtraQueryTime
Constructor.
extraValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 

F

F<A,​B> - Class in org.intermine.webservice.server.core
A type for a function from A -> B.
F() - Constructor for class org.intermine.webservice.server.core.F
 
F.Constant<X,​R> - Class in org.intermine.webservice.server.core
An implementation of a constant function.
FacetListService - Class in org.intermine.webservice.server
A web service for returning all the facet list
FacetListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.FacetListService
Constructor
FacetListServlet - Class in org.intermine.webservice.server
A web service for returning all the facet list
FacetListServlet() - Constructor for class org.intermine.webservice.server.FacetListServlet
 
FacetService - Class in org.intermine.webservice.server
A web service for returning facet related to particular query
FacetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.FacetService
Constructor
FacetServlet - Class in org.intermine.webservice.server
A web service for returning facet related to particular query
FacetServlet() - Constructor for class org.intermine.webservice.server.FacetServlet
 
fairTerm - Variable in class org.intermine.metadata.AttributeDescriptor
 
FALSE - Static variable in class org.intermine.objectstore.query.QueryValue
The false value
fanOutCombinations(List<Collection<E>>) - Static method in class org.intermine.util.CollectionUtil
Returns a collection containing all possible combinations of the input values.
FastPathObject - Interface in org.intermine.model
A root interface for all objects that can be stored in a InterMine database.
fatalError(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
}
FavouritesController - Class in org.intermine.web.struts
Controller for the starTemplate tile.
FavouritesController() - Constructor for class org.intermine.web.struts.FavouritesController
 
features(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
FEATURES - org.intermine.webservice.server.jbrowse.Commands.Action
features
FeedbackService - Class in org.intermine.webservice.server
Send feedback from users
FeedbackService(InterMineAPI) - Constructor for class org.intermine.webservice.server.FeedbackService
Constructor
FeedbackServlet - Class in org.intermine.webservice.server
Send feedback from users
FeedbackServlet() - Constructor for class org.intermine.webservice.server.FeedbackServlet
 
fetchBatchFromObjectStore(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets a batch from the ObjectStore.
fetchByIds(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Class<?>, Collection<Integer>, ExtraQueryTime) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Fetches a group of objects from the database by ID.
fetchCollectionPathExpression(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Query, QueryCollectionPathExpression, List<ResultsRow<Object>>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Fetches the QueryCollectionPathExpression data for a query.
fetchObjectPathExpression(ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, Query, QueryObjectPathExpression, List<ResultsRow<Object>>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
Fetches the contents of a QueryObjectPathExpression for a query.
field - Variable in class org.intermine.api.results.ResultElement
 
field() - Method in class org.intermine.sql.query.SqlParser
 
field(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
Field - Class in org.intermine.sql.query
A representation of a field in a table.
Field(String, AbstractTable) - Constructor for class org.intermine.sql.query.Field
Constructor for this Field object.
FIELD - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
FIELD - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
field_alias() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
field_alias() - Method in class org.intermine.sql.query.SqlParser
 
field_alias(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
FIELD_ALIAS - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
FIELD_ALIAS - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
field_name() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
field_name() - Method in class org.intermine.sql.query.SqlParser
 
field_name(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
FIELD_NAME - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
FIELD_NAME - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
FIELD_PATH_EXPRESSION - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
FieldConfig - Class in org.intermine.web.logic.config
The webapp configuration for one field of a class.
FieldConfig() - Constructor for class org.intermine.web.logic.config.FieldConfig
 
FieldConfigHelper - Class in org.intermine.web.logic.config
Helper methods for the FieldConfig class.
FieldDescriptor - Class in org.intermine.metadata
Abstract representation of a field within a class - could be an attribute, an object reference or a collection.
FieldDescriptor(String) - Constructor for class org.intermine.metadata.FieldDescriptor
Construct, name of field must not be null and must be a valid Java variable name.
FieldExporter - Interface in org.intermine.web.logic.export
An interface implemented by objects that can export the value of a particular.
FieldInfo(String, Method, Method, Method, Method, Method) - Constructor for class org.intermine.metadata.TypeUtil.FieldInfo
Construct a new FieldInfo object.
fieldIsPrimaryKey(Model, Class<?>, String, Source) - Static method in class org.intermine.dataloader.DataLoaderHelper
Returns true if the given field is a member of any primary key on the given class, for the given source.
fieldName - Variable in class org.intermine.objectstore.query.QueryForeignKey
 
fieldName - Variable in class org.intermine.objectstore.query.QueryReference
 
fields - Variable in class org.intermine.sql.logging.DatabaseWriter
 
file - Variable in class org.intermine.codegen.JavaModelOutput
 
file - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
file - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
file - Variable in class org.intermine.task.FullXmlConverterTask
 
FileConverter - Class in org.intermine.dataconversion
Parent class for DataConverters that read from files
FileConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.FileConverter
Constructor
FileConverterTask - Class in org.intermine.task
Initiates retrieval and conversion of data from a source file.
FileConverterTask() - Constructor for class org.intermine.task.FileConverterTask
 
FileDirectDataLoaderTask - Class in org.intermine.task
A DirectDataLoaderTask for files.
FileDirectDataLoaderTask() - Constructor for class org.intermine.task.FileDirectDataLoaderTask
 
FileDownloadAction - Class in org.intermine.web.struts
This is a generic action to download file from any given directory.
FileDownloadAction() - Constructor for class org.intermine.web.struts.FileDownloadAction
 
fileName - Variable in class org.intermine.web.task.DumpDefaultTemplatesTask
 
fileName - Variable in class org.intermine.web.task.ProfileWriteTask
 
fileName - Variable in class org.intermine.web.task.TemplateTrackWriteTask
 
FILENAME_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The parameter for setting the filename
fileSet - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
fileSet - Variable in class org.intermine.task.FileConverterTask
 
fileSet - Variable in class org.intermine.task.FullXmlConverterTask
 
fileSets - Variable in class org.intermine.task.FileDirectDataLoaderTask
 
filter - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
filter - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
filter(List<Constraint>, FromElement, boolean) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Return a subset of the given List that contains only Constraints that relate to the given FromElement or constraints associated with nothing if fromElement is null.
filterByList(Map<String, WebSearchable>, String) - Static method in class org.intermine.web.struts.WebSearchableListController
Filters websearchables.
filterByTags(Map<String, W>, List<String>, String, String, TagManager) - Method in class org.intermine.api.search.SearchFilterEngine
Given a Map from name to WebSearchable, return a Map that contains only those name, WebSearchable pairs where the name is tagged with all of the tags listed.
filterByTags(Map<String, W>, List<String>, String, String, TagManager, boolean) - Method in class org.intermine.api.search.SearchFilterEngine
Given a Map from name to WebSearchable, return a Map that contains only those name, WebSearchable pairs where the name is tagged with all of the tags listed.
filterConfig - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter
The filter configuration object we are associated with.
FilteringResultIterator - Class in org.intermine.webservice.server.output
A result iterator that skips things we aren't interested in.
FilteringResultIterator(Results) - Constructor for class org.intermine.webservice.server.output.FilteringResultIterator
Construct a new iterator which does no filtering.
FilteringResultIterator(Results, int, int, String) - Constructor for class org.intermine.webservice.server.output.FilteringResultIterator
Construct a new iterator which filters to things that match a filter term and only returns results in a given window.
filterOutInvalidTemplates(Map<String, ? extends WebSearchable>) - Static method in class org.intermine.api.search.SearchResults
Filter out invalid templates from a map.
filterWebSearchables(String, String, List<String>, String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Given a scope, type, tags and some filter text, produce a list of matching WebSearchable, in a format useful in JavaScript.
finalize() - Method in class org.intermine.api.tracker.TrackerDelegate
clean up threads
finalize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Overrides Object.finalize - release the DB log connection.
finalize() - Method in class org.intermine.sql.Database
findAndCodes(Set<String>, LogicExpression.Node) - Static method in class org.intermine.api.query.MainHelper
Finds all the codes in a constraint logic that are ANDed in the given constraint logic.
findClassKeyValue(Map<String, List<FieldDescriptor>>, InterMineObject) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the first non-null class key field for the object with the given id.
findCombinations(Set<T>, Set<T>, Comparator<? super T>) - Static method in class org.intermine.util.MappingUtil
Produces a Set of possible mappings from items in the firstSet onto items in the secondSet, where the mapping maps from one item to another item that is equal according to the comparator.
findCombinations(Set<T>, Set<T>, Comparator<? super T>, MappingUtilChecker<T>) - Static method in class org.intermine.util.MappingUtil
Produces a Set of possible mappings from items in the firstSet onto items in the secondSet, where the mapping maps from one item to another item that is equal according to the comparator.
findCommonClasses(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils
Return a list of the classes which present in the inheritance tree of all the given classes.
findCommonClasses(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
 
findCommonSuperclass(Collection<Class<?>>) - Static method in class org.intermine.util.CollectionUtil
Finds a common superclass or superinterface for all the classes specified in the arguments.
findCommonSuperclasses(Collection<Class<?>>) - Static method in class org.intermine.util.CollectionUtil
Finds common superclasses and superinterfaces for all the classes specified in the arguments.
findCommonSuperTypeOf(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
Finds the common class for a set of classes.
findFairTerm(Model, String) - Static method in class org.intermine.metadata.ClassDescriptor
Return the fair term for the given class name defined in the model.
findForcedInnerJoins(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Get a list of paths that should be forced to inner join.
findInherithance(Model, String, String) - Static method in class org.intermine.metadata.ClassDescriptor
Return true if the superClassName given in input is a super class of className
FindInListAction - Class in org.intermine.web.struts
Action to search a list for an identifier and then highlight it on the list details page.
FindInListAction() - Constructor for class org.intermine.web.struts.FindInListAction
 
FindInListForm - Class in org.intermine.web.struts
Form for FindInListAction.
FindInListForm() - Constructor for class org.intermine.web.struts.FindInListForm
Construct a new Form.
findIntersectionType(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils
Find the ClassDescriptor for the type that any two or more objects must be of where those objects are randomly selected from a collection containing objects which are of the types represented by the class descriptors in the provided collection.
findLockedPaths(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Get a list of paths that should not be removed from the query by the user.
findMostSpecificCommonTypeOf(Set<ClassDescriptor>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
 
findMultipleCombinations(Set<Map<T, T>>) - Static method in class org.intermine.util.MappingUtil
Produces a Set of possible combinations of multiple mappings (as produced by findCombinations), where all mappings in a multiple mapping combination map onto distinct objects.
findNewQueryName(Set<String>) - Static method in class org.intermine.api.util.NameUtil
Return a query name that isn't currently in use.
findNewQueryName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil
Return a query name that isn't currently in use, returning the given name if it is available.
findParentPaths(String, PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Returns a List of paths, being the given path and all its parents.
findParticipatingLoops(LogicExpression, Map<PathConstraint, String>) - Static method in class org.intermine.api.query.MainHelper
Returns the Set of PathConstraintLoop objects that will participate in the QueryClass collapsing mechanism.
findReferencedDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor
sort out references from this class
findResourcesMatching(Pattern) - Method in class org.intermine.web.struts.ResourceFinder
Find all resources matching a pattern in the WEB-INF directory.
findSumType(Collection<ClassDescriptor>) - Static method in class org.intermine.metadata.DescriptorUtils
Find the ClassDescriptor for the type that any random element selected from a collection of objects must be an instance of, where each object is an instance of one of the classes represented by the class descriptors in the input collection.
findSuperClassNames(Model, String) - Static method in class org.intermine.metadata.ClassDescriptor
Return a list of the super class names for the given class name.
findTableForAlias(String, Set<AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Finds a table in a Set with the given alias.
findTableNames(Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a Set of all table names that are touched by a given query.
findTableNames(Query, DatabaseSchema, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Builds a Set of all table names that are touched by a given query.
finish() - Method in class org.intermine.util.ObjectPipe
Marks the ObjectPipe as finished - that is, no further Objects will be put into the ObjectPipe.
finishedItem(Item) - Method in class org.intermine.xml.full.FullHandler
Method that does something useful with the finished Item
fireEvent(OriginatingEvent) - Method in class org.intermine.api.profile.StorableBag
 
fireEvent(OriginatingEvent) - Method in interface org.intermine.api.search.WebSearchable
Notify all your observers of this event which originates at this web searchable.
fireEvent(OriginatingEvent) - Method in class org.intermine.api.template.ApiTemplate
 
firstOrderByHasNoNulls - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
firstPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the first page
fixedEnumOps(Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
For an argument type which an enumerated value set, return the list of operators for which it makes sense only to provide the enumerated values and not allow the user to enter an arbitrary string.
fixEntityNames(String) - Static method in class org.intermine.util.XmlUtil
Replace greek character entity names with entity names that work in HTML.
fixInvalidBag(String, String) - Method in class org.intermine.api.profile.Profile
Fix this bag by changing its type
fixUpForJoinStyle() - Method in class org.intermine.pathquery.PathQuery
Fixes up the order by list and the constraint logic, given the arrangement of outer joins in the query.
FLAT_FILES - Static variable in enum org.intermine.webservice.server.Format
Flat file formats: TSV, CSV
FlatFileFormatter - Class in org.intermine.webservice.server.output
A class to define behaviour common to flat files (csv, tsv)
FlatFileFormatter() - Constructor for class org.intermine.webservice.server.output.FlatFileFormatter
 
FlatFileWidgetResultProcessor - Class in org.intermine.webservice.server.widget
A widget result processor that produces results in flat file format (tsv/csv)
FlatListFormatter - Class in org.intermine.webservice.server.lists
Formats a list into its name.
FlatListFormatter() - Constructor for class org.intermine.webservice.server.lists.FlatListFormatter
 
flatten(Object) - Static method in class org.intermine.metadata.TypeUtil
Make all nested objects top-level in returned collection
FlatWidgetProcessor - Class in org.intermine.webservice.server.widget
 
FLOAT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
FLOAT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
FLOOR - Static variable in class org.intermine.objectstore.query.QueryFunction
Greatest integer value less than input.
flush() - Method in class org.intermine.dataloader.DataTracker
Flushes everything to the backing database.
flush() - Method in class org.intermine.sql.logging.DatabaseWriter
Flush completed rows to the database
flush() - Method in class org.intermine.sql.precompute.OptimiserCache
Removes all entries from the cache.
flush() - Method in interface org.intermine.sql.writebatch.FlushJob
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobBatchCommit
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobPostgresCopyImpl
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobStatementBatchImpl
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.sql.writebatch.FlushJobUpdateStatistics
Performs the flush of all data represented by this object.
flush() - Method in class org.intermine.webservice.server.output.HTMLOutput
Prints html closing tags.
flush() - Method in class org.intermine.webservice.server.output.MemoryOutput
Does nothing because MemoryOutput serves as a storage of results during execution.
flush() - Method in class org.intermine.webservice.server.output.Output
Flushes output.
flush() - Method in class org.intermine.webservice.server.output.StreamedOutput
Finish writing.
flush(Connection) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server.
flush(Connection, Set<String>) - Method in class org.intermine.sql.writebatch.Batch
Flushes the batch out to the database server.
FlushJob - Interface in org.intermine.sql.writebatch
An interface representing a job to be performed when actually flushing data to a database.
FlushJobBatchCommit - Class in org.intermine.sql.writebatch
A FlushJob that commits and re-opens a transaction on the database.
FlushJobBatchCommit(Connection) - Constructor for class org.intermine.sql.writebatch.FlushJobBatchCommit
Constructor for this class
FlushJobPostgresCopyImpl - Class in org.intermine.sql.writebatch
An implementation of the FlushJob interface that represents a batch created in a Statement.
FlushJobPostgresCopyImpl(CopyManager, String, byte[], int) - Constructor for class org.intermine.sql.writebatch.FlushJobPostgresCopyImpl
Constructor for this class
FlushJobStatementBatchImpl - Class in org.intermine.sql.writebatch
An implementation of the FlushJob interface that represents a batch created in a Statement.
FlushJobStatementBatchImpl(Statement) - Constructor for class org.intermine.sql.writebatch.FlushJobStatementBatchImpl
Constructor for this class
FlushJobUpdateStatistics - Class in org.intermine.sql.writebatch
An interface representing a job to be performed when actually flushing data to a database.
FlushJobUpdateStatistics(Map<String, Integer>, BatchWriter, Connection) - Constructor for class org.intermine.sql.writebatch.FlushJobUpdateStatistics
Constructor for this class
flushLogTable() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows the log table to be flushed, guaranteeing that all log entries are committed to the database.
flushObjectById() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Completely empties the getObjectById cache.
flushObjectById() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Completely empties the getObjectById cache.
flushObjectById() - Method in interface org.intermine.objectstore.ObjectStore
Completely empties the getObjectById cache.
flushObjectById() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Completely empties the getObjectById cache.
flushObjectById() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Completely empties the getObjectById cache.
flushOldTempBagTables(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Removes any temporary bag tables that are no longer reachable.
FORM - org.intermine.web.struts.oauth2.ResponseType
This provider responds with url-encoded data
format() - Method in class org.intermine.webservice.server.user.JSONUserFormatter
Format a user into a map.
format(double, StringBuffer, FieldPosition) - Method in class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
 
format(long, StringBuffer, FieldPosition) - Method in class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
 
format(String) - Static method in class org.intermine.pathquery.ConstraintValueParser
Converts a Date to ISO date format.
format(List<? extends Object>) - Method in interface org.intermine.web.logic.export.RowFormatter
Format row to string.
format(List<? extends Object>) - Method in class org.intermine.web.logic.export.RowFormatterImpl
Formats objects to string.
format(Job) - Method in class org.intermine.webservice.server.idresolution.BagResultCategoryKeyFormatter
 
format(Job) - Method in interface org.intermine.webservice.server.idresolution.BagResultFormatter
Turn a job into a serialisable structure.
format(Job) - Method in class org.intermine.webservice.server.idresolution.BagResultOutputKeyFormatter
 
format(InterMineBag) - Method in class org.intermine.webservice.server.lists.FlatListFormatter
 
format(InterMineBag) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter
 
format(InterMineBag) - Method in class org.intermine.webservice.server.lists.JSONListFormatter
 
format(InterMineBag) - Method in interface org.intermine.webservice.server.lists.ListFormatter
Format a list into a list of string values.
format(PermanentToken) - Static method in class org.intermine.webservice.server.user.PermaTokens
Format a permanent token as a map.
Format - Enum in org.intermine.webservice.server
 
FORMAT_PARAMETER_ANY - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The parameter for accepting any format
FORMAT_PARAMETER_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants comma separated output to be returned.
FORMAT_PARAMETER_CSV - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants comma separated output to be returned.
FORMAT_PARAMETER_HTML - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants html output to be returned.
FORMAT_PARAMETER_JSON - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data
FORMAT_PARAMETER_JSON_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data suitable for using to construct tables with - this returns the rows of the table
FORMAT_PARAMETER_JSON_DATA_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data in a data table
FORMAT_PARAMETER_JSON_OBJ - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as nested objects representing records
FORMAT_PARAMETER_JSON_ROW - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data suitable for using to construct tables with - this returns the rows of the table
FORMAT_PARAMETER_JSON_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data suitable for using to construct tables with
FORMAT_PARAMETER_JSONP - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants jsonp data
FORMAT_PARAMETER_JSONP_COUNT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_JSONP_DATA_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants jsonp data in a data table
FORMAT_PARAMETER_JSONP_OBJ - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above, but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_JSONP_ROW - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_JSONP_TABLE - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants json data as above but in a format suitable for cross site ajax calls
FORMAT_PARAMETER_TAB - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants tab separated output to be returned.
FORMAT_PARAMETER_TEXT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants plain text to be returned.
FORMAT_PARAMETER_TSV - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants tab separated output to be returned.
FORMAT_PARAMETER_XML - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Value of parameter when user wants xml output to be returned.
FORMAT_VERSION - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput
The version number of the database format
formatAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.JSONFormatter
Format the header attributes.
formatAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.JSONResultFormatter
This differs from the JSONFormatter implementation in that it will output a representation of all keys in the attributes map.
formatBioEntity(HttpServletRequest, int) - Static method in class org.intermine.web.fair.SemanticMarkupFormatter
Returns bioschema.org markups to be added to the report page of bio entities
formatClass(ClassDescriptor, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a class name, using the web-config to produce configured labels.
formatColumnName(String) - Static method in class org.intermine.web.logic.WebUtil
Formats column name.
formatExtraAttributes(Map<String, Map<String, Object>>) - Method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor
Format the value of extraAttribute.
formatField(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a path into a displayable field name.
formatField(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a path into a displayable field name.
formatFieldChain(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a path represented as a string to the formatted fields, without the class name.
formatFieldChain(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a sequence of fields in a chain.
formatFooter(String, int) - Method in class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.jbrowse.util.ObjectFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.Formatter
Returns formatted footer.
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.JSONFormatter
Put on the final brace, and close the call-back bracket if needed.
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.PlainFormatter
 
formatFooter(String, int) - Method in class org.intermine.webservice.server.output.XMLFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.jbrowse.util.ObjectFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
Returns formatted header.
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Formatter
Returns formatted header.
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONFormatter
Add the opening brace, and a call-back if any
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.PlainFormatter
 
formatHeader(Map<String, Object>) - Method in class org.intermine.webservice.server.output.XMLFormatter
 
formatInstance(HttpServletRequest, Profile) - Static method in class org.intermine.web.fair.SemanticMarkupFormatter
Returns schema.org markups to be added to the home page
formatIsFlatFile() - Method in class org.intermine.webservice.server.WebService
 
formatIsJSON() - Method in class org.intermine.webservice.server.WebService
 
formatIsJsonObj() - Method in class org.intermine.webservice.server.query.AbstractQueryService
 
formatIsJSONP() - Method in class org.intermine.webservice.server.WebService
 
formatIsXML() - Method in class org.intermine.webservice.server.WebService
 
formatKVPair(String, Object) - Method in class org.intermine.pathquery.PathQuery
Format a key-value pair in a JSON compatible way.
formatPath(String, HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPath(String, InterMineAPI, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPath(String, Model, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPath(String, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the given query to construct a path according to the current state of its subclasses.
formatPath(Path, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Formats a column name, using the webconfig to produce configured labels.
formatPathDescription(String, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Return a string suitable for displaying a PathQuery's path, taking any path descriptions it has configured into account.
formatPathDescription(Path, PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Return a string suitable for displaying a PathQuery's path, taking any path descriptions it has configured into account.
formatPathQueryView(PathQuery, HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
Format a query's view into a list of displayable strings, taking both the query's path descriptions and the application's web configuration into account.
formatPathQueryView(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.WebUtil
Format a query's view into a list of displayable strings, taking both the query's path descriptions and the application's web configuration into account.
formatResult(List<String>) - Method in class org.intermine.webservice.server.jbrowse.util.ArrayFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.Formatter
Returns formatted result item.
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.JSONCountFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.JSONFormatter
In normal cases a list with a single JSON string item is expected.
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.PlainFormatter
 
formatResult(List<String>) - Method in class org.intermine.webservice.server.output.XMLFormatter
Returns formatted result item.
formatResult(List<String>) - Method in class org.intermine.webservice.server.user.UserDataFormatter
 
formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchJSONProcessor
 
formatResult(KeywordSearchResult, boolean) - Method in interface org.intermine.webservice.server.search.QuickSearchResultProcessor
They take a results, and return one or more strings.
formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchTextProcessor
 
formatResult(KeywordSearchResult, boolean) - Method in class org.intermine.webservice.server.search.QuickSearchXMLProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor
 
formatRow(List<Object>) - Method in interface org.intermine.webservice.server.widget.EnrichmentResultProcessor
Format a row of results.
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.EnrichmentXMLProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.FlatFileWidgetResultProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.GraphJSONProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.GraphXMLProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.TableJSONProcessor
 
formatRow(List<Object>) - Method in class org.intermine.webservice.server.widget.TableXMLProcessor
 
formatRow(List<Object>) - Method in interface org.intermine.webservice.server.widget.WidgetResultProcessor
Format a list of objects into a string representation.
FormattedTextParser - Class in org.intermine.util
Class for methods and util methods for parsing csv files and others.
Formatter - Class in org.intermine.webservice.server.output
Abstract class for formatting result data.
Formatter() - Constructor for class org.intermine.webservice.server.output.Formatter
 
formFile - Variable in class org.intermine.web.struts.ImportXMLForm
 
ForseenProblem - Exception in org.intermine.web.struts.oauth2
An exception type to plaster over the absence of first-class continuations in java.
ForseenProblem(String) - Constructor for exception org.intermine.web.struts.oauth2.ForseenProblem
Construct one of these objects.
ForseenProblem(String, Object...) - Constructor for exception org.intermine.web.struts.oauth2.ForseenProblem
Construct one of these objects.
forward() - Method in class org.intermine.web.struts.ForwardParameters
Construct the resulting ActionForward.
ForwardParameters - Class in org.intermine.web.struts
Utility wrapper class for programatically adding parameters to ActionForward paths.
ForwardParameters(String, boolean) - Constructor for class org.intermine.web.struts.ForwardParameters
Creates a new instance of ForwardParameters with a given path and redirect settings.
ForwardParameters(ActionForward) - Constructor for class org.intermine.web.struts.ForwardParameters
Creates a new instance of ForwardParameters.
FrictionlessDataPackage - Class in org.intermine.webservice.server.query.result
Exports Frictionless Data Package if the parameter exportDataPackage is true.
FrictionlessDataPackage() - Constructor for class org.intermine.webservice.server.query.result.FrictionlessDataPackage
 
FRIENDLY - org.intermine.webservice.server.ColumnHeaderStyle
 
friendlyMineManager - Variable in class org.intermine.api.InterMineAPI
 
FriendlyMineManager - Class in org.intermine.api.mines
Class to manage friendly mines
from - Variable in class org.intermine.sql.query.Query
 
FROM_DB - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
from_list() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
from_list() - Method in class org.intermine.sql.query.SqlParser
 
from_list(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
FROM_LIST - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
FROM_LIST - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
FromElement - Interface in org.intermine.objectstore.query
An element that can appear in the FROM clause of a query
full - Variable in class org.intermine.sql.precompute.BestQueryLogger
 
full - Variable in class org.intermine.task.AnalyseDbTask
 
FULL - org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity
Very verbose - with cells as objects with class names and stuff.
FullHandler - Class in org.intermine.xml.full
Extension of DefaultHandler to handle parsing full XML.
FullHandler() - Constructor for class org.intermine.xml.full.FullHandler
Create a new FullHandler object.
FullParser - Class in org.intermine.xml.full
Unmarshal XML Full format data into java business objects.
FullRenderer - Class in org.intermine.xml.full
Render an object in InterMine Full XML format
FullXmlConverter - Class in org.intermine.dataconversion
Loads InterMine XML into an items database.
FullXmlConverter(ItemWriter, Model) - Constructor for class org.intermine.dataconversion.FullXmlConverter
Constructor.
FullXmlConverterTask - Class in org.intermine.task
Load InterMine Items XML file(s) into a target items database.
FullXmlConverterTask() - Constructor for class org.intermine.task.FullXmlConverterTask
 
Function - Class in org.intermine.sql.query
A representation of a function in an SQL query.
Function<A,​B> - Interface in org.intermine.webservice.server.core
An interface for defining a thing that can take something and return something else.
Function(int) - Constructor for class org.intermine.sql.query.Function
Constructor for this Function object.

G

gcd(int, int) - Static method in class org.intermine.metadata.Util
Takes two integers, and returns the greatest common divisor, using euclid's algorithm.
GE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
GE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
generate() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Generate a string that contains the torque data for the given schema.
generate(WebserviceCodeGenInfo) - Method in interface org.intermine.api.query.codegen.WebserviceCodeGenerator
This method will generate web service source code from a path query or template query.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
This method will generate web service source code in Java from a path query or template query.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator
This method will generate code that can be run in a browser.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
This method will generate web service source code in Perl from a path query or template query.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
This method will generate code that will run using the python webservice client library.
generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
generate(AttributeDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates code for a single attribute.
generate(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Generate a string that describes the given ClassDescriptor.
generate(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generate the output for a ClassDescriptor.
generate(CollectionDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates code for a single collection.
generate(ReferenceDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates code for a single reference.
generate(Query, int, int, DatabaseSchema, Database, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a Query object into an SQL String.
generate(Query, DatabaseSchema, Database, Constraint, int, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a Query object into an SQL String.
generate24hrKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
Generate a day token
generateAddCollectionElement(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the addCollectionElement method.
generateApiKey(String) - Method in class org.intermine.dwr.AjaxServices
Generate a new API key for a given user.
generateApiKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
Generate a new API access key for this profile and return it.
generateCertificate(String, PublicKey) - Method in class org.intermine.web.security.KeySigner
Create a self-signed X.509 Certificate Should be eventually replaced with X509v3CertificateBuilder.
generateClassDescriptors(Reader, String) - Method in class org.intermine.metadata.InterMineModelParser
Read source model information in InterMine XML format and create a set of ClassDescriptors.
generateClassDescriptors(Reader, String) - Method in interface org.intermine.metadata.ModelParser
Read source information and construct a list of InterMine ClassDescriptors
generateClassName(String, String) - Static method in class org.intermine.metadata.TypeUtil
Generate the full class name, eg.
generateClassNames(String, Model) - Static method in class org.intermine.xml.full.ItemHelper
Generate a package qualified class name within the specified model from a space separated list of namespace qualified names
generateEquals(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generate a .equals() method for the given class.
generateFieldDescriptors(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generate all FieldDescriptors for a class/interface
generateGetElementType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getElementType method.
generateGetFieldType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getFieldType method.
generateGetFieldValue(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getFieldValue method.
generateGetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the getoBJECT method for producing NotXml.
generateGetSet(FieldDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
Write code for getters and setters for given field.
generateHashCode(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generate a .hashCode() method for the given class.
generateIndirectionTable(CollectionDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Generate an indirection table
generateJdbcType(String) - Static method in class org.intermine.objectstore.intermine.TorqueModelOutput
Convert java primitive and object names to those compatible with torque.
generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.api.LinkRedirectManager
 
generateListFromQuery(PathQuery, ListInput, Profile) - Method in class org.intermine.webservice.server.query.QueryListAppendService
 
generateListFromQuery(PathQuery, ListInput, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService
Generate a list from a pathquery.
generateListFromQuery(PathQuery, ListInput, Profile) - Method in class org.intermine.webservice.server.template.TemplateListAppendService
 
generateNewName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil
Generate a new name for a list.
generatePassword() - Static method in class org.intermine.web.task.LoadDefaultTemplatesTask
Generate a random 8-letter String of lower-case characters
generatePermaLink(FastPathObject, String, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper
Generate a perma-link to a report page for an InterMine object.
generatePermaPath(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper
Generate a link suitable for use as an external, permanent link, in that the link should work between rebuilds of the database.
generatePortalLink(FastPathObject, InterMineAPI, HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper
Generate a stable link to a report page for the given object, this will create a portal link with the correct class and a value from a non-null class key field of the object.
generatePortalPath(FastPathObject, InterMineAPI) - Static method in class org.intermine.web.logic.PortalHelper
Generate an external portal link (perma-link) for an InterMine object.
generateQueryForId(Integer, Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Generates a query to retrieve a single object from the database, by id.
generateRandomUniqueString() - Static method in class org.intermine.api.util.TextUtil
 
generateRandomUniqueString(int) - Static method in class org.intermine.api.util.TextUtil
 
generateReadOnlyAccessToken(Profile, String) - Method in class org.intermine.api.profile.ProfileManager
Return a permanent user access token, with ReadOnly permission.
generateReportLink(ResultElement, String) - Static method in class org.intermine.web.logic.PortalHelper
Generate a link to the object details page using the internal id.
generateReportPath(ResultCell) - Static method in class org.intermine.web.logic.PortalHelper
Get the path fragment (starting with "/") for the report page for an object in the mine.
generateSetFieldValue(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the setFieldValue method.
generateSetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generates the setoBJECT method for deserialising objects.
generateSingleUseKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
Generate a single use API key and store it in memory, before returning it.
generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Create temporary tables for the bag in the BagConstraints of the given Query, then call SqlGenerator.generate().
generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Create temporary tables for the bag in the BagConstraints of the given Query, then call SqlGenerator.generate().
generateSql(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Generate sql from a Query
generateSqlCompatibleName(String) - Static method in class org.intermine.sql.DatabaseUtil
Convert any sql keywords to valid names for tables/columns.
generateSqlForCount(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Generate SQL only for counting; no need to order by and no need to calculate LIMIT and OFFSET Create temporary tables for the bag in the BagConstraints of the given Query, then call directly SqlGenerator.generate() using as Query type the value QUERY_FOR_COUNTING
generateToString(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Generate a .toString() method for the given class .
GenerateUpdateTriggersTask - Class in org.intermine.task
 
GenerateUpdateTriggersTask() - Constructor for class org.intermine.task.GenerateUpdateTriggersTask
 
generationSqlString - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
get(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
get(int) - Method in class org.intermine.api.results.WebResults
get(int) - Method in class org.intermine.objectstore.query.Results
get(int) - Method in class org.intermine.util.IntToIntMap
Retrieves a mapping from the object
get(Integer) - Method in class org.intermine.util.IntToIntMap
Retrieves a mapping from the object.
get(Object) - Method in class org.intermine.util.AlwaysMap
get(Object) - Method in class org.intermine.util.IdentityMap
get(Object) - Method in class org.intermine.util.ReferenceMap
get(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory
Get a ReportObject for the given InterMineObject.
get(String) - Method in class org.intermine.web.security.KeyStorePublicKeySource
 
get(String) - Method in interface org.intermine.web.security.PublicKeySource
Get a specific key by name.
get(PathConstraint, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory
Get a display constraint.
get(Path, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory
Get a display constraint.
GET - org.intermine.webservice.server.core.WebServiceServlet.Method
GET
getAbbreviation(String) - Static method in class org.intermine.webservice.server.CodeTranslator
Returns corresponding abbreviation of translated operation.
getAcceptableFormats(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Get the list of formats that this request finds acceptable.
getAccepted() - Method in class org.intermine.api.bag.SharingInvite
 
getAccepted() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite
 
getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getAccessCounter() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the rank associated to the templates
getAccessCounter(Connection) - Method in class org.intermine.api.tracker.TemplateTracker
Return the number of executions for each public template
getAction() - Method in class org.intermine.api.search.TaggingEvent
 
getAction() - Method in class org.intermine.web.struts.WidgetForm
 
getAction() - Method in class org.intermine.webservice.server.jbrowse.Command
 
getActionMessage() - Method in exception org.intermine.web.struts.oauth2.ForseenProblem
Get a struts action message, rather than a simple string message.
getActionMessage(String, int, String, String) - Method in class org.intermine.web.logic.bag.BagConverter
Get the ActionMessage to display in the webapp
getActionType() - Method in class org.intermine.web.struts.TemplateSettingsForm
 
getAdder() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the adder Method.
getAdder(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the adder for the field name
getAddIssues() - Method in class org.intermine.webservice.server.lists.ListCreationInput
 
getAdditionalBeanInfo() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getAdditionalBeanInfo() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getAdditionalConverters(String) - Method in class org.intermine.api.bag.BagQueryConfig
Return a Map from a converter Class name (such as org.intermine.bio.web.logic.OrthologueConverter) to set of additional converters.
getAdditionalFields() - Method in class org.intermine.web.search.KeywordSearchResult
additional display field expressions
getAdditionalParameter(HttpServletRequest, String) - Static method in class org.intermine.web.logic.PortalHelper
Searches a request for additional parameters that might match an additional converter.
getAdditionalProperties() - Method in class org.intermine.web.registry.model.Instance
 
getAdditionalProperties() - Method in class org.intermine.web.registry.model.RegistryResponse
 
getAlgorithm() - Method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
 
getAlias() - Method in class org.intermine.sql.query.AbstractTable
Returns the alias for this AbstractTable object.
getAlias() - Method in class org.intermine.sql.query.SelectValue
Gets the alias from this object.
getAliasedColumnHeaders(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Get the view for a path query reformatted to obey the labels given in webconfig.
getAliases() - Method in class org.intermine.objectstore.query.Query
Returns the map of QuerySelectables and FromElements to String aliases
getAll() - Method in class org.intermine.web.security.KeyStorePublicKeySource
 
getAll() - Method in interface org.intermine.web.security.PublicKeySource
 
getAllAttributeDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets all AttributeDescriptors for this class and its super classes - i.e.
getAllBags() - Method in class org.intermine.api.profile.Profile
Get all bags associated with this profile, both valid and invalid.
getAllClassDescriptors() - Method in class org.intermine.xml.full.Item
Return the ClassDescriptors of the class of this Item (as given by className) and all the implementations.
getAllCollectionDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets all CollectionDescriptors for this class - i.e.
getAllFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets the FieldDescriptors for this class and all superclasses and interfaces.
getAllNullAttributes() - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the attributes that are always null or empty.
getAllNullReferencesAndCollections() - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of reference and collection names that are always null or empty.
getAllReferenceDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets all ReferenceDescriptors for this class - i.e.
getAllReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager
Get all displayers for the given type regardless of placement.
getAllRows() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return all the resultElementRows of the table as a List of Lists.
getAllSelected() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getAllSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
If a whole column is selected, return its index, otherwise return -1.
getAllSubs(ClassDescriptor) - Method in class org.intermine.metadata.Model
Get the ClassDescriptors for the all subclasses of a class
getAllSuperclassNames() - Method in class org.intermine.metadata.ClassDescriptor
Get the full inheritance list for this class.
getAllSuperDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Get the full inheritance list for this class.
getAllSuperUsers() - Method in class org.intermine.api.profile.ProfileManager
 
getAlteredViews(PathQuery) - Static method in class org.intermine.webservice.server.query.result.FrictionlessDataPackage
Get the views for the transformed query.
getAlteredViews(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Get the views for the transformed query.
getAnalysedTotal() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the number of items in the sample that had an attribute value.
getAnnotatedCountsInPopulation() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
For each attribute give a count of items in the whole population that have that attribute assigned to them, M.
getAnnotatedCountsInPopulation() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getAnnotatedCountsInSample() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
For each attribute give a count of items in the sample that have that attribute assigned to them, k.
getAnnotatedCountsInSample() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getAPI() - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getApiKey() - Method in class org.intermine.api.profile.Profile
 
getApiKey() - Method in class org.intermine.api.userprofile.UserProfile
 
getApiVersion() - Method in class org.intermine.web.registry.model.Instance
 
getAppendConfig() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
 
getApproximateType() - Method in class org.intermine.objectstore.query.QueryCast
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in interface org.intermine.objectstore.query.QueryEvaluable
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryExpression
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryField
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryForeignKey
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryFunction
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.QueryValue
Returns an integer representing the approximate type of this QueryEvaluable, in the case where an accurate type cannot be ascertained.
getApproximateType() - Method in class org.intermine.objectstore.query.UnknownTypeValue
Returns the approximate type of the argument.
getArg1() - Method in class org.intermine.objectstore.query.ClassConstraint
Returns the QueryClass argument 1
getArg1() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the left argument of the expression.
getArg1() - Method in class org.intermine.objectstore.query.SimpleConstraint
Returns the left argument of the constraint.
getArg2() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the right argument, or the position argument of the substring.
getArg2() - Method in class org.intermine.objectstore.query.SimpleConstraint
Returns the right argument of the constraint.
getArg2Object() - Method in class org.intermine.objectstore.query.ClassConstraint
Returns the Object argument 2
getArg2QueryClass() - Method in class org.intermine.objectstore.query.ClassConstraint
Returns the QueryClass argument 2
getArg3() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the length argument of a substring expression.
getAspect(String) - Static method in class org.intermine.api.tag.AspectTagUtil
Extracts aspect from tag name.
getAspectDisplayers() - Method in class org.intermine.web.logic.config.Type
 
getAspects() - Method in class org.intermine.web.logic.config.Displayer
Get the aspects of this displayer
getAspects(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the Map of aspects.
getAspectSources() - Method in class org.intermine.web.logic.aspects.Aspect
Get the AspectSources.
getAspectTemplates(String) - Method in class org.intermine.api.template.TemplateManager
Get public templates for a particular aspect.
getAspectTemplates(String, Integer) - Method in class org.intermine.api.template.TemplateManager
Get public templates for a particular aspect.
getAttribute(String) - Static method in class org.intermine.web.context.InterMineContext
Get the value of a stored attribute.
getAttribute(String) - Method in class org.intermine.xml.full.Item
Get a named attribute.
GetAttributeAsFileAction - Class in org.intermine.web.struts
Provide an attribute value as a file
GetAttributeAsFileAction() - Constructor for class org.intermine.web.struts.GetAttributeAsFileAction
 
getAttributeDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Gets an AttributeDescriptor for a field of the given name.
getAttributeDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor
Gets an AttributeDescriptor for a field of the given name.
getAttributeDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets AttributeDescriptors for this class - i.e.
getAttributeDescriptors() - Method in class org.intermine.web.logic.results.ReportObject
Get attribute descriptors.
getAttributeIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask
Add indexes for all fields to the relevant tables for a given ClassDescriptor.
getAttributeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of attributeOp
getAttributeOps() - Method in class org.intermine.web.struts.TemplateForm
Get the attribute ops
getAttributeOps(String) - Method in class org.intermine.web.struts.TemplateForm
Get an attribute op
getAttributeOptions() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of attributeValue
getAttributePrefixes() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getAttributes() - Method in class org.intermine.api.searchengine.ClassAttributes
attributes associated with the class
getAttributes() - Method in class org.intermine.model.fulldata.Item
 
getAttributes() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields
Returns the Set of attributes
getAttributes() - Method in class org.intermine.web.logic.results.ReportObject
Get the attribute fields and values for this object
getAttributes() - Method in class org.intermine.xml.full.Item
Get all the attributes.
getAttributesFromBag(InterMineBag, ObjectStore, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper
Used by esyn tool
getAttributesFromBag(InterMineBag, ObjectStore, String, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper
 
getAttributeValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of attributeValue
getAttributeValues() - Method in class org.intermine.web.struts.TemplateForm
Get the attribute values
getAttributeValues(String) - Method in class org.intermine.web.struts.TemplateForm
Get an attribute value
getAuthenticatedUser() - Method in class org.intermine.webservice.server.WebService
Get a profile that is a true authenticated user that exists in the database.
getAutoCompleter() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the autocompleter for this path if one is available.
getAutoCompleter(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the AutoCompleter stored on the ServletContext.
getBag() - Method in class org.intermine.api.bag.SharingInvite
 
getBag() - Method in class org.intermine.objectstore.query.BagConstraint
Get the bag Collection.
getBag() - Method in interface org.intermine.objectstore.query.ConstraintWithBag
Returns the bag that the constraint is using.
getBag() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
Returns the bag that this object was constructed with.
getBag() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns the bag of objects.
getBag() - Method in class org.intermine.pathquery.PathConstraintBag
Returns the bag name that the constraint is constraining to.
getBag() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
the bag that this widget is using
getBag(String) - Method in class org.intermine.web.struts.TemplateForm
Get the bag name selected.
getBag(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch a global or user or shared bag by name.
getBagConverter(InterMineAPI, WebConfig, String) - Static method in class org.intermine.web.logic.PortalHelper
Returns a BagConverter for the given parameters.
getBagCreationQuery() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return a Query that produces a Results object of the selected objects.
getBagDisplayers() - Method in class org.intermine.web.logic.config.Type
Get the List of bag Displayers
getBagId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getBagId() - Method in class org.intermine.objectstore.query.ObjectStoreBag
Returns the identifier of the bag.
getBagManager() - Method in interface org.intermine.api.API
 
getBagManager() - Method in class org.intermine.api.InterMineAPI
 
getBagManager() - Static method in class org.intermine.api.query.PathQueryAPI
Returns a BagManager.
getBagName() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getBagName() - Method in class org.intermine.web.struts.FindInListForm
 
getBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Get the value of bagName
getBagName() - Method in class org.intermine.web.struts.WidgetForm
 
getBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
Get the name of the bag
getBagNames() - Method in class org.intermine.pathquery.PathQuery
Returns all bag names used in constraints on this query.
getBagOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of bagOp
getBagOp(String) - Method in class org.intermine.web.struts.TemplateForm
Get the bag operation selected.
getBagOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the valid constraint ops when constraining on a bag.
getBagQueries() - Method in class org.intermine.api.bag.BagQueryHandler
Return the bag queries from the XML file.
getBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig
Return a list of BagQuerys to run for a given type
getBagQueryConfig() - Method in interface org.intermine.api.API
 
getBagQueryConfig() - Method in class org.intermine.api.bag.BagQueryHandler
Return the BagQueryConfig created from the XML.
getBagQueryConfig() - Method in class org.intermine.api.InterMineAPI
 
getBagQueryConfig() - Static method in class org.intermine.api.query.PathQueryAPI
Returns a BagQueryConfig configured in WEB-INF/bag-queries.xml.
getBagQueryResult() - Method in class org.intermine.api.bag.BagQueryUpgrade
 
getBagQueryRunner() - Method in interface org.intermine.api.API
 
getBagQueryRunner() - Method in class org.intermine.api.InterMineAPI
The bag-query runner is the object that performs look-up queries used when constructing bags from lists of identifiers, and in path-queries when LOOKUP constraints are used.
getBags() - Method in class org.intermine.api.bag.operations.BagOperation
 
getBags() - Method in class org.intermine.api.profile.BagSet
 
getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Returns the List of bags.
getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
Returns the Collection of bags.
getBags() - Method in class org.intermine.web.logic.query.DisplayConstraint
Get a list of public and user bag names available and currentfor this path.
getBags(Profile) - Method in class org.intermine.api.bag.BagManager
Fetch all global bags, user bags and shared bags combined in the same map.
getBagsAndClasses(Set<ClassDescriptor>, Set<InterMineBag>, Profile, BagManager, Model, String[]) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
Given an array of bag names, populate both a set of bags, and a set of class-descriptors with the objects these names refer to.
getBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags of the specified type or a subclass of the specified type.
getBagsOfType(Profile, String, boolean) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags of the specified type or a subclass of the specified type.
getBagTableNames() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getBagType() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the bag type that the constraint can be constrained to.
getBagType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getBagType() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Get the bag type - hidden form value.
getBagType() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getBagType() - Method in class org.intermine.web.struts.WidgetForm
 
getBagValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of bagValue
getBaseEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns the base equivalent object fetcher.
getBaseLink() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getBaseUrl() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getBaseUrl(HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper
Get the base url for this web-app.
getBaseURL() - Method in class org.intermine.web.util.AttributeLinkURL
 
getBaseURL() - Method in class org.intermine.web.util.URLGenerator
 
getBasicInstanceInfo(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the instance to use
getBatch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets a batch by whatever means - maybe batches, maybe the ObjectStore.
getBatchFromCache(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the given batch, if it is already in the batch cache.
getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.Results
Gets the batch for a particular row
getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the batch for a particular row
getBatchSize() - Method in class org.intermine.objectstore.query.Results
Gets the batch size being used.
getBatchSize() - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the batch size being used.
getBeanDescriptor() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getBeanDescriptor() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getBest() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the best Candidate found so far.
getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the ExpainResult for the best Query found so far.
getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryFallback
Gets the ExpainResult for the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQuery
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryFallback
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryLogger
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryStorer
Gets the best Query found so far
getBestQuery() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Gets the best Query found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQuery
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer
Gets the best query String found so far.
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryFallback
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryLogger
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryStorer
Gets the best query String found so far
getBestQueryString() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
Gets the best query String found so far
getBgcolor() - Method in class org.intermine.api.mines.LocalMine
 
getBgcolor() - Method in interface org.intermine.api.mines.Mine
 
getBgcolor() - Method in class org.intermine.api.mines.RemoteMine
 
getBinsParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
 
getBottomUpLevelTraversal() - Method in class org.intermine.metadata.Model
Return the classes in the model in level order from deepest to shallowest, the order of nodes at any given level is undefined.
getBuffer() - Method in class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
Returns the byte buffer without copying it.
getBuildMode() - Method in class org.intermine.api.tracker.track.ListTrack
Return the way the list is built
getButton() - Method in class org.intermine.web.logic.query.MetadataNode
Gets the value of button
getByToken(InterMineAPI, String) - Static method in class org.intermine.api.bag.SharingInvite
 
getCallback() - Method in class org.intermine.webservice.server.WebService
Get the value of the callback parameter.
getCanCreateConstraint() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if there is any possibility of creating a constraint on this path.
getCandidateLoops() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the set of paths that could feasibly be loop constrained onto the constraint's path, given the query's outer join situation.
getCandidateLoops(String) - Method in class org.intermine.pathquery.PathQuery
Returns the set of paths that could feasibly be loop constrained onto the given path, given the current outer join situation.
getCaseSensitive() - Method in interface org.intermine.api.idresolution.JobInput
 
getCaseSensitive() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getCaseSensitive() - Method in class org.intermine.web.struts.BuildBagForm
 
getCategories(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Gets the aspect categories from the servlet context.
getCategory() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns the category of this PrecomputedTable
getCategoryPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getCauseElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getCauseElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getChildren() - Method in class org.intermine.pathquery.LogicExpression.Operator
Get an unmodifiable copy of the node's children.
getChildren(ClassDescriptor) - Static method in class org.intermine.web.struts.InitialiserPlugin
Get the names of the type of this ClassDescriptor and all its descendants
getChildren(ClassDescriptor, Set<String>) - Static method in class org.intermine.web.struts.InitialiserPlugin
Add the names of the descendents of a ClassDescriptor to a Set
getClass(String) - Static method in class org.intermine.metadata.TypeUtil
Instantiate a class by unqualified name The name should be "Date" or that of a primitive container class such as "Integer"
getClass(String, Model) - Static method in class org.intermine.metadata.TypeUtil
Instantiate a class by unqualified name The name should be "InterMineObject" or the name of class in the model provided
getClassBoost() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getClassConfig() - Method in class org.intermine.web.logic.config.FieldConfig
 
getClassCount(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get the number of instances of a particular class in the ObjectStore.
getClassDescriptor() - Method in class org.intermine.metadata.FieldDescriptor
Get the ClassDescriptor for this field's class.
getClassDescriptor() - Method in class org.intermine.metadata.PrimaryKey
Return the ClassDescriptor for class this key is defined for
getClassDescriptor() - Method in class org.intermine.web.logic.results.ReportObject
Get the class descriptor for this object
getClassDescriptorByName(String) - Method in class org.intermine.metadata.Model
Get a ClassDescriptor by name, null if no ClassDescriptor of given name in Model.
getClassDescriptorByName(String) - Method in class org.intermine.xml.full.Item
Throw a RuntimeException if any of the named class isn't in the Model set by setModel().
getClassDescriptors() - Method in class org.intermine.api.profile.InterMineBag
Return the class descriptors for the type of this bag.
getClassDescriptors() - Method in class org.intermine.metadata.Model
Get all ClassDescriptors in this model.
getClassDescriptorsForClass(Class<?>) - Method in class org.intermine.metadata.Model
Takes a Class, and generates a Set of all ClassDescriptors that are the Class or any of its parents.
getClasses() - Method in class org.intermine.api.bag.operations.BagOperation
 
getClasses() - Method in class org.intermine.metadata.Model.ModelAST
 
getClassesForBags(Collection<InterMineBag>) - Method in class org.intermine.webservice.server.lists.AbstractListService
Get the classes represented by a collection of bags.
getClassFieldConfigs(ClassDescriptor) - Method in class org.intermine.web.logic.results.InlineResultsTable
Find the FieldConfig objects for the the given ClassDescriptor.
getClassFieldConfigs(WebConfig, ClassDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
Find the FieldConfig objects for the the given ClassDescriptor (or generate them).
getClassFromString(String) - Static method in class org.intermine.metadata.Util
Returns the class (not primitive) associated with the given String type.
getClassIndex(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
 
getClassIndexes(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
 
getClassKeys() - Method in interface org.intermine.api.API
 
getClassKeys() - Method in class org.intermine.api.bag.operations.BagOperation
 
getClassKeys() - Method in class org.intermine.api.InterMineAPI
The class keys are the list of fields used to identify objects in the data base, so for Employee it would include "name", and for Gene it would include "symbol".
getClassKeys() - Static method in class org.intermine.api.query.PathQueryAPI
Returns classkeys configured in class_keys.properties.
getClassKeys() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getClassKeys() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
Get the classKeys
getClassName() - Method in class org.intermine.api.bag.AdditionalConverter
 
getClassName() - Method in class org.intermine.api.searchengine.ClassAttributes
name of the class
getClassName() - Method in class org.intermine.api.searchengine.ObjectValueContainer
className
getClassName() - Method in class org.intermine.model.fulldata.Item
 
getClassName() - Method in class org.intermine.web.logic.config.TableExportConfig
Get the class name of the exporter eg.
getClassName() - Method in class org.intermine.web.logic.config.Type
Get the class name
getClassName() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
 
getClassName() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getClassName() - Method in class org.intermine.web.struts.QueryClassSelectForm
Get the class name
getClassName() - Method in class org.intermine.web.uri.InterMineLUI
Get the className
getClassName() - Method in class org.intermine.xml.full.Item
Get the class name of this item.
getClassName(Object, Model) - Static method in class org.intermine.xml.XmlHelper
Get the class name if object represents a material class in model.
getClassNames() - Method in class org.intermine.metadata.Model
Get a Set of fully qualified class names in this model (i.e.
getClassNames(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Given a String, perform a one of a set of expansions and return a Set of unqualified class names.
getClazz() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
Returns the class.
getClientId() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getClientId() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getClientId() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getClientInstance(ObjectStore) - Static method in class org.intermine.api.searchengine.solr.SolrClientManager
Static method to get the solr client instance
getClientSecret() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getClientSecret() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getClientSecret() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getClob() - Method in class org.intermine.objectstore.query.ClobAccess
Return the Clob that this object is accessing.
getClob() - Method in class org.intermine.objectstore.query.PendingClob
Return the Clob that this object is accessing.
getClobId() - Method in class org.intermine.objectstore.query.Clob
Returns the identifier of the Clob.
getCode() - Method in class org.intermine.web.logic.query.DisplayConstraint
If editing an existing constraint get the code for this constraint in the query, return null if creating a new constraint.
getCode() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get the code associated with this constraint in the query.
getCode() - Method in class org.intermine.web.logic.template.ConstraintInput
 
getCode() - Method in class org.intermine.webservice.server.output.Output
Gets the error code
getCode(String) - Static method in class org.intermine.webservice.server.CodeTranslator
Returns corresponding code of translated operation.
getCollection() - Method in class org.intermine.web.logic.results.DisplayCollection
 
getCollection() - Method in class org.intermine.web.logic.results.ReportInList
 
getCollection(String) - Method in class org.intermine.xml.full.Item
Get a named collection.
getCollectionDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Gets a CollectionDescriptor for a collection of the given name.
getCollectionDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor
Gets a CollectionDescriptor for a field of the given name.
getCollectionDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets CollectionDescriptors for this class.
getCollections() - Method in class org.intermine.model.fulldata.Item
 
getCollections() - Method in class org.intermine.web.logic.results.ReportObject
Get the collection fields and values for this object
getCollections() - Method in class org.intermine.xml.full.Item
Get all the collections.
getCollectionsForClass(Class<?>) - Method in class org.intermine.metadata.Model
Takes a Class, and generates a Map of all the collections that are in the Class or any of its parents.
getColNames() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the column names.
getColumnAliases(Query) - Static method in class org.intermine.objectstore.query.QueryHelper
Returns a list of aliases, where each alias corresponds to each element of the SELECT list of the Query object.
getColumnClasses(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper
 
getColumnFieldClasses() - Method in class org.intermine.task.DelimitedFileConfiguration
Return a List of Class objects corresponding to the fields returned by getColumnFieldDescriptors().
getColumnFieldDescriptors() - Method in class org.intermine.task.DelimitedFileConfiguration
Return a List of the configured AttributeDescriptors.
getColumnHeaders() - Method in class org.intermine.pathquery.PathQuery
Returns the paths descriptions for the view.
getColumnHeaderStyle() - Method in class org.intermine.webservice.server.WebService
Get an enum which represents the column header style (path, friendly, or none)
getColumnId() - Method in class org.intermine.api.results.Column
 
getColumnIdentifier() - Method in class org.intermine.api.results.Column
Used in the view to match this element
getColumnName(FieldDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Creates a column name for a field descriptor
getColumnNames() - Method in class org.intermine.api.results.WebResults
Return the names of the columns of the results.
getColumnNames() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the column names
getColumnNames() - Method in class org.intermine.web.tags.table.TableTag
 
getColumnPaths(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper
Return a List containing the Path objects from the Columns of this PagedTable.
getColumns() - Method in class org.intermine.api.results.ExportResultsIterator
Allows test to access column info.
getColumns() - Method in class org.intermine.api.results.WebResults
Returns the columns for these results.
getColumns() - Method in interface org.intermine.api.results.WebTable
Returns the Column objects for this table.
getColumns() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the list of column configurations
getColumns() - Method in class org.intermine.web.logic.widget.TableWidget
Get the columns
getColumns() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Get the columnNames
getColumns() - Method in class org.intermine.webservice.server.core.SubTable
 
getColumnsPath() - Method in class org.intermine.api.results.WebResults
 
getColumnsPath() - Method in interface org.intermine.api.results.WebTable
 
getColumnsSize() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getColumnSummary(String, String) - Static method in class org.intermine.dwr.AjaxServices
Get the summary for the given column
getColumnTitle() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getColumnTypes(Query) - Static method in class org.intermine.objectstore.query.QueryHelper
Returns a list of Class objects, where each object corresponds to the type of each element of the SELECT list of the Query object.
getColumnTypeString(Class<?>) - Method in class org.intermine.sql.Database
Return the SQL type used to store objects of the given Class.
getCommand(String, Map<String, String>) - Static method in class org.intermine.webservice.server.jbrowse.Commands
return null if not a suitable command.
getComment() - Method in class org.intermine.template.TemplateQuery
Get the private comment for this template.
getComment() - Method in class org.intermine.web.struts.TemplateSettingsForm
Return the comment
getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Get the JSON prefix common to all constraints.
getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.template.TemplateQuery
 
getCompatibleCurrentBags(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags current of the specified type or a subclass or any superclass of the specified type.
getComplete() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the estimated amount of time taken to produce the entire set of results.
getComplete() - Method in class org.intermine.sql.query.ExplainResult
Returns the number of page requests before the query is completed, estimated by the database for this query.
getComponentsForQuery(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in interface org.intermine.objectstore.ObjectStore
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Returns a Set of independent components that affect the results of the given Query.
getComponentsForQuery(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Returns a Set of independent components that affect the results of the given Query.
getConfig(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
Return the TableExportConfig for the given id.
getConfigClassDescriptor() - Method in class org.intermine.task.DelimitedFileConfiguration
Return the ClassDescriptor of the class to modify.
getConfigId() - Method in class org.intermine.web.logic.widget.Widget
Get the ID of the corresponding WidgetConfig
getConfiguredTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the unqualified class names for which this displayer should be displayed.
getConnectField() - Method in class org.intermine.api.bag.BagQueryConfig
Return the connecting field.
getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns a Connection.
getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns a Connection.
getConnection() - Method in class org.intermine.sql.Database
Gets a Connection to this Database
getConstrainField() - Method in class org.intermine.api.bag.BagQueryConfig
Return the constrain field.
getConstraint() - Method in class org.intermine.objectstore.query.Query
Get the current constraint on this Query
getConstraint() - Method in interface org.intermine.objectstore.query.Queryable
Returns the additional constraint.
getConstraint() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the additional constraint.
getConstraint() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the additional constraint.
getConstraint() - Method in class org.intermine.sql.query.NotConstraint
Returns the contained constraint.
getConstraint() - Method in class org.intermine.template.TemplateValue
Returns the constraint that this object was constructed with.
getConstraintCodes() - Method in class org.intermine.pathquery.PathQuery
Return the constraint codes used in the query, some constraint types (subclasses) don't get assigned a code, these are not included.
getConstraintDescription(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns the description attached to the given constraint.
getConstraintDescriptions() - Method in class org.intermine.template.TemplateQuery
Returns the constraint descriptions for this query.
getConstraintForCode(String) - Method in class org.intermine.pathquery.PathQuery
Returns the PathConstraint associated with a given code.
getConstraintGroups() - Method in class org.intermine.pathquery.PathQuery
Returns the outer join constraint codes groups map for this query, if the query verifies correctly.
getConstraintLogic() - Static method in class org.intermine.dwr.AjaxServices
Get the grouped constraint logic
getConstraintLogic() - Method in class org.intermine.pathquery.PathQuery
Returns the current constraint logic.
getConstraintLogicForEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Return the constraint logic modified to contain only the blocks with editable constraints
getConstraintLogicForGroup(String) - Method in class org.intermine.pathquery.PathQuery
Returns the constraint logic for the given outer join group, if the query verifies correctly.
getConstraintOp() - Method in class org.intermine.web.logic.template.ConstraintInput
Returns constraint operation
getConstraintOp(String) - Static method in class org.intermine.metadata.ConstraintOp
Get ConstraintOp for given operation code.
getConstraintPath() - Method in class org.intermine.api.bag.AdditionalConverter
 
getConstraints() - Method in class org.intermine.objectstore.query.ConstraintSet
Returns the Set of constraints.
getConstraints() - Method in class org.intermine.pathquery.PathQuery
Returns a Map of all the constraints in this query, from PathConstraint to the constraint code used in the constraint logic.
getConstraints() - Method in class org.intermine.sql.query.ConstraintSet
Returns the Set of constraints forming this object.
getConstraints() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Return summary representations of constraints on this path or an empty list if none exist.
getConstraints() - Method in class org.intermine.web.logic.template.TemplateResultInput
Returns constraints.
getConstraintsForPath(String) - Method in class org.intermine.pathquery.PathQuery
Returns a list of PathConstraints applied to a given path or an empty list.
getConstraintSwitchOffAbility() - Method in class org.intermine.template.TemplateQuery
Returns the constraint SwitchOffAbility for this query.
getContainsOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the CONTAINS options are same as the WITHIN options with the left and right operators swapped.
getContent() - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
Get the content of the widget.
getContent(String, boolean, String, String) - Method in class org.intermine.dwr.AjaxServices
 
getContents() - Method in class org.intermine.api.profile.InterMineBag
Returns a List of BagValue (key field value and extra value) of the objects contained by this bag.
getContents() - Method in class org.intermine.api.profile.StorableBag
Returns a List of BagValue (key field value and extra value) of the objects contained by this bag.
getContentsAsIds() - Method in class org.intermine.api.profile.InterMineBag
Returns a List which contains the contents of this bag as Integer IDs.
getContentsOrderByExtraValue() - Method in class org.intermine.api.profile.StorableBag
 
getContentType() - Method in enum org.intermine.webservice.server.Format
 
getConversionMapQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter
Get conversion query for the types provided, edited so that the first type is constrained to be in the bag.
getConversionQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter
Get conversion query for the types provided, edited so that the first type is constrained to be in the bag and the first type is removed from the view list so that the query only returns the converted type.
getConversionTemplates() - Method in class org.intermine.api.bag.BagQueryRunner
Fetch conversion template queries from the template manager.
getConversionTemplates() - Method in class org.intermine.api.template.TemplateManager
Return template queries used for converting between types in bag upload and lookup queries, these are Superuser templates that have been tagged with TagNames.IM_CONVERTER.
getConversionTemplates(List<ApiTemplate>, Class) - Static method in class org.intermine.api.bag.TypeConverter
Return a Map from typeB to a TemplateQuery that will convert from typeA to typeB.
getConvertCountForBag(String, String) - Static method in class org.intermine.dwr.AjaxServices
For a given bag name and a type different from the bag type, give the number of converted objects
getConvertedObjectIds(Profile, String, List<Integer>, String) - Method in class org.intermine.web.logic.bag.BagConverter
 
getConvertedObjectMap(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object, ObjectStore) - Static method in class org.intermine.api.bag.TypeConverter
Converts a List of objects from one type to another type using a TemplateQuery, returns a map from an original object to the converted object(s).
getConvertedObjects(HttpSession, List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, InterMineBag) - Static method in class org.intermine.web.logic.bag.BagConversionHelper
Converts a List of objects from one type to another type using a TemplateQuery, returns the converted objects.
getConvertedValue(Class<?>) - Method in class org.intermine.objectstore.query.UnknownTypeValue
Returns the value, converted (if possible) into the object type given by the input class.
getCorrection() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
 
getCorrection() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getCount() - Method in class org.intermine.api.profile.TagHandler
Return a count of the number of tags read.
getCount() - Method in class org.intermine.api.tracker.track.ListTrack
Return the number of items contained into the list
getCount() - Method in class org.intermine.web.logic.results.ReportInList
 
getCount() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
Return the count set with setCount().
getCountItemsWithLengthNotNull() - Method in class org.intermine.api.profile.InterMineBag
Return the number of items contained in the bag with length not null If the type bag is not a subclass of SequenceFeature, return 0
getCounts() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the count of each attribute value found in the sample.
getCounts(Profile, InterMineBag) - Method in class org.intermine.web.logic.bag.BagConverter
Method to return list of values and the counts of converted objects for that object used for display on list analysis page.
getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite
 
getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getCreatedAt() - Method in class org.intermine.web.registry.model.Instance
 
getCurrentBags(Profile) - Method in class org.intermine.api.bag.BagManager
Get the bags this user has access to, as long as they are current.
getCurrentBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
Fetch the current user or global or shared bags that contain the given id.
getCurrentBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch global and user bags current of the specified type or a subclass of the specified type.
getCurrentFile() - Method in class org.intermine.dataconversion.FileConverter
Return the File that is currently being converted.
getCurrentPage() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getCurrentSavedBags() - Method in class org.intermine.api.profile.Profile
Get the value of savedBags current
getCurrentSelectedIdStrings() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return selected object ids of the current page as a String[], needed for jsp multibox.
getCurrentSelectedIdStringsList() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return selected object ids of the current page as a List.
getCurrentUserBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch user bags current of the specified type or a subclass of the specified type.
getCustomConverterCounts(String, String) - Static method in class org.intermine.dwr.AjaxServices
For a list and a converter, return types and related counts
getDatabase() - Method in class org.intermine.dataconversion.DBConverter
Get the Database that was passed to the constructor.
getDatabase() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the Database used by this ObjectStore
getDatabase(String) - Static method in class org.intermine.sql.DatabaseFactory
Returns a connection to the named database
getDataSource() - Method in class org.intermine.sql.Database
Gets the DataSource object for this Database
getDataTracker() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Returns the data tracker being used.
getDateCreated() - Method in class org.intermine.api.profile.InterMineBag
Return the creation date that was passed to the constructor.
getDateCreated() - Method in class org.intermine.api.profile.InvalidBag
 
getDateCreated() - Method in class org.intermine.api.profile.SavedQuery
Get the date on which the query was created.
getDateCreated() - Method in class org.intermine.api.profile.StorableBag
Get the date that this bag was created at.
getDateCreated() - Method in class org.intermine.api.userprofile.PermanentToken
 
getDateCreated() - Method in class org.intermine.api.userprofile.SavedBag
 
getDayToken() - Method in class org.intermine.api.profile.Profile
Get a token with at least an hour of validity, and up to 24 hours.
getDayToken() - Method in class org.intermine.api.util.AnonProfile
 
getDb() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getDbDescription() - Method in class org.intermine.objectstore.query.ClobAccess
Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.
getDbDescription() - Method in class org.intermine.objectstore.query.PendingClob
Returns a String that describes this object sufficiently for it to be recreated given an ObjectStore.
getDefaultClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the QueryClass that represents the collection in this object.
getDefaultClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the QueryClass that represents the collection in this object.
getDefaultEventIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getDefaultEventIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getDefaultFileName() - Method in class org.intermine.webservice.server.query.CodeService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.SchemaListService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.SummaryService
 
getDefaultFileName() - Method in class org.intermine.webservice.server.WebService
 
getDefaultFilterValue(WidgetConfig, InterMineBag, String) - Method in class org.intermine.webservice.server.widget.WidgetService
Get the default filter value for a widget.
getDefaultFormat() - Method in class org.intermine.webservice.server.core.JSONService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.lists.AvailableListsService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.lists.JaccardIndexService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.model.ModelService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.CodeService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryToListService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.TableRowService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.template.SystemTemplatesService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.user.DeregistrationService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.VersionService
 
getDefaultFormat() - Method in class org.intermine.webservice.server.WebService
 
getDefaultOperator(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the default operator to apply to new constraints.
getDefaultOutput(PrintWriter, OutputStream) - Method in class org.intermine.webservice.server.WebService
Make the default output for this service.
getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.webservice.server.WebService
Make the default output for this service.
getDefaultPermission(Profile) - Static method in class org.intermine.api.profile.ProfileManager
Wrap a profile in the default permission level.
getDefaultPropertyIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getDefaultPropertyIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns default style class.
getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag
Returns default style class.
getDefaultValue() - Method in class org.intermine.api.mines.LocalMine
 
getDefaultValue() - Method in interface org.intermine.api.mines.Mine
get first default value.
getDefaultValue() - Method in class org.intermine.api.mines.RemoteMine
 
getDefaultValues() - Method in class org.intermine.api.mines.LocalMine
 
getDefaultValues() - Method in interface org.intermine.api.mines.Mine
 
getDefaultValues() - Method in class org.intermine.api.mines.RemoteMine
 
getDefaultViewForClass(String, Model, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Return a list of string paths that are defined as WebConfig to be shown in results.
getDefaultViewForClass(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Return a list of string paths that are defined as WebConfig to be shown in results.
getDeletedClasses() - Method in class org.intermine.api.profile.ModelUpdate
Return a set containing all the deleted classes
getDescr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getDescription() - Method in class org.intermine.api.mines.LocalMine
 
getDescription() - Method in interface org.intermine.api.mines.Mine
 
getDescription() - Method in class org.intermine.api.mines.RemoteMine
 
getDescription() - Method in class org.intermine.api.profile.InterMineBag
Return the description of this bag.
getDescription() - Method in class org.intermine.api.profile.InvalidBag
 
getDescription() - Method in class org.intermine.api.profile.StorableBag
 
getDescription() - Method in interface org.intermine.api.search.WebSearchable
Return the description of this object.
getDescription() - Method in class org.intermine.api.userprofile.SavedBag
 
getDescription() - Method in class org.intermine.pathquery.PathQuery
Gets the description for this PathQuery.
getDescription() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the label associated with a constraint if editing a template query constraint.
getDescription() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get the description for a constraint.
getDescription() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getDescription() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Get the description
getDescription() - Method in class org.intermine.web.registry.model.Instance
 
getDescription() - Method in class org.intermine.web.struts.TemplateSettingsForm
Return the description.
getDescription() - Method in class org.intermine.webservice.server.lists.ListInput
 
getDescription(int) - Static method in class org.intermine.webservice.server.StatusDictionary
 
getDescription(String) - Method in class org.intermine.pathquery.PathQuery
Returns the description for a given path, or null if no description is registered.
getDescriptions() - Method in class org.intermine.pathquery.PathQuery
Returns an unmodifiable Map which is a copy of the current set of path descriptions of this query at the time of execution of this method.
getDescriptiveString() - Method in class org.intermine.pathquery.PathConstraintLoop
Returns a descriptive string for this constraint, mainly useful for checking uniqueness.
getDescriptor() - Method in class org.intermine.web.logic.results.DisplayCollection
Get ReferenceDescriptor for this reference.
getDescriptor() - Method in class org.intermine.web.logic.results.DisplayReference
Get ReferenceDescriptor for this reference.
getDescriptor() - Method in class org.intermine.web.logic.results.InlineList
 
getDescriptors(Model) - Static method in class org.intermine.dataloader.DataLoaderHelper
Build a map from class and field names to a priority-ordered List of source name Strings.
getDirectDataLoader() - Method in class org.intermine.task.DirectDataLoaderTask
Return the DirectDataLoader for this Task.
getDirection() - Method in class org.intermine.pathquery.OrderElement
Returns the order direction of this OrderElement.
getDirectSubs(ClassDescriptor) - Method in class org.intermine.metadata.Model
Get the ClassDescriptors for the direct subclasses of a class
getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the disableResultsCache configuration option.
getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the disableResultsCache configuration option.
getDisplayer() - Method in class org.intermine.web.logic.config.FieldConfig
Get the displayer for that field
getDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer
Gimme my name
getDisplayerPage() - Method in class org.intermine.web.logic.results.ReportObjectField
Return path to a custom displayer
getDisplayFields() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getDisplayName() - Method in class org.intermine.web.logic.config.FieldConfig
Get the label to display in the webapp for this field.
getDisplayName() - Method in class org.intermine.web.logic.config.Type
 
getDisplayName() - Method in class org.intermine.web.logic.results.ReportObjectField
Get the label to display in the webapp for this field.
getDisplaySummary(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
Create summary information of the paths currently in a query and their constraints for display in the QueryBuilder summary section.
getDocument() - Method in class org.intermine.api.searchengine.KeywordSearchResultContainer
document Type generic Eg: SolrInputDocument, Document
getDoesntContainOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the DOES NOT CONTAINS options are negation of the CONTAINS options.
getDoesntOverlapOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the DOES NOT OVERLAP options are negation of the OVERLAPS options.
getDoGzip() - Method in class org.intermine.web.struts.TableExportForm
Get whether the output should be GZIPped.
getDomain() - Method in class org.intermine.api.beans.PartnerLink
 
getDomain() - Method in class org.intermine.api.mines.ObjectRequest
 
getDomain() - Method in class org.intermine.webservice.server.jbrowse.Command
 
getDomainLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the domainLabel
getDoneAlready() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Returns the doneAlready Set, for logging purposes
getDoNotTruncate() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the doNotTruncate flag.
getDoNotTruncate() - Method in class org.intermine.web.logic.results.ReportObjectField
 
getDriver() - Method in class org.intermine.sql.Database
Gets the driver this Database
geteditable() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Returns the list of all editable constraints.
getEditableConstraints(String) - Method in class org.intermine.template.TemplateQuery
For a path with editable constraints, get all the editable constraints as a List, or the empty list if there are no editable constraints on that path.
getEditablePaths() - Method in class org.intermine.template.TemplateQuery
Get the paths of all editable constraints in this template.
getEditingConstraintCode() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the constraint that is being edited or null if creating a new constraint.
getEditingView(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the view list that the user is currently editing.
getEffectiveOrderBy() - Method in class org.intermine.objectstore.query.Query
Gets the effective ORDER BY clause of this Query, such as may be used to create SQL.
getEffectiveView() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
getElementClassDescriptors() - Method in class org.intermine.pathquery.Path
Return a List of the ClassDescriptor objects for each element of the path.
getElementId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Return the table identifier if isTable==true.
getElements() - Method in class org.intermine.pathquery.Path
Return a list of field names, one per path element (except for the first, which is a class).
getElementsContainingField(String, String) - Method in class org.intermine.pathquery.Path
Return the indexes of elements containing the field given in input
getElementType() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the collection element type of the field.
getElementType(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the element type of a collection given the field name.
getElementType(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
getElementType(String) - Method in class org.intermine.api.userprofile.SavedBag
 
getElementType(String) - Method in class org.intermine.api.userprofile.SavedQuery
 
getElementType(String) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getElementType(String) - Method in class org.intermine.api.userprofile.Tag
 
getElementType(String) - Method in class org.intermine.api.userprofile.TemplateSummary
 
getElementType(String) - Method in class org.intermine.api.userprofile.UserProfile
 
getElementType(String) - Method in class org.intermine.model.fulldata.Item
 
getElementType(String) - Method in interface org.intermine.model.InterMineFastPathObject
Returns the element type of a collection by name.
getElementType(String) - Method in interface org.intermine.model.InterMineObject
Returns the element type of a collection by name.
getElementType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the element type of a collection by name.
getEmail() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getEmail() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
 
getEmailAddress() - Method in class org.intermine.api.profile.Profile
Get this user's preferred email address.
getEmailer(Properties) - Static method in class org.intermine.web.context.EmailerFactory
 
getEnableOptimize() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getEnd() - Method in interface org.intermine.api.query.range.Range
 
getEnd() - Method in class org.intermine.objectstore.query.OverlapRange
Returns the right parameter.
getEnd() - Method in class org.intermine.webservice.server.core.Page
 
getEnd() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getEndClassDescriptor() - Method in class org.intermine.pathquery.Path
If the last element in the path is a reference or collection return the ClassDescriptor that the reference or collection references.
getEndClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getEndFieldDescriptor() - Method in class org.intermine.pathquery.Path
Return the FieldDescriptor of the last element in the path or null if the path has just one element.
getEndRow() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the index of the last row of this page
getEndType() - Method in class org.intermine.pathquery.Path
Return the type of the last element in the path, regardless of whether it is an attribute or a class.
getEnrich() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
The enrich property is the path to the value that should be enriched.
getEnrichIdentifier() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the equivalent object fetcher.
getEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns a Set of objects from the idMap or database that are equivalent to the given object, according to the primary keys defined by the given Source.
getEquivalentsFor(List<ResultsRow<Object>>) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches the equivalent object information for a whole batch of objects.
getEquivalentsForObjects(List<FastPathObject>) - Method in class org.intermine.dataloader.BatchingFetcher
Fetches the equivalent object information for a whole batch of objects.
getError() - Method in interface org.intermine.api.idresolution.Job
 
getError() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getError() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getError() - Method in class org.intermine.webservice.server.output.Output
Gets the error message.
getError() - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
 
getErrorCorrection() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
which method of errorcorrection the user chose.
getErrorCorrection() - Method in class org.intermine.web.struts.WidgetForm
 
getErrorElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getErrorElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Gets the blocking error codes from the servlet context.
getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidator
Returns errors occurred during parsing xml.
getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
Returns errors occurred during parsing xml.
getErrorsAndWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator
Returns errors and warning occurred during parsing xml.
getEscapeXml() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the escapeXml flag.
getEscapeXml() - Method in class org.intermine.web.logic.results.ReportObjectField
 
getEstimatedRows() - Method in class org.intermine.sql.query.ExplainResult
Returns the best current estimate for the number of rows for this query.
getEstimatedSize() - Method in class org.intermine.api.results.WebResults
Get the estimated number of rows of this table
getEstimatedSize() - Method in interface org.intermine.api.results.WebTable
Get the estimated number of rows of this table
getEstimatedSize() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the (possibly estimated) number of resultElementRows of this table
getEvaluables() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
Returns the evaluables that this object was constructed with.
getEvent() - Method in class org.intermine.api.tracker.track.ListTrack
Return the type of event to track (creation or list execution )
getEventSetDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getEventSetDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getExactSize() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the exact number of resultElementRows of this table
getException() - Method in class org.intermine.api.searchengine.solr.SolrObjectHandler
Get the error that occurred during processing, if any.
getExcludeList() - Method in class org.intermine.task.ConverterTask
Return the list set by setExcludeList().
getExecutionTime() - Method in class org.intermine.web.registry.model.RegistryResponse
 
getExistingBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Gets the value of existingBagName
getExistingBagName() - Method in class org.intermine.web.struts.SaveBagForm
Gets the value of existingBagName
getExistingLoops() - Method in class org.intermine.pathquery.PathQuery
Returns the set of loop constraint descriptive strings, for the purpose of checking for uniqueness.
getExpiry() - Method in class org.intermine.webservice.server.user.DeletionToken
 
getExplain() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the ExplainResult of this Candidate, fetching the data if not already present.
getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Internal method that creates an ExplainResult.
getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Internal method that creates an ExplainResult.
getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Internal method that creates an ExplainResult.
getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Internal method that creates an ExplainResult.
getExplainText() - Method in class org.intermine.sql.query.PostgresExplainResult
Returns the text of the explain result, in human readable form.
getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter
Do the export.
getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
Do the export.
getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.TabHttpExporter
Do the export.
getExporter(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
Return the exporter class for the given id.
getExportField() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getExportQuery(List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.GraphWidget
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidget
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getExportResults(String[]) - Method in class org.intermine.web.logic.widget.Widget
 
getExporttype() - Method in class org.intermine.web.struts.WidgetForm
 
getExtension() - Method in class org.intermine.webservice.server.query.CodeService
 
getExtension() - Method in class org.intermine.webservice.server.WebService
 
getExternalLink() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getExternalLink() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
getExternalLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getExternalLinkLabel() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
getExtra() - Method in class org.intermine.api.profile.BagValue
 
getExtraAttribute() - Method in class org.intermine.web.logic.widget.PopulationInfo
 
getExtraAttribute() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
 
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
Do-nothing implementation of superclass method
getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getExtraAttributes(ObjectStore, InterMineBag) - Method in interface org.intermine.web.logic.widget.WidgetHelper
Get the extra attributes needed for the DataSetLoader
getExtraConnectFieldPath() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getExtraConstraintClassName() - Method in class org.intermine.api.bag.BagQueryConfig
Return the class name that was passed to the constructor.
getExtraConstraintClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint
If a LOOKUP constraint and an extra value constraint is available return the classname of the extra constraint so it can be displayed.
getExtraConstraintValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
If a LOOKUP constraint and an extra constraint is available for this path, return a list of the possible values for populating a dropdown.
getExtraCorrectionCoefficient() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
 
getExtraCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
getExtraCorrectionCoefficient() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getExtraFieldValue() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the extra field value - the optional constraint on the bag upload page
getExtraFieldValue() - Method in class org.intermine.web.struts.BuildBagForm
Get the value to use when creating an extra constraint on a BagQuery, configured in BagQueryConfig.
getExtraFieldValue() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
 
getExtraParams() - Method in class org.intermine.web.struts.TableExportForm
Extra parameters map for use by sub classes.
getExtraValue() - Method in interface org.intermine.api.idresolution.JobInput
 
getExtraValue() - Method in class org.intermine.pathquery.PathConstraintLookup
Returns the extra value for this constraint.
getExtraValue() - Method in class org.intermine.template.TemplateValue
 
getExtraValue() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getExtraValue() - Method in class org.intermine.web.logic.template.ConstraintInput
Returns extra value.
getExtraValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of extraValue
getExtraValue() - Method in class org.intermine.webservice.server.lists.ListInput
 
getExtraValue() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
 
getExtraValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
A static method for getting the extra-value if there is one, or null if there is none to be got.
getExtraValueFieldClass() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getExtraValues() - Method in class org.intermine.web.struts.TemplateForm
Get the extra values
getExtraValues(String) - Method in class org.intermine.web.struts.TemplateForm
Get an extra value
getFacets() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getFacets() - Method in class org.intermine.api.searchengine.KeywordSearchResults
 
getFairTerm() - Method in class org.intermine.metadata.AttributeDescriptor
Get the term for the attribute - a URI pointing to an ontology term describing this attribute.
getFairTerm() - Method in class org.intermine.metadata.ClassDescriptor
Returns the URI for this data type.
getFastList(String, String, String, int) - Method in class org.intermine.web.autocompletion.AutoCompleter
Returns n search results
getField() - Method in interface org.intermine.api.results.ResultCell
 
getField() - Method in class org.intermine.api.results.ResultElement
Get the field value
getField() - Method in class org.intermine.api.searchengine.KeywordSearchFacet
internal field name
getField() - Method in class org.intermine.api.searchengine.KeywordSearchFacetData
get single/first field or null
getField() - Method in class org.intermine.webservice.server.core.TableCell
 
getFieldConfig() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getFieldConfig(String) - Method in class org.intermine.web.logic.config.Type
Return a FieldConfig for a particular field if it has been specified, otherwise return null
getFieldConfig(String, String) - Method in class org.intermine.web.logic.config.WebConfig
Return the FieldConfig for a particular field of the specified field, or null if field not configured.
getFieldConfig(WebConfig, ClassDescriptor, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
Get a field config object for a particular descriptor.
getFieldConfig(WebConfig, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
Get a field config object for a particular descriptor.
getFieldConfigMap() - Method in class org.intermine.web.logic.config.Type
Return a Map from FieldConfig.fieldName to FieldConfig objects.
getFieldConfigs() - Method in class org.intermine.web.logic.config.Type
Get the List of FieldConfig objects
getFieldConfigs() - Method in class org.intermine.web.logic.results.ReportObject
Return a list of field configs
getFieldConfigs() - Method in class org.intermine.web.search.KeywordSearchResult
fieldConfigs
getFieldConfigs(String) - Method in class org.intermine.web.logic.config.WebConfig
Return a FieldConfigs for a particular class or an empty list if no config is defined.
getFieldDescriptor() - Method in class org.intermine.pathquery.Node
 
getFieldDescriptor() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Return the last field descriptor (the last element) of the path.
getFieldDescriptor() - Method in class org.intermine.web.logic.results.InlineResultsTable
Get the fields descriptor this list represents.
getFieldDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Retrieve a FieldDescriptor by name.
getFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets the FieldDescriptors for this class (but not superclasses).
getFieldDescriptorsForClass(Class<?>) - Method in class org.intermine.metadata.Model
Takes a Class, and generates a Map of all FieldDescriptors that are the class fields or any of its parents.
getFieldDisplayName(String) - Method in class org.intermine.web.logic.results.ReportObject
Return a string to display as the name of a field.
getFieldExporter() - Method in class org.intermine.web.logic.config.FieldConfig
Return the class name of the FieldExporter to use when this field is viewed.
getFieldExpr() - Method in class org.intermine.web.logic.config.FieldConfig
Return the JSTL expression for the object.
getFieldInfo(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns a FieldInfo object for the given class and field name.
getFieldInfos(Class<?>) - Static method in class org.intermine.metadata.TypeUtil
Returns the Map from field name to TypeUtil.FieldInfo objects for all the fields in a given class.
getFieldName() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the name of the field.
getFieldName() - Method in class org.intermine.objectstore.query.QueryField
Returns the name of the field.
getFieldName() - Method in class org.intermine.objectstore.query.QueryForeignKey
Gets the fieldname of this QueryReference.
getFieldName() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the name of the field.
getFieldName() - Method in class org.intermine.objectstore.query.QueryReference
Gets the fieldname of this QueryReference.
getFieldName() - Method in class org.intermine.pathquery.Node
Gets the value of fieldName
getFieldName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the fieldname for this path.
getFieldNames() - Method in class org.intermine.api.searchengine.solr.SolrObjectHandler
get list of fields contained in the fetched documents
getFieldNames() - Method in class org.intermine.metadata.PrimaryKey
Return the Set of field names
getFieldNumber() - Method in class org.intermine.objectstore.query.PathExpressionField
Returns the field number.
getFieldProxy(Object, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the value of a public or protected Field of an Object given by the field name without dereferencing any ProxyReference objects.
getFieldProxy(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
getFieldProxy(String) - Method in class org.intermine.api.userprofile.SavedBag
 
getFieldProxy(String) - Method in class org.intermine.api.userprofile.SavedQuery
 
getFieldProxy(String) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getFieldProxy(String) - Method in class org.intermine.api.userprofile.Tag
 
getFieldProxy(String) - Method in class org.intermine.api.userprofile.TemplateSummary
 
getFieldProxy(String) - Method in class org.intermine.api.userprofile.UserProfile
 
getFieldProxy(String) - Method in interface org.intermine.model.FastPathObject
Returns the value of a field without dereferencing any ProxyReference objects.
getFieldProxy(String) - Method in class org.intermine.model.fulldata.Attribute
 
getFieldProxy(String) - Method in class org.intermine.model.fulldata.Item
 
getFieldProxy(String) - Method in class org.intermine.model.fulldata.Reference
 
getFieldProxy(String) - Method in class org.intermine.model.fulldata.ReferenceList
 
getFieldProxy(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the value of a field without dereferencing any ProxyReference objects.
getFields() - Method in class org.intermine.api.searchengine.KeywordSearchFacetData
array of field names, only used for path right now
getFieldToAlias(FromElement) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getFieldType(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the type of a field given the field name.
getFieldType(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
getFieldType(String) - Method in class org.intermine.api.userprofile.SavedBag
 
getFieldType(String) - Method in class org.intermine.api.userprofile.SavedQuery
 
getFieldType(String) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getFieldType(String) - Method in class org.intermine.api.userprofile.Tag
 
getFieldType(String) - Method in class org.intermine.api.userprofile.TemplateSummary
 
getFieldType(String) - Method in class org.intermine.api.userprofile.UserProfile
 
getFieldType(String) - Method in interface org.intermine.model.FastPathObject
Returns the type of a field by name.
getFieldType(String) - Method in class org.intermine.model.fulldata.Attribute
 
getFieldType(String) - Method in class org.intermine.model.fulldata.Item
 
getFieldType(String) - Method in class org.intermine.model.fulldata.Reference
 
getFieldType(String) - Method in class org.intermine.model.fulldata.ReferenceList
 
getFieldType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the type of a field by name.
getFieldValue(Object, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the value of a public or protected Field of an Object given the field name
getFieldValue(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
getFieldValue(String) - Method in class org.intermine.api.userprofile.SavedBag
 
getFieldValue(String) - Method in class org.intermine.api.userprofile.SavedQuery
 
getFieldValue(String) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getFieldValue(String) - Method in class org.intermine.api.userprofile.Tag
 
getFieldValue(String) - Method in class org.intermine.api.userprofile.TemplateSummary
 
getFieldValue(String) - Method in class org.intermine.api.userprofile.UserProfile
 
getFieldValue(String) - Method in interface org.intermine.model.FastPathObject
Returns the value of a field by name.
getFieldValue(String) - Method in class org.intermine.model.fulldata.Attribute
 
getFieldValue(String) - Method in class org.intermine.model.fulldata.Item
 
getFieldValue(String) - Method in class org.intermine.model.fulldata.Reference
 
getFieldValue(String) - Method in class org.intermine.model.fulldata.ReferenceList
 
getFieldValue(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the value of a field by name.
getFieldValue(String) - Method in class org.intermine.web.logic.results.ReportObject
Get field value for a field name (expression)
getFieldValues() - Method in class org.intermine.web.search.KeywordSearchResult
values of all fields
getFieldValues(String, String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the possible values (as Strings) for a given field in a given class.
getFieldValues(ObjectStore, ObjectStoreSummary, String, String) - Static method in class org.intermine.web.struts.BagBuildController
Return a list of the possible field values for the given class/field name combination.
getFilename(String, String) - Static method in class org.intermine.metadata.Util
Given a key and model name, return filename for reading/writing.
getFilename(String, String) - Static method in class org.intermine.modelproduction.MetadataManager
Given a key and model name, return filename for reading/writing.
getFileName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Returns the filename that should be associated with this query.
getFilter() - Method in interface org.intermine.web.logic.widget.WidgetOptions
 
getFilter() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
filter values get used in the query to constrain the results in some way, and they can be changed by the user.
getFilter() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getFilterLabel() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getFilterLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
the label for the filter.
getFilters() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getFilters() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
filter values get used in the query to constrain the results in some way, and they can be changed by the user.
getFiltersValues(ObjectStore, InterMineBag, String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getFilterWebSearchables(HttpServletRequest, String, String, String) - Static method in class org.intermine.web.struts.WebSearchableListController
Get all the WebSearchables in the given scope and of the given type.
getFirstColumnForClass(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
Find the first column index for the specified class or a subclass in the page table (may be a parent class of a field being displayed).
getFirstOrderByHasNoNulls() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns true if the first element of the ORDER BY clause is a column that contains no nulls.
getFirstSelectedFields(ObjectStore, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the fields for the first selected objects.
getFixedOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
If a dropdown is available for a constraint fewer operations are possible, return the list of operations.
getFlatSelect() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
Converts a SELECT list from a normal query into a representation of the columns returned in this converted list.
getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidget
Get the flattened results
getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
get the flattened results
getFlattenedSourceName(String) - Static method in class org.intermine.metadata.StringUtil
Flattens source name.
getFooter() - Static method in class org.intermine.xml.full.FullRenderer
Return the Full XML file footer
getFormat() - Method in enum org.intermine.api.mines.ContentType
 
getFormat() - Method in class org.intermine.web.struts.CSVExportForm
Return the format field ("csv", "tab", ...)
getFormat() - Method in class org.intermine.webservice.server.WebService
Returns required output format.
getFormatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue
Get the formatted version, with e.g.
getFormattedClassName() - Method in class org.intermine.web.logic.config.Type
 
getFormattedClassName(String) - Static method in class org.intermine.web.logic.config.Type
 
getFormattedName() - Method in class org.intermine.web.logic.config.FieldConfig
 
getFormattedName(String) - Static method in class org.intermine.web.logic.config.FieldConfig
 
getFormattedTrack() - Method in class org.intermine.api.tracker.track.KeySearchTrack
 
getFormattedTrack() - Method in class org.intermine.api.tracker.track.ListTrack
Return the track formatted into an array of String to be saved in the database
getFormattedTrack() - Method in class org.intermine.api.tracker.track.LoginTrack
Return the track formatted into an array of String to be saved in the database
getFormattedTrack() - Method in class org.intermine.api.tracker.track.QueryTrack
 
getFormattedTrack() - Method in class org.intermine.api.tracker.track.TemplateTrack
Return the track formatted into an array of String to be saved in the database
getFormattedTrack() - Method in interface org.intermine.api.tracker.track.Track
Return the track formatted into an array of String to be saved in the database
getFormatter() - Static method in class org.intermine.webservice.server.core.ISO8601DateFormat
 
getFormatType() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
getFormFile() - Method in class org.intermine.web.struts.BuildBagForm
Get the FormFile.
getFormFile() - Method in class org.intermine.web.struts.ImportXMLForm
Get the FormFile.
getFragmentFromURI(String) - Static method in class org.intermine.util.XmlUtil
Return the fragment portion of a URI string (i.e.
getFriendlyDesc(Object) - Static method in class org.intermine.util.DynamicUtil
Creates a friendly description of an object - that is, the class and the ID (if it has one).
getFriendlyMineLinks(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
used on REPORT page For a gene, generate links to other intermines.
getFriendlyMines() - Method in class org.intermine.api.mines.FriendlyMineManager
Return a list of Mines listed in config.
getFriendlyName() - Method in class org.intermine.pathquery.Node
Gets a friendly name for display on the web site.
getFriendlyName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the last element of the path.
getFriendlyName(Class<?>) - Static method in class org.intermine.metadata.Util
Creates a friendly name for a given class.
getFrom() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getFrom() - Method in class org.intermine.objectstore.query.Query
Returns all FromElements in the FROM clause
getFrom() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the additional FROM list.
getFrom() - Method in class org.intermine.sql.query.Query
Gets the Set of from tables for this query.
getFromElement() - Method in class org.intermine.objectstore.query.QueryField
Gets the FromElement of which the field is a member
getFrontcolor() - Method in class org.intermine.api.mines.LocalMine
 
getFrontcolor() - Method in interface org.intermine.api.mines.Mine
 
getFrontcolor() - Method in class org.intermine.api.mines.RemoteMine
 
getFullName(String) - Static method in class org.intermine.webservice.server.CodeTranslator
Returns corresponding fullName of translated operation.
getGeneratedPathDescription(String) - Method in class org.intermine.pathquery.PathQuery
Returns the path description for the given path.
getGetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the getter Method.
getGetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the getter for the field name.
getGetters(Class<?>) - Static method in class org.intermine.metadata.TypeUtil
Gets the getter methods for the bean properties of a class
getGlobalBag(String) - Method in class org.intermine.api.bag.BagManager
Fetch a global bag by name.
getGlobalBags() - Method in class org.intermine.api.bag.BagManager
Fetch globally available bags - superuser public bags that are available to everyone.
getGlobalBagsContainingId(Integer) - Method in class org.intermine.api.bag.BagManager
Fetch global bags that contain the given id.
getGlobalBagsWithTags(List<String>) - Method in class org.intermine.api.bag.BagManager
Fetch globally available bags - superuser public bags that are available to everyone with a particular tag assigned to them
getGlobalSearchRepositories() - Static method in class org.intermine.api.search.SearchRepository
Get the search repositories registered as global repositories.
getGlobalSearchRepository(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the SearchRepository for global (public) objects.
getGlobalSearchRepository(Profile) - Static method in class org.intermine.api.search.SearchRepository
Get the search repository registered as global repositories for the user specified in input.
getGlobalTemplate(String) - Method in class org.intermine.api.template.TemplateManager
Fetch a global template by name.
getGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager
Return a map from template name to template query containing superuser templates that are tagged as public.
getGlobalTemplates(boolean) - Method in class org.intermine.api.template.TemplateManager
Return a map from template name to template query containing superuser templates that are tagged as public.
getGraphType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the type of this graph, e.g.
getGroupBy() - Method in class org.intermine.objectstore.query.Query
Gets the GROUP BY clause of this Query
getGroupBy() - Method in class org.intermine.sql.query.Query
Gets the Set of fields in the GROUP BY clause of this query.
getGroupedConstraintLogic() - Method in class org.intermine.pathquery.PathQuery
Returns a List of logic Strings according to the different outer join sections of the query.
getHasAvailableBags() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if there are any available bags for the type of this path.
getHasClassKeys() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if the type of this path has class keys configured.
getHasDisplayer() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getHasHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
Used from JSP
getHasMoreThanOneType() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getHasNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
Used from JSP
getHasPossibleLoops() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if this path in the query has possible loop constraints that are not already in the query.
getHasResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
getHasResults() - Method in class org.intermine.web.logic.widget.GraphWidget
getHasResults() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getHasResults() - Method in class org.intermine.web.logic.widget.TableWidget
getHasResults() - Method in class org.intermine.web.logic.widget.Widget
 
getHasSubclasses() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if the original type has subclasses in the model.
getHaving() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getHaving() - Method in class org.intermine.sql.query.Query
Gets the set of constraints forming the HAVING clause of this query.
getHavingBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getHeadAttributes() - Method in class org.intermine.api.template.ApiTemplate
 
getHeadAttributes() - Method in class org.intermine.pathquery.PathQuery
 
getHeadAttributes() - Method in class org.intermine.template.TemplateQuery
 
getHeader() - Static method in class org.intermine.xml.full.FullRenderer
Return the Full XML file header
getHeaderAttributes() - Method in class org.intermine.webservice.server.clob.SequenceService
Why is the results key "features", pray? and not something more sensible, like, "results", say.
getHeaderAttributes() - Method in class org.intermine.webservice.server.core.JSONService
Get the header attributes to apply to the formatter.
getHeaderAttributes() - Method in class org.intermine.webservice.server.jbrowse.Endpoint
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListTagService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListUploadService
Gets the header attributes on the output object.
getHeaderAttributes() - Method in class org.intermine.webservice.server.output.Output
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.search.QuickSearch
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.template.TemplateTagService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.user.NewUserService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.VersionService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
 
getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.WidgetService
 
getHeaderConfigLink() - Method in class org.intermine.web.logic.config.Type
 
getHeaderConfigTitle() - Method in class org.intermine.web.logic.config.Type
 
getHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
 
getHeaderLink() - Method in class org.intermine.web.logic.results.ReportObject
 
getHeadResources(String, Map<String, String>) - Static method in class org.intermine.web.logic.WebUtil
Returns the resources for a particular section of the head element.
getHelper(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
 
getHelpMessage() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return a help message to display alongside the constraint, this will examine the constraint type and generate and appropriate message, e.g.
getHelpMessage(DisplayConstraint) - Static method in class org.intermine.web.logic.query.DisplayConstraintHelpMessages
Generate a context sensitive help message for a constraint.
getHelpPage(HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
Look at the current webapp page and subtab and return the help page and tab.
getHide() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the hide flag.
getHighlight() - Method in class org.intermine.web.struts.WidgetForm
 
getHighlightedLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns html formatted link in which are highlighted parameters that are to be replaced.
getHintCount(String) - Method in class org.intermine.web.logic.results.WebState
Get the number of times a particular hint has been shown.
getHistory() - Method in class org.intermine.api.profile.Profile
Get the session query history.
getHits() - Method in class org.intermine.api.searchengine.KeywordSearchResults
 
getHtmlHeadTitle() - Method in class org.intermine.web.logic.results.ReportObject
Fetch a header string to use as the page title.
getHtmlLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Generates TemplateResultService web service link.
getHttpErrorCode() - Method in exception org.intermine.webservice.server.exceptions.ServiceException
 
getHumanReadableText() - Method in class org.intermine.metadata.ClassDescriptor
Returns a String that contains a multi-line human-readable description of the ClassDescriptor.
getIcon(int) - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getIcon(int) - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getIconImage() - Method in class org.intermine.web.logic.aspects.Aspect
Get the icon Image.
getId() - Method in interface org.intermine.api.results.ResultCell
 
getId() - Method in class org.intermine.api.results.ResultElement
Get the Id.
getId() - Method in class org.intermine.api.userprofile.PermanentToken
 
getId() - Method in class org.intermine.api.userprofile.SavedBag
 
getId() - Method in class org.intermine.api.userprofile.SavedQuery
 
getId() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getId() - Method in class org.intermine.api.userprofile.Tag
 
getId() - Method in class org.intermine.api.userprofile.TemplateSummary
 
getId() - Method in class org.intermine.api.userprofile.UserProfile
 
getId() - Method in class org.intermine.model.fulldata.Item
 
getId() - Method in interface org.intermine.model.InterMineFastPathObject
Getter for the ID field - ensures that every object in the database has an ID.
getId() - Method in interface org.intermine.model.InterMineObject
Getter for the ID field - ensures that every object in the database has an ID.
getId() - Method in class org.intermine.objectstore.proxy.ProxyReference
Gets the ID value
getId() - Method in class org.intermine.web.logic.config.InlineListObject
 
getId() - Method in class org.intermine.web.logic.config.TableExportConfig
Return the id of this TableExportConfig.
getId() - Method in class org.intermine.web.logic.results.DisplayReference
Get the id of the object
getId() - Method in class org.intermine.web.logic.results.ReportObject
Get the id of this object
getId() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getId() - Method in class org.intermine.web.registry.model.Instance
 
getId() - Method in class org.intermine.web.search.KeywordSearchResult
intermine ID
getId() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getId() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Gets element id.
getId() - Method in class org.intermine.webservice.server.core.TableCell
 
getID() - Method in class org.intermine.api.mines.LocalMine
 
getIdentifier() - Method in class org.intermine.api.beans.ObjectDetails
 
getIdentifier() - Method in class org.intermine.api.mines.ObjectRequest
 
getIdentifier() - Method in class org.intermine.model.fulldata.Item
 
getIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Used from JSP
getIdentifier() - Method in class org.intermine.web.uri.InterMineLUI
Get the identifier
getIdentifier() - Method in class org.intermine.xml.full.Item
Get the identifier of this item.
getIdentifier(String) - Method in class org.intermine.web.uri.ClassNameURIIdentifierMapper
Given the className, returns the identifier (e.g.
getIdentity() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
 
getIdField() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the idField.
getIdMap() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns the IdMap used.
getIds() - Method in interface org.intermine.api.idresolution.JobInput
 
getIds() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns the Set of object IDs present in the bag that correspond to the type specified.
getIds() - Method in class org.intermine.pathquery.PathConstraintIds
Returns the id collection that the constraint is constraining to.
getIds() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getIds() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getIds(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
Get the ids for a constraint.
getIdsContained(Collection<Integer>) - Method in class org.intermine.api.profile.InterMineBag
Returns a List which contains the ids given in input and contained in this bag as Integer IDs.
getIdsToDelete() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the delete set.
getIdsToInsert() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the insert map.
getIdsToRemove(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the IDs to remove.
getIgnoreConfig() - Method in interface org.intermine.api.idresolution.JobInput
There is config that allows mines to configure match behaviour.
getIgnoreConfig() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getIgnoredClasses() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getIgnoredFields() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getImage() - Method in class org.intermine.web.logic.config.HeaderConfigLink
 
getImplementations() - Method in class org.intermine.model.fulldata.Item
 
getImplementations() - Method in class org.intermine.xml.full.Item
Get the interfaces implemented by this item.
getImplementClassDescriptors(String) - Method in class org.intermine.xml.full.Item
Returns the ClassDescriptors for the given implementations.
getImplements(Object, Model) - Static method in class org.intermine.xml.full.ItemFactory
Get all interfaces that an object implements.
getIncludeHeaders() - Method in class org.intermine.web.struts.TableExportForm
Return the current value of the includeHeaders flag.
getIndentation() - Method in class org.intermine.pathquery.Node
Gets the value of indentation
getIndentation() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the number of elements in the path, where a simple class is zero.
getIndentation() - Method in class org.intermine.web.logic.TreeNode
Get the indentation
getIndex() - Method in class org.intermine.api.results.Column
Gets the value of index
getIndex() - Method in class org.intermine.metadata.ConstraintOp
Get an index for this ConstraintOp TODO: expunge this horror.
getIndexBatchSize() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getIndirectAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getIndirectionTableName(CollectionDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Creates an indirection table name for a many-to-many collection descriptor
getIndirectionTableNames(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Given a ClassDescriptor find names of all related indirection tables.
getInfo() - Method in class org.intermine.api.results.WebResults
Return the ResultsInfo object from the underlying Results object.
getInfo() - Method in interface org.intermine.api.results.WebTable
Gets the underlying results object info
getInfo() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Returns Returns the current best estimate of the characteristics of the LazyCollection
getInfo() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Returns Returns the current best estimate of the characteristics of the LazyCollection
getInfo() - Method in class org.intermine.objectstore.query.Results
Gets the best current estimate of the characteristics of the query.
getInfo() - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the best current estimate of the characteristics of the query.
getInfoCache() - Method in class org.intermine.api.query.WebResultsExecutor
Returns the entire infoCache, which is an unmodifiable Map from PathQuery (by identity) to ResultsInfo.
getInitialExportPaths(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
The initial export path list is just the paths from the columns of the PagedTable.
getInitialExportPaths(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
Return a list of the Paths to show the user as initial export columns or header contents.
getInlineListConfig() - Method in class org.intermine.web.logic.config.Type
 
getInput() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getInput() - Method in class org.intermine.webservice.server.lists.AbstractListService
 
getInput() - Method in interface org.intermine.webservice.server.lists.ListMaker
 
getInput() - Method in class org.intermine.webservice.server.lists.ListOperationService
 
getInput() - Method in class org.intermine.webservice.server.lists.ListsRequestParser
Returns parameters of web service as a parameter object.
getInput() - Method in class org.intermine.webservice.server.lists.ListSubtractionService
 
getInput() - Method in class org.intermine.webservice.server.lists.ListUploadService
Parse the parameters for this request.
getInput() - Method in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Returns parsed parameters in parameter object - so this values can be easily get from this object.
getInput() - Method in class org.intermine.webservice.server.template.result.TemplateResultRequestParser
Returns parsed parameters in parameter object - so this values can be easily obtained from this object.
getInput(HttpServletRequest) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
Returns parameters of web service as a parameter object.
getInputIdent() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
 
getInputIdentifiersForIssue(String) - Method in class org.intermine.api.bag.BagQueryResult
 
getInstance() - Static method in class org.intermine.api.idresolution.IDResolver
 
getInstance() - Static method in class org.intermine.pathquery.PathLengthComparator
 
getInstance() - Static method in class org.intermine.util.AlwaysSet
Returns a new AlwaysSet with the correct type parameters.
getInstance() - Static method in class org.intermine.util.IdentityMap
Obtain an instance of this class
getInstance() - Static method in class org.intermine.util.ShutdownHook
Get the instance of this ShutdownHook.
getInstance() - Method in class org.intermine.web.registry.model.RegistryResponse
 
getInstance() - Static method in class org.intermine.webservice.server.user.DeletionTokens
 
getInstance(String, Connection) - Static method in class org.intermine.sql.query.ExplainResult
Constructs an instance of ExplainResult for a given query String and database Connection.
getInstance(String, Properties) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Creates a new instance of this class, given the properties defining it.
getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Gets an ObjectStoreFastCollectionsForTranslatorImpl instance for the given properties
getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Gets an ObjectStoreFastCollectionsImpl instance for the given properties
getInstance(String, Properties) - Static method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets a ObjectStoreInterMineImpl instance for the given underlying properties
getInstance(String, Properties) - Static method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Gets an ObjectStore for the given underlying properties.
getInstance(String, Properties, Class<? extends IntegrationWriterDataTrackingImpl>, Class<? extends DataTracker>) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Creates a new IntegrationWriter instance of the specified class and with a specified DataTracker class plus properties.
getInstance(Connection) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
Gets a PrecomputedTableManager instance for the given underlying Connection.
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.KeySearchTracker
Return an instance of the KeySearchTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.ListTracker
Return an instance of the ListTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.LoginTracker
Return an instance of the LoginTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.QueryTracker
Return an instance of the QueryTracker
getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.TemplateTracker
Return an instance of the TemplateTracker
getInstance(PreparedStatement) - Static method in class org.intermine.sql.query.ExplainResult
Constructs an instance of ExplainResult given a PreparedStatement object.
getInstance(InterMineAPI, Properties) - Static method in class org.intermine.api.mines.FriendlyMineManager
Get an instance of FriendlyMineManager.
getInstance(ProfileManager) - Static method in class org.intermine.api.bag.SharedBagManager
Return the singleton SharedBagManager instance
getInstance(ObjectStore) - Static method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
static method to get one instance of KeywordSearchProperties Manager
getInstance(Database) - Static method in class org.intermine.sql.precompute.OptimiserCache
Returns an OptimiserCache object relevant to the database given.
getInstance(Database) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
Gets a PrecomputedTableManager instance for the given underlying database.
getInstance(Query, Connection) - Static method in class org.intermine.sql.query.ExplainResult
Constructs an instance of ExplainResult for a given Query and database Connection.
getInstance(WebConfig, InterMineAPI) - Static method in class org.intermine.web.displayer.DisplayerManager
Fetch the DisplayerManager, a single instance is held.
getInstanceByName(String) - Static method in class org.intermine.metadata.Model
Return a Model for specified model name (loading Model if necessary)
getIntegrationWriter() - Method in class org.intermine.dataloader.DataLoader
Return the IntegrationWriter that was passed to the constructor.
getIntegrationWriter() - Method in class org.intermine.task.DirectDataLoaderTask
Return the IntegrationWriter for this task.
getIntegrationWriter(String) - Static method in class org.intermine.dataloader.IntegrationWriterFactory
Return an IntegrationWriter configured using properties file
getInterMineAPI() - Static method in class org.intermine.web.context.InterMineContext
 
getInterMineAPI() - Method in class org.intermine.web.uri.InterMineLUIConverter
Returns the InterMineAPI
getInterMineAPI(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the InterMineAPI which provides the core features of an InterMine application.
getInterMineAPI(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the InterMineAPI which provides access to core features of an InterMine application.
getInterMineAPI(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the InterMineAPI which provides access to core features of an InterMine application.
getInterMineID(InterMineLUI) - Method in class org.intermine.web.uri.InterMineLUIConverter
Given a InterMineLUI (compact uri, e.g.
getInterMineLUI(Integer) - Method in class org.intermine.web.uri.InterMineLUIConverter
Generate the InterMineLUI associated to the internal interMine ID
getInterMineResults() - Method in class org.intermine.api.results.WebResults
Return the underlying results object.
getIntermineVersion() - Method in class org.intermine.web.registry.model.Instance
 
getIntParameter(String) - Method in class org.intermine.webservice.server.WebService
Get the value of a parameter that should be interpreted as an integer.
getIntParameter(String, Integer) - Method in class org.intermine.webservice.server.WebService
Get the value of a parameter that should be interpreted as an integer.
getIntro(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getIntroText() - Method in class org.intermine.web.logic.aspects.Aspect
Get the introduction text.
getIntSessionProperty(HttpSession, String, int) - Static method in class org.intermine.web.logic.WebUtil
Lookup an Integer property from the SessionContext and return it.
getInvalidBags() - Method in class org.intermine.api.profile.BagSet
 
getInvalidBags() - Method in class org.intermine.api.profile.Profile
 
getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
getInvite() - Method in class org.intermine.web.struts.InvitationForm
 
getInviteData(ProfileManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite
 
getInvitee() - Method in class org.intermine.api.bag.SharingInvite
 
getInvitee() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getInviterId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getInvites(InterMineAPI, Profile) - Static method in class org.intermine.api.bag.SharingInvite
Get the invitations this profile has made.
getInvites(ProfileManager, BagManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite
Get the invitations this profile has made.
getInwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil
Creates a column name for the "inward" key of a many-to-many collection descriptor.
getIqlQuery() - Method in class org.intermine.objectstore.query.Query
Returns an IqlQuery object representing this query, that may have been cached.
getIsDottedPath() - Method in class org.intermine.web.logic.config.FieldConfig
 
getIsKeyField() - Method in class org.intermine.web.logic.results.InlineTableResultElement
 
getIsNull() - Method in class org.intermine.web.logic.query.MetadataNode
 
getIsRelative() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getIssueIds() - Method in class org.intermine.api.bag.BagQueryResult
Get ids of all InterMineObjects returned that were issues for this bag query lookup.
getIssueIds(String) - Method in class org.intermine.api.bag.BagQueryResult
Get ids of all InterMineObjects returned that were registered as issues of this particular type for this bag query lookup.
getIssuer() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
 
getIssueResults(String) - Method in class org.intermine.api.bag.BagQueryResult
 
getIssues() - Method in class org.intermine.api.bag.BagQueryResult
Get any results that require some user input before adding to the bag.
getItem() - Method in class org.intermine.api.search.SearchResult
Get the web searchable item that was found.
getItem() - Method in class org.intermine.model.fulldata.Attribute
 
getItem() - Method in class org.intermine.model.fulldata.Reference
 
getItem() - Method in class org.intermine.model.fulldata.ReferenceList
 
getItemElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getItemElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getItems() - Method in class org.intermine.api.searchengine.KeywordSearchFacet
list of all values and counts
getItems() - Method in class org.intermine.dataconversion.MockItemWriter
Get the items that have been stored This method is not part of ItemWriter, and for testing convenience returns XML Items
getItems() - Method in class org.intermine.web.logic.results.InlineList
 
getItems() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
 
getItems() - Method in class org.intermine.xml.full.FullHandler
Return the Items that have been read with this handler.
getItemWriter() - Method in class org.intermine.dataconversion.DataConverter
Return the ItemWriter that was passed to the constructor.
getIterator() - Method in class org.intermine.api.searchengine.InterMineResultsContainer
the iterator on the results
getJavaClass() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the Java class name of the controller for this displayer.
getJobById(String) - Method in class org.intermine.api.idresolution.IDResolver
 
getJobById(UUID) - Method in class org.intermine.api.idresolution.IDResolver
 
getJobs() - Method in class org.intermine.api.idresolution.IDResolver
 
getJoinPath() - Method in class org.intermine.webservice.server.core.SubTable
 
getJoinType() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getJson() - Method in class org.intermine.pathquery.PathQuery
toJson synonym for JSPs.
getJspName() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the name of the JSP associated with this displayer.
getJspPage() - Method in class org.intermine.web.displayer.ReportDisplayer
The JSP page that will be called with the request to render output.
getKey() - Method in interface org.intermine.util.ReferenceMap.ReferenceWithKey
Returns the key in the entry.
getKey() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getKey() - Method in class org.intermine.webservice.server.core.Pair
 
getKeyFieldNames() - Method in class org.intermine.api.profile.InterMineBag
Return a list containing the keyFieldNames for the bag
getKeyFieldNames(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
Return names of the key fields for a given class.
getKeyFields() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the key fields for this path as a formatted string, for use in LOOKUP help message.
getKeyFields() - Method in class org.intermine.web.search.KeywordSearchResult
key field expressions
getKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
Return the key fields of a given class.
getKeyFieldValue(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper
Get a key field value for the given object.
getKeyFieldValues(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper
Get a list of key field values for the given object.
getKeyProperties(String) - Static method in class org.intermine.metadata.PrimaryKeyUtil
Return the Properties that specify the key fields for the classes in this Model
getKeyProperties(Source) - Static method in class org.intermine.dataloader.DataLoaderHelper
Return the Properties that enumerate the keys for this Source
getKeyStore() - Static method in class org.intermine.web.context.InterMineContext
 
getKeywordSearches() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the number of search for each keyword
getKeywordSearches(Connection) - Method in class org.intermine.api.tracker.KeySearchTracker
Return the number of search for each keyword
getLabel() - Method in class org.intermine.web.logic.config.FieldConfig
The human readable label for this field.
getLabel() - Method in class org.intermine.web.logic.config.Type
Get the label property's value.
getLabel() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
Get the value to be displayed in the dropdown for this operation.
getLabel() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
label for the results table.
getLabel() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Get the label for this trail element.
getLabels() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
getLabels(GraphWidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
Get the labels for Graph widgets.
getLargeImage() - Method in class org.intermine.web.logic.aspects.Aspect
Webapp relative path to large image.
getLastClassDescriptor() - Method in class org.intermine.pathquery.Path
Returns the last ClassDescriptor in the path.
getLastClassName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Fetch the unqualified class name of the final class on this path, if the path represents an attribute this will be the parent class of that attribute.
getLastElement() - Method in class org.intermine.pathquery.Path
Return the last string element of this path, throw an exception of there is only one element, i.e.
getLastTimeUpdated() - Method in class org.intermine.web.registry.model.Instance
 
getLayout() - Method in class org.intermine.web.logic.template.TemplateResultInput
 
getLayout() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
 
getLdr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
getLeft() - Method in class org.intermine.objectstore.query.OverlapConstraint
Returns the left OverlapRange.
getLeft() - Method in class org.intermine.sql.query.Constraint
Returns the left argument of the constraint.
getLeft() - Method in class org.intermine.sql.query.InListConstraint
Returns the left AbstractValue.
getLeft() - Method in class org.intermine.sql.writebatch.Row
Returns left.
getLeftArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Get the left argument of the given constraint, will return null if passed a ConstraintSet or a MultipleInBagConstraint.
getLeftColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the left column name.
getLeftField() - Method in class org.intermine.api.query.range.ConstraintOptions
Defaults to "start".
getLeftOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getLength() - Method in class org.intermine.web.logic.results.InlineList
 
getLengthWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the (possibly uninitialised) length internal parameter in this object, for use by subclass constructors.
getLevel() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
getLevel() - Method in class org.intermine.api.userprofile.PermanentToken
 
getLimit() - Method in class org.intermine.objectstore.query.Query
Returns the LIMIT parameter for this query.
getLimit() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Getter for limit.
getLimit() - Method in class org.intermine.sql.query.Query
Gets the LIMIT number for this query.
getLimit() - Method in class org.intermine.webservice.server.WebServiceInput
Returns maximum number of results the user will accept.
getLineBreak() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getLineBreak() - Method in class org.intermine.webservice.server.WebService
 
getLineLength() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getLineLength() - Method in class org.intermine.web.logic.results.InlineList
 
getLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
the link is the class that generates the url for each result.
getLink() - Method in class org.intermine.web.struts.WidgetForm
 
getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
 
getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns link switching between displayed and hidden state.
getLink(String, String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Generates QueryResultService web service link.
getLinkPath(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Get the link path for a query.
getLinkPath(TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns the path section of the link for this template.
getLinkPath(TemplateQuery, String) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns the path section of the link for this template.
getLinkPath(TemplateQuery, String, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns the path section of the link for this template.
getLinkRedirect() - Method in class org.intermine.api.results.ResultElement
 
getLinkRedirect() - Method in class org.intermine.web.search.KeywordSearchResult
URL set in web.properties.
getLinkRedirector() - Method in interface org.intermine.api.API
 
getLinkRedirector() - Method in class org.intermine.api.InterMineAPI
 
getLinks(MultiKey) - Method in class org.intermine.api.mines.FriendlyMineManager
 
getLinks(FriendlyMineManager, String, String, String) - Method in class org.intermine.web.util.InterMineLinkGenerator
Query other intermines for this object
getLinks(Mine, Mine, ObjectRequest) - Method in interface org.intermine.web.displayer.InterMineLinkGenerator
Query other intermines for this object
getList(Profile, String) - Method in class org.intermine.webservice.server.query.QueryListAppendService
Get a list from a profile, throwing a service forbidden exception if the list is not accessible.
getListCreationTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getListCreationTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getListExecutionTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getListExecutionTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getListLeft() - Method in class org.intermine.web.struts.ModifyBagForm
 
getListManager() - Method in class org.intermine.webservice.server.WebService
 
getListMap() - Method in class org.intermine.webservice.server.core.ListManager
Returns the lists available to the current user in a Map.
getListName() - Method in class org.intermine.webservice.server.lists.ListInput
 
getListOfTypes() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getListOperations() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the operations done for each list (execution or creation)
getListOperations(Connection) - Method in class org.intermine.api.tracker.ListTracker
Return the operations done for each list (execution or creation)
getListPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getListRight() - Method in class org.intermine.web.struts.ModifyBagForm
 
getLists() - Method in class org.intermine.webservice.server.core.ListManager
Returns the lists available to the current user.
getLists() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput
 
getLists() - Method in class org.intermine.webservice.server.lists.AvailableListsService
Get the lists for this request.
getLists() - Method in class org.intermine.webservice.server.lists.JaccardIndexService
Get the lists for this request.
getLists() - Method in class org.intermine.webservice.server.lists.ListInput
 
getLists() - Method in class org.intermine.webservice.server.lists.ListsService
Executes service specific logic.
getListsButton() - Method in class org.intermine.web.struts.ModifyBagForm
 
getListsContaining(Integer) - Method in class org.intermine.webservice.server.core.ListManager
Returns the current lists available to the current user which contain the specified object.
getListsMatching(ListManager, String) - Method in class org.intermine.webservice.server.lists.AvailableListsService
Get the lists that match the current filter.
getListsNames(Integer) - Method in class org.intermine.webservice.server.core.ListManager
Returns public current lists that contain object with specified id.
getListUploadTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser
Return a tokeniser suitable for parsing tokens received from a list upload context.
getLocalAccount() - Method in class org.intermine.api.userprofile.UserProfile
 
getLocalMine() - Method in class org.intermine.api.mines.FriendlyMineManager
 
getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the log used by this objectstore.
getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns the log used by this objectstore.
getLogarithmMap(String, String, TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker
Return a map containing the logarithm of accesses for each template.
getLogarithmMap(String, TemplateManager) - Method in class org.intermine.api.tracker.TemplatesExecutionMap
Return a map containing the logarithm's sum of the templates executions launched by the same users or during the same sessions.
getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the logBeforeExecute configuration option.
getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the logBeforeExecute configuration option.
getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the logEverything configuration option.
getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the logEverything configuration option.
getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the logExplains configuration option.
getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the logExplains configuration option.
getLogicExpression() - Method in class org.intermine.pathquery.PathQuery
 
getLoginTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getLogo() - Method in class org.intermine.api.mines.LocalMine
 
getLogo() - Method in interface org.intermine.api.mines.Mine
 
getLogo() - Method in class org.intermine.api.mines.RemoteMine
 
getLongDisplayers() - Method in class org.intermine.web.logic.config.Type
Get the List of long Displayers
getLookupOp() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the LOOKUP constraint op.
getLookupOs() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns the objectstore that contains the equivalent objects.
getLookupTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser
Return a tokeniser suitable for parsing tokens received from a lookup constraint context.
getLoopPath() - Method in class org.intermine.pathquery.PathConstraintLoop
Returns the path that the constraint is constraining to.
getLoopQueryOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of loopQueryOp
getLoopQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the set of operators valid for loop constraints.
getLoopQueryValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of loopQueryValue
getLuceneName() - Method in class org.intermine.api.searchengine.ObjectValueContainer
generate the name to be used as a field name in lucene
getMailinglist() - Method in class org.intermine.web.struts.CreateAccountForm
 
getMainSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getMainSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter
Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.
getMainSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Converts a string describing the data source into a Source object suitable for passing to the store method as the main source.
getMaintainerEmail() - Method in class org.intermine.web.registry.model.Instance
 
getMaintainerGithubUrl() - Method in class org.intermine.web.registry.model.Instance
 
getMaintainerOrgName() - Method in class org.intermine.web.registry.model.Instance
 
getMaintainerUrl() - Method in class org.intermine.web.registry.model.Instance
 
getMainTitles() - Method in class org.intermine.web.logic.config.Type
 
getMap() - Method in class org.intermine.util.DynamicBean
Getter for the map, for testing purposes
getMapper() - Static method in class org.intermine.web.uri.ClassNameURIIdentifierMapper
Static method to create the instance of ClassNameURIIdentifierMapper class
getMapper(TagMapper.Field) - Static method in class org.intermine.api.profile.TagMapper
Get a tag mapper.
getMatchAndIssueIds() - Method in class org.intermine.api.bag.BagQueryResult
Get ids of all InterMineObjects returned that were matches or issues for this bag query lookup.
getMatcher() - Method in class org.intermine.webservice.server.lists.ListUploadService
Get the String Matcher for parsing the list of identifiers.
getMatches() - Method in class org.intermine.api.bag.BagQueryResult
Get any exact matches found by the queries [id -> [input strings].
getMatchIDs() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Get the encoded match ids (hidden form field).
getMatchOnFirst() - Method in class org.intermine.api.bag.BagQueryConfig
If flag is true, bagqueryrunner queries for identifier until match is found, returning only that first matching record.
getMaterialisedCollection() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Gets the collection if it is a real materialised collection.
getMax() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the maximum possible number of rows in the results.
getMax() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
maximum value to display.
getMax() - Method in class org.intermine.web.struts.WidgetForm
 
getMaxLimit() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxLimit() - Method in interface org.intermine.objectstore.ObjectStore
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxLimit() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxLimit() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get the maximum LIMIT that can be used in an SQL query without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in interface org.intermine.objectstore.ObjectStore
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxOffset() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get the maximum range start index a that can be accessed in a Results object without throwing an ObjectStoreLimitReachedException
getMaxParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
 
getMaxPValue() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
 
getMaxPValue() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getMaxQueryParseTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
getMaxQueryParseTime() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Get the maximum time in milliseconds that the optimiser should spend parsing a query from SQL string to an org.intermine.sql.Query object.
getMaxRetrievableIndex() - Method in class org.intermine.api.results.WebResults
Returns the ObjectStore's maximum allowable offset.
getMaxRetrievableIndex() - Method in interface org.intermine.api.results.WebTable
Return the maximum retrievable index for this PagedTable.
getMaxRetrievableIndex() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the maximum retrievable index for this PagedTable.
getMaxSize() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the current maximum number of rows in the results
getMaxTime() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxTime() - Method in interface org.intermine.objectstore.ObjectStore
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxTime() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
getMaxValues() - Method in class org.intermine.objectstore.ObjectStoreSummary
Return the configured maximum number of values to show in a dropdown.
getMd5checksum(String) - Static method in class org.intermine.metadata.Util
 
getMessage() - Method in class org.intermine.api.bag.BagQuery
Return the message that was passed to the constructor.
getMessage() - Method in class org.intermine.api.userprofile.PermanentToken
 
getMessage() - Method in class org.intermine.web.struts.ContactForm
 
getMessage() - Method in exception org.intermine.webservice.server.exceptions.ServiceException
getMessageElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getMessageElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getMessageFormat() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getMessageFormat() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getMessageFormat() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getMethodDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getMethodDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getMimeType() - Method in enum org.intermine.api.mines.ContentType
 
getMin() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the minimum possible number of rows in the results.
getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the cutoff value used to decide if a bag should be put in a table.
getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns the cutoff value used to decide if a bag should be put in a table.
getMine(String) - Method in class org.intermine.api.mines.FriendlyMineManager
 
getMineId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
 
getMineResultsLink(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Get the link for a query that shows the results in a mine.
getMineResultsLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Get a link that takes the user to a results page in the originating mine.
getMineResultsPath(String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
Get the link path for a query that shows the results in a mine.
getMineResultsPath(TemplateQuery, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Get a link that takes the user to a results page in the originating mine.
getMinimalPath() - Method in class org.intermine.pathquery.Node
 
getMinParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
 
getMinSize() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the current minimum number of rows in the results
getMissingTables() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the Set of table names which are tables missing from the database.
getMode() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Returns the optimiser mode of operation.
getModel() - Method in interface org.intermine.api.API
 
getModel() - Method in class org.intermine.api.InterMineAPI
 
getModel() - Method in class org.intermine.api.mines.LocalMine
 
getModel() - Method in interface org.intermine.api.mines.Mine
Get the main model associated with this application.
getModel() - Method in class org.intermine.api.mines.RemoteMine
 
getModel() - Method in class org.intermine.dataconversion.DataConverter
Return the data Model that was passed to the constructor.
getModel() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns the Model used.
getModel() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.metadata.ClassDescriptor
Return the model this class is a part of.
getModel() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the model.
getModel() - Method in interface org.intermine.objectstore.ObjectStore
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return the metadata associated with this ObjectStore
getModel() - Method in class org.intermine.pathquery.Path
Return the model that this path is created for.
getModel() - Method in class org.intermine.pathquery.PathQuery
Returns the Model object stored in this object.
getModel() - Method in class org.intermine.web.uri.InterMineLUIConverter
Returns the model
getModel() - Method in class org.intermine.xml.full.Item
Return the model that was passed to the constructor or set with setModel().
getModelFromClasspath(String, Properties) - Static method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Read the Model from the classpath.
getModelName() - Method in class org.intermine.task.ConverterTask
Return the model name
getModifiableEditableConstraints() - Method in class org.intermine.template.TemplateQuery
Returns the list of all editable constraints.
getMonkey() - Method in class org.intermine.web.struts.ContactForm
 
getMostPopularTemplateOrder(Integer) - Method in class org.intermine.api.template.TemplateManager
Return the list of public templates ordered by rank descendant.
getMostPopularTemplateOrder(String, String, Integer) - Method in class org.intermine.api.template.TemplateManager
Return the template list ordered by rank descendant for the user/sessionid specified in the input
getMrlv() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Returns the MultiRowLaterValue corresponding to this object.
getMultiValueAttribute() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Returs the value of multiValueAttribute
getMultiValueAttribute(String) - Method in class org.intermine.web.struts.TemplateForm
Returns the multivalueattribute given a key
getMultivalues() - Method in class org.intermine.web.logic.template.ConstraintInput
Return multivalues
getMultiValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the value collection if the constraint is a multivalue, otherwise return null.
getMultiValues() - Method in class org.intermine.web.struts.TemplateForm
Returns the multiValues
getMultiValues(String) - Method in class org.intermine.web.struts.TemplateForm
Get a multi value
getMultiValuesAsString() - Method in class org.intermine.web.logic.query.DisplayConstraint
If the constraint is a multivalue, returns the value collection represented as string separated by ', ', otherwise return an empty String.
getName() - Method in class org.intermine.api.beans.ObjectDetails
 
getName() - Method in class org.intermine.api.mines.LocalMine
 
getName() - Method in interface org.intermine.api.mines.Mine
 
getName() - Method in class org.intermine.api.mines.RemoteMine
 
getName() - Method in class org.intermine.api.profile.InterMineBag
Returns the value of name
getName() - Method in class org.intermine.api.profile.InvalidBag
 
getName() - Method in class org.intermine.api.profile.Profile
Return a first part of the username before the "@" sign (used in metabolicMine)
getName() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
getName() - Method in class org.intermine.api.profile.SavedQuery
Get the name of the saved query.
getName() - Method in class org.intermine.api.profile.StorableBag
 
getName() - Method in interface org.intermine.api.profile.Taggable
The name (or identifier) used as the primary key for storing this object.
getName() - Method in exception org.intermine.api.query.BagNotFound
 
getName() - Method in class org.intermine.api.results.Column
Get the name (title) of the column.
getName() - Method in class org.intermine.api.searchengine.KeywordSearchFacet
user-friendly name
getName() - Method in class org.intermine.api.searchengine.KeywordSearchFacetData
name of the facet (displayed on page)
getName() - Method in class org.intermine.api.searchengine.ObjectValueContainer
name
getName() - Method in class org.intermine.api.tracker.AbstractTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.KeySearchTracker
 
getName() - Method in class org.intermine.api.tracker.ListTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.LoginTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.QueryTracker
Return the tracker's name
getName() - Method in class org.intermine.api.tracker.TemplateTracker
Return the tracker's name
getName() - Method in interface org.intermine.api.tracker.Tracker
Return the tracker's name
getName() - Method in class org.intermine.api.userprofile.SavedBag
 
getName() - Method in class org.intermine.dataloader.Source
Getter for name.
getName() - Method in class org.intermine.metadata.ClassDescriptor
Returns the fully qualified class name described by this ClassDescriptor.
getName() - Method in class org.intermine.metadata.FieldDescriptor
Get the name of the described field.
getName() - Method in class org.intermine.metadata.Model
Get the name of this model - i.e.
getName() - Method in class org.intermine.metadata.PrimaryKey
Return the name
getName() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the field name
getName() - Method in class org.intermine.model.fulldata.Attribute
 
getName() - Method in class org.intermine.model.fulldata.Reference
 
getName() - Method in class org.intermine.model.fulldata.ReferenceList
 
getName() - Method in class org.intermine.pathquery.LogicExpression.Variable
Get variable name.
getName() - Method in class org.intermine.sql.Database
Gets the database name only, not the full URL.
getName() - Method in class org.intermine.sql.precompute.PrecomputedTable
Gets the name of this PrecomputedTable
getName() - Method in class org.intermine.sql.query.Field
Returns the name of the field.
getName() - Method in class org.intermine.sql.query.Table
Returns the name of the table
getName() - Method in class org.intermine.template.TemplateQuery
Get the query short name.
getName() - Method in class org.intermine.web.logic.aspects.Aspect
Get the name of the data set.
getName() - Method in class org.intermine.web.logic.aspects.AspectSource
Get the source name.
getName() - Method in class org.intermine.web.logic.results.ReportObjectField
Get field name
getName() - Method in class org.intermine.web.logic.template.TemplateResultInput
Returns template name.
getName() - Method in class org.intermine.web.registry.model.Instance
 
getName() - Method in class org.intermine.web.struts.ContactForm
 
getName() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getName() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getName() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getName() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getName() - Method in class org.intermine.web.struts.TemplateForm
Get the template name.
getName() - Method in class org.intermine.web.struts.TemplateSettingsForm
 
getName() - Method in class org.intermine.xml.full.Attribute
Get the name of this field
getName() - Method in class org.intermine.xml.full.Reference
Get the name of this field
getName() - Method in class org.intermine.xml.full.ReferenceList
Get the name of this field.
getNamespace() - Method in class org.intermine.web.registry.model.Instance
 
getNeighbours() - Method in class org.intermine.web.registry.model.Instance
 
getNewBagName() - Method in class org.intermine.api.bag.operations.BagOperation
 
getNewBagName() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Get the bag name.
getNewBagName() - Method in class org.intermine.web.struts.ModifyBagForm
Get the new bag name.
getNewBagName() - Method in class org.intermine.web.struts.SaveBagForm
Gets the value of newBagName
getNewBagType() - Method in class org.intermine.api.bag.operations.BagOperation
 
getNewBagType() - Method in class org.intermine.api.bag.operations.Intersection
 
getNewBagType() - Method in class org.intermine.api.bag.operations.RelativeComplement
 
getNewBagType() - Method in class org.intermine.api.bag.operations.SymmetricDifference
 
getNewBagType() - Method in class org.intermine.api.bag.operations.Union
 
getNewBagType() - Method in class org.intermine.web.struts.TriageBagForm
Get the new bag name.
getNewData() - Method in class org.intermine.dataloader.ObjectDescription
Returns the new data, which needs to be written back into the backing database.
getNewId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
 
getNewIds(InterMineObject, ObjectStore) - Method in interface org.intermine.api.bag.IdUpgrader
For the given object from an old ObjectStore, find the corresponding InterMineObjects in a new ObjectStore.
getNewIds(InterMineObject, ObjectStore) - Method in class org.intermine.api.bag.PkQueryIdUpgrader
For the given object from an old ObjectStore, find the corresponding InterMineObjects in a new ObjectStore.
getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService
Calculate the type of the new list.
getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService
 
getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListUploadService
 
getNewObject() - Method in class org.intermine.api.bag.ConvertedObjectPair
Get the newObject that was passed to the constructor.
getNewpassword() - Method in class org.intermine.web.struts.ChangePasswordForm
The new password
getNewpassword() - Method in class org.intermine.web.struts.PasswordResetForm
Gets the value of newpassword.
getNewpassword2() - Method in class org.intermine.web.struts.ChangePasswordForm
New password verification
getNewpassword2() - Method in class org.intermine.web.struts.PasswordResetForm
Gets the value of newpassword2.
getNewsPreview(String) - Static method in class org.intermine.dwr.AjaxServices
Work as a proxy for fetching remote file (RSS)
getNewTemplateQuery() - Method in class org.intermine.api.profile.TemplateQueryUpdate
 
getNewWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in interface org.intermine.objectstore.ObjectStore
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNewWriter() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Create an ObjectStoreWriter that writes into this ObjectStore.
getNextLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getNicerDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer
A JSP wants a nice name to display while the Displayer is loading
getNoConstraintsString() - Method in class org.intermine.pathquery.Path
Required for jsp
getNoResultsMessage() - Method in class org.intermine.web.tags.table.TableTag
 
getNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
 
getNoseyObjectStore(ObjectStore) - Method in class org.intermine.dataloader.BatchingFetcher
Returns an ObjectStore layered on top of the given ObjectStore, which reports to this fetcher which objects are being loaded.
getNotAnalysed() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getNotAnalysed() - Method in class org.intermine.web.logic.widget.Widget
 
getNullAttributes(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the attributes that, for a given class, are always null or empty.
getNullConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the null/not null constraint value.
getNullConstraint() - Method in class org.intermine.web.struts.TemplateForm
Get the nullConstraint
getNullConstraint(String) - Method in class org.intermine.web.struts.TemplateForm
Get a nullConstraint
getNullReferencesAndCollections(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
Get a list of the reference and collection names that, for a given class, are always null or empty.
getNumberOfBins() - Static method in class org.intermine.api.query.MainHelper.SummaryConfig
Returns the number of bins to split a histogram into.
getNumberOfMainTitlesToShow() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
 
getNumberOfTableRowsToShow() - Method in class org.intermine.web.logic.results.ReportObject
The said function will resolve the maximum number of rows to show (in Collections) from webProperties.
getNumberOpt() - Method in class org.intermine.web.struts.WidgetForm
 
getOAuth2Providers(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the set of accepted Open-ID providers.
getoBJECT() - Method in class org.intermine.api.userprofile.PermanentToken
 
getoBJECT() - Method in class org.intermine.api.userprofile.SavedBag
 
getoBJECT() - Method in class org.intermine.api.userprofile.SavedQuery
 
getoBJECT() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getoBJECT() - Method in class org.intermine.api.userprofile.Tag
 
getoBJECT() - Method in class org.intermine.api.userprofile.TemplateSummary
 
getoBJECT() - Method in class org.intermine.api.userprofile.UserProfile
 
getoBJECT() - Method in class org.intermine.model.fulldata.Item
 
getoBJECT() - Method in interface org.intermine.model.InterMineFastPathObject
Returns the NotXml serialised version of this object.
getoBJECT() - Method in interface org.intermine.model.InterMineObject
Returns the NotXml serialised version of this object.
getoBJECT() - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the NotXml serialised version of this object.
getObject() - Method in interface org.intermine.api.results.ResultCell
 
getObject() - Method in class org.intermine.api.results.ResultElement
Return the Object contained in this result element.
getObject() - Method in class org.intermine.api.searchengine.KeywordSearchResultContainer
object
getObject() - Method in class org.intermine.objectstore.proxy.ProxyReference
Gets the real object from the database.
getObject() - Method in class org.intermine.objectstore.query.ContainsConstraint
Returns the InterMineObject of the constraint.
getObject() - Method in class org.intermine.web.logic.config.InlineListObject
Fetch the InterMine object (if needed)
getObject() - Method in class org.intermine.web.logic.results.DisplayReference
Get the referenced object
getObject() - Method in class org.intermine.web.logic.results.ReportObject
Get InterMine object
getObject() - Method in class org.intermine.web.logic.TreeNode
Get the Object
getObject() - Method in class org.intermine.web.search.KeywordSearchResult
returns original intermine object
getObject() - Method in class org.intermine.webservice.server.core.TableCell
 
getObjectByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
getObjectByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore
Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
 
getObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Search database for object matching the given object id
getObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Get an object from the ObjectStore by giving an ID.
getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get an object from the ObjectStore by giving an ID.
getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get an object from the ObjectStore by giving an ID.
getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Search database for object matching the given object id and class
getObjectById(Integer, Class<? extends InterMineObject>) - Method in interface org.intermine.objectstore.ObjectStore
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
getObjectHits - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectId() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
Used from JSP
getObjectId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Get the object id for this trail element.
getObjectIdentifier() - Method in class org.intermine.api.userprofile.Tag
 
getObjectIdsFromSearch(InterMineAPI, String, int, Map<String, String>, List<Integer>, int) - Method in interface org.intermine.api.searchengine.KeywordSearchHandler
A method specifically designed to be used in SaveFromIdsToBagAction class
getObjectIdsFromSearch(InterMineAPI, String, int, Map<String, String>, List<Integer>, int) - Method in class org.intermine.api.searchengine.solr.SolrKeywordSearchHandler
 
getObjectOps - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectPrefetches - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjects() - Method in class org.intermine.api.beans.PartnerLink
 
getObjects(InterMineAPI, Set<Integer>) - Static method in class org.intermine.api.data.Objects
Resolve a set of ids to mapping from ID to object.
getObjectsByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
getObjectsByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore
Return an object from the objectstore that has the fields mentioned in the list set to the same values as the fields in the provided example object.
getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
 
getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
 
getObjectsByIds(Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectsByIds(Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStore
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Get an objects from the ObjectStore that have the IDs in the ids colection
getObjectStore() - Method in interface org.intermine.api.API
 
getObjectStore() - Method in class org.intermine.api.InterMineAPI
 
getObjectStore() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the production ObjectStore configured in webapp.os.alias.
getObjectStore() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Retrieve this Writer's ObjectStore.
getObjectStore() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Retrieve this Writer's ObjectStore.
getObjectStore() - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Returns the ObjectStore that this ParallelPrecomputer uses.
getObjectStore() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Retrieve this Writer's ObjectStore.
getObjectStore() - Method in interface org.intermine.objectstore.proxy.Lazy
Returns the ObjectStore that this lazy object will use
getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Returns the ObjectStore that this proxy will use
getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyReference
Returns the ObjectStore that this proxy will use
getObjectStore() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the ObjectStore that this object will use to access data.
getObjectStore() - Method in class org.intermine.objectstore.query.PendingClob
Returns the ObjectStore that this object will use to access data.
getObjectStore() - Method in class org.intermine.objectstore.query.Results
Returns the ObjectStore that this Results object will use
getObjectStore() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the ObjectStore that this ResultsBatches object will use
getObjectStore(String) - Static method in class org.intermine.objectstore.ObjectStoreFactory
Return an ObjectStore configured using properties
getObjectStoreSummary() - Method in interface org.intermine.api.API
 
getObjectStoreSummary() - Method in class org.intermine.api.InterMineAPI
 
getObjectStoreWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Returns the underlying ObjectStoreWriter.
getObjectStoreWriter() - Method in class org.intermine.postprocess.PostProcessor
Return the ObjectStoreWriter that was passed to the constructor.
getObjectStoreWriter(String) - Static method in class org.intermine.objectstore.ObjectStoreWriterFactory
Return an ObjectStoreWriter configured using properties file
getObjectSummaryFields() - Method in class org.intermine.web.logic.results.ReportObject
A listing of object fields as pieced together from the various ReportObject methods
getObjectTagNames(String, String, String) - Method in class org.intermine.api.profile.TagManager
Returns names of tagged tags for specified object.
getObjectTagNames(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
Returns names of tagged tags for specified object.
getObjectTags(String, String) - Static method in class org.intermine.dwr.AjaxServices
Returns all tags by which is specified object tagged.
getObjectTags(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
Get the tags for a specific object.
getOffset() - Method in class org.intermine.objectstore.query.ClobAccess
Return the offset into the underlying clob that this object is using.
getOffset() - Method in class org.intermine.objectstore.query.PendingClob
Return the offset into the underlying clob that this object is using.
getOffset() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Getter for offset.
getOffset() - Method in class org.intermine.sql.query.Query
Gets the OFFSET number for this query.
getOffsetConstraint(Query, QueryOrderable, Object, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Create a constraint to add to the main query to deal with offset - this is based on the first element in the order by (field) and a given value (x).
getOldId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
 
getOldObject() - Method in class org.intermine.api.bag.ConvertedObjectPair
Get the objObject that was passed to the constructor.
getOldpassword() - Method in class org.intermine.web.struts.ChangePasswordForm
The old password
getOnClick() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
 
getOp() - Method in class org.intermine.objectstore.query.Constraint
Get op of constraint
getOp() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Returns the op of this combination.
getOp() - Method in class org.intermine.pathquery.PathConstraint
Returns the operation that this constraint performs.
getOp() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get a string representation of the constraint operation.
getOpened() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns true if disclosure is opened else false.
getOpenIdProviders(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the set of accepted Open-ID providers.
getOperands() - Method in class org.intermine.sql.query.Function
Returns the List of operands of this function.
getOperation() - Method in class org.intermine.objectstore.query.QueryExpression
Returns the operation.
getOperation() - Method in class org.intermine.objectstore.query.QueryFunction
Returns the operation of the function.
getOperation() - Method in class org.intermine.sql.query.Constraint
Returns the operation of the constraint.
getOperation() - Method in class org.intermine.sql.query.Function
Returns the operation of the function.
getOperation() - Method in class org.intermine.template.TemplateValue
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListDifferenceService
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListIntersectionService
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService
Get the BagOperation that will create the list.
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListSubtractionService
 
getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListUnionService
 
getOperationButton() - Method in class org.intermine.web.struts.SaveBagForm
 
getOperationCode() - Method in class org.intermine.api.bag.operations.BagOperation
 
getOperationCode() - Method in class org.intermine.api.bag.operations.Intersection
 
getOperationCode() - Method in class org.intermine.api.bag.operations.RelativeComplement
 
getOperationCode() - Method in class org.intermine.api.bag.operations.SymmetricDifference
 
getOperationCode() - Method in class org.intermine.api.bag.operations.Union
 
getOperator() - Method in class org.intermine.pathquery.LogicExpression.And
Override to provide text symbol for this operator.
getOperator() - Method in class org.intermine.pathquery.LogicExpression.Operator
Override to provide text symbol for this operator.
getOperator() - Method in class org.intermine.pathquery.LogicExpression.Or
Override to provide text symbol for this operator.
getOperator() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the operator.
getOpForIndex(Integer) - Static method in class org.intermine.metadata.ConstraintOp
Convert an index to a ConstraintOp (Only for use in webapp)
getOptimised() - Method in class org.intermine.sql.precompute.OptimiserCacheLine
Gets the optimised query (minus the LIMIT and OFFSET) from this cache line.
getOptionalParameter(String) - Method in class org.intermine.webservice.server.WebService
Get a parameter this service deems to be optional, or null.
getOptionalParameter(String, String) - Method in class org.intermine.webservice.server.WebService
Get a parameter this service deems to be optional, or the default value.
getOptions() - Method in class org.intermine.web.task.IssueTokenTask
 
getOptions() - Method in class org.intermine.web.task.KeyStoreTask
Get the options as configured for this task
getOptionsTileName() - Method in class org.intermine.web.logic.config.TableExportConfig
Get the optionsTileName of this TableExportConfig - ie.
getOrderBy() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getOrderBy() - Method in class org.intermine.objectstore.query.Query
Gets the ORDER BY clause of this Query
getOrderBy() - Method in class org.intermine.pathquery.PathQuery
Returns the current order by list.
getOrderBy() - Method in class org.intermine.sql.query.Query
Gets the list of fields forming the ORDER BY clause of this query.
getOrderByAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getOrderByField() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns the name of the order by field, if it exists.
getOrderPath() - Method in class org.intermine.pathquery.OrderElement
Returns the path of this OrderElement.
getOrganisms() - Method in class org.intermine.web.registry.model.Instance
 
getOrig() - Method in class org.intermine.dataloader.ObjectDescription
Returns the original data, as reflected in the backing database.
getOrigin() - Method in class org.intermine.api.search.OriginatingEvent
Get the web searchable involved in this event.
getOriginal() - Method in class org.intermine.sql.precompute.OptimiserCacheLine
Returns the original SQL string.
getOriginalSql() - Method in class org.intermine.sql.precompute.PrecomputedTable
Returns the original SQL text stored in the index for this PrecomputedTable
getOriginalValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
getOrigType() - Method in class org.intermine.web.logic.query.MetadataNode
Returns the type of this node if it did not have a subclass constraint.
getOs() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the ObjectStore that this object uses.
getOsb() - Method in class org.intermine.api.profile.InterMineBag
Returns the ObjectStoreBag, so that elements can be added and removed.
getOsb() - Method in class org.intermine.api.profile.InvalidBag
 
getOsb() - Method in class org.intermine.api.profile.StorableBag
Return a reference to the object store bag contained in the production database.
getOsb() - Method in class org.intermine.objectstore.query.BagConstraint
Get the ObjectStoreBag.
getOsb() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns the ObjectStoreBag.
getOsbId() - Method in class org.intermine.api.userprofile.SavedBag
 
getOsName() - Method in class org.intermine.task.ConverterTask
Return the object store alias set by setOsName().
getOuterInSummary() - Method in class org.intermine.web.logic.config.FieldConfig
 
getOuterJoinGroup() - Method in class org.intermine.pathquery.Node
Returns a String describing the outer join group that this Node is in.
getOuterJoinGroup(String) - Static method in class org.intermine.pathquery.Node
Returns a String describing the outer join group that the given path string is in.
getOuterJoinGroup(String) - Method in class org.intermine.pathquery.PathQuery
Returns the outer join group that the given path is in.
getOuterJoinGroups() - Method in class org.intermine.pathquery.PathQuery
Returns the outer join groups map for this query, if the query verifies correctly.
getOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery
Returns an unmodifiable Map which is a copy of the current outer join status of this query at the time of execution of this method.
getOuterJoinStatus(String) - Method in class org.intermine.pathquery.PathQuery
Returns the outer join status of the last part of a given path in this query.
getOuterMap() - Method in class org.intermine.pathquery.PathQuery
Returns a Map from path to TRUE for all paths that are outer joined.
getOutputInfo(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Return the key value pairs to put in the webservice result
getOutro(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getOutsideOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the OUTSIDE options are the negation of the WITHIN options, with the right and left fields swapped.
getOutwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil
Creates a column name for the "outward" key of a many-to-many collection descriptor.
getOverlapsOptions() - Method in class org.intermine.api.query.range.AbstractHelper
By default the OVERLAPS options are the same as the WITHIN options with the right and left fields swapped.
getPackageName() - Method in class org.intermine.metadata.Model
Return name of the model's package.
getPackageName() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Get the package name
getPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the page index.
getPagedTable() - Method in class org.intermine.web.logic.query.PageTableQueryMonitor
Return the PagedTable that was passed to the constructor.
getPagedTable(HttpServletRequest, HttpSession) - Method in class org.intermine.web.struts.TableExportAction
 
getPageLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getPageName() - Method in class org.intermine.web.struts.ModifyBagForm
 
getPageName() - Method in class org.intermine.web.struts.ModifyTemplateForm
 
getPageSize() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the page size of the current page
getPageSize() - Method in class org.intermine.web.struts.ChangeTableSizeForm
Get the page size
getPageSize() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getParam() - Method in class org.intermine.objectstore.query.QueryFunction
Returns the QueryEvaluable of the function.
getParam2() - Method in class org.intermine.objectstore.query.QueryFunction
Returns the second evaluable, where these is one.
getParameter(String) - Method in class org.intermine.webservice.server.jbrowse.Command
 
getParameter(String, String) - Method in class org.intermine.webservice.server.jbrowse.Command
 
getParameterJson() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the parameters for this displayer as a JSONObject
getParameterName() - Method in class org.intermine.web.logic.template.ConstraintInput
 
getParameters() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Get the parameters
getParameters() - Method in class org.intermine.web.util.AttributeLinkURL
 
getParameterString() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
A JSON string representing custom parameters for this displayer.
getParams() - Method in class org.intermine.web.logic.config.Displayer
Return the parameters stored in this Displayer.
getParent() - Method in class org.intermine.objectstore.query.OverlapRange
Returns the parent parameter.
getParent() - Method in class org.intermine.pathquery.Node
Get the parent node.
getParent() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns a new DisplayPath that represents the parent path, or null if this path is just a root class.
getParentType() - Method in class org.intermine.pathquery.Node
Type of parent node.
getParentType() - Method in class org.intermine.web.logic.results.InlineResultsTable
Get the parent's type
getPartialString(List<String>) - Method in class org.intermine.pathquery.LogicExpression
Produce an expression for this branch of the tree displaying only the children containing the variable in input
getPassword() - Method in class org.intermine.api.profile.Profile
Get the value of password
getPassword() - Method in class org.intermine.api.userprofile.UserProfile
 
getPassword() - Method in class org.intermine.sql.Database
Gets the password for this Database
getPassword() - Method in class org.intermine.web.struts.CreateAccountForm
 
getPassword() - Method in class org.intermine.web.struts.LoginForm
Gets the value of password
getPassword() - Method in class org.intermine.webservice.server.WebServiceInput
 
getPassword(String) - Method in class org.intermine.api.profile.ProfileManager
Get a user's password A check should be made prior to this call to ensure a Profile exists
getPassword2() - Method in class org.intermine.web.struts.CreateAccountForm
 
getPath() - Method in class org.intermine.api.results.Column
Get the Path set by setPath().
getPath() - Method in interface org.intermine.api.results.ResultCell
 
getPath() - Method in class org.intermine.api.results.ResultElement
 
getPath() - Method in class org.intermine.pathquery.PathConstraint
Returns the path that this constraint is attached to.
getPath() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
The path that should be in the title, with style removed.
getPath() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getPath() - Method in class org.intermine.web.logic.query.DisplayConstraint
Get a representation of the path that is being constraint.
getPath() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Return the underlying path object.
getPath() - Method in class org.intermine.web.logic.results.InlineList
 
getPath() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of path
getPath() - Method in class org.intermine.webservice.server.core.TableCell
 
getPathConstraint() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
Returns the pathConstraint based on the enrichmentIdentifier will be applied on the pathQUery
getPathConstraints() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getPathConstraintsForView() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getPathId() - Method in class org.intermine.web.logic.template.ConstraintInput
 
getPathQuery() - Method in class org.intermine.api.profile.SavedQuery
Get the saved PathQuery.
getPathQuery() - Method in class org.intermine.api.results.WebResults
 
getPathQuery() - Method in interface org.intermine.api.results.WebTable
Get the PathQuery associated with this WebTable
getPathQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
 
getPathQuery() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getPathQuery() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
Returns the pathquery based on the views set in config file and the bag constraint Executed when the user selects any item in the matches column in the enrichment widget.
getPathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget
Returns the pathquery based on the views set in config file and the bag constraint.
getPathQuery() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getPathQuery() - Method in class org.intermine.web.logic.widget.TableWidget
 
getPathQuery() - Method in class org.intermine.web.logic.widget.Widget
Return the PathQuery generated dynamically by the attribute views in the configuration file
getPathQueryExecutor() - Method in class org.intermine.api.InterMineAPI
 
getPathQueryExecutor() - Static method in class org.intermine.api.query.PathQueryAPI
Returns a PathQueryExecutor, using properties.
getPathQueryExecutor() - Method in class org.intermine.web.uri.InterMineLUIConverter
Returns the PathQueryExecutor
getPathQueryExecutor() - Method in class org.intermine.webservice.server.query.result.QueryResultService
Return the PathQueryExecutor
getPathQueryExecutor(Profile) - Method in interface org.intermine.api.API
 
getPathQueryExecutor(Profile) - Method in class org.intermine.api.InterMineAPI
 
getPathQueryForMatches() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
Returns the pathquery based on the startClassDisplay, constraintsForView set in config file and the bag constraint Executed when the user click on the matches column in the enrichment widget.
getPathsString() - Method in class org.intermine.web.struts.TableExportForm
Get the paths string in the format: "Class.field Class.field2 Class.ref.field"
getPathString() - Method in class org.intermine.pathquery.Node
Gets the String value of pathString of this node (eg.
getPathString() - Method in exception org.intermine.pathquery.PathException
Return the path String that was passed to the constructor.
getPathString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the full path string for this path.
getPathString() - Method in class org.intermine.web.logic.results.ReportObjectField
Get a path string to fetch field descriptions
getPathStrings() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
Comma separated list of path strings to appear in the widget, ie Employee.firstName, Employee.lastName
getPathToBagQueryResult() - Method in class org.intermine.api.results.WebResults
Returns the pathToBagQueryResult Map.
getPathToBagQueryResult() - Method in interface org.intermine.api.results.WebTable
Returns the pathToBagQueryResult Map.
getPathToIndex() - Method in class org.intermine.api.results.WebResults
Create a map from string paths to index of QueryNodes in the ObjectStore query
getPathToQueryNode() - Method in class org.intermine.api.results.WebResults
Returns the pathToQueryNode Map.
getPathUpdated(String, Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
Update the path given in input with the renamed classes and fields
getPathWithoutSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
 
getPerlWSModuleVer() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getPermanentBaseURI() - Method in class org.intermine.web.logic.PermanentURIHelper
Returns the permanent base URI
getPermanentBaseURL() - Method in class org.intermine.web.util.URLGenerator
Generates base url.
getPermanentTokens() - Method in class org.intermine.api.userprofile.UserProfile
 
getPermanentURI(InterMineLUI) - Method in class org.intermine.web.logic.PermanentURIHelper
Returns the permanent URI given the intermine lui, e.g.
getPermanentURL(Integer, Profile) - Method in class org.intermine.web.logic.PermanentURIHelper
Returns the permanent URL given the class name and the primary identifier The permanent URL is used in the Share button, to set the url in Schema.org
getPermanentURL(InterMineLUI) - Method in class org.intermine.web.logic.PermanentURIHelper
Returns the permanent URL given the lui The permanent URL is used in the Share button, to set the url in Schema.org
getPermission() - Method in class org.intermine.webservice.server.WebService
Return the permission object representing the authorisation state of the request.
getPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Authenticate a user using username/password credentials.
getPermission(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Get the level of permission granted by an access token.
getPermission(PermanentToken, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
 
getPlacement() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the data category name under which this displayer should appear.
getPlatform() - Method in class org.intermine.sql.Database
Gets the platform of this Database
getPoints() - Method in class org.intermine.web.search.KeywordSearchResult
return points
getPopularTemplatesByAspect(String, int) - Method in class org.intermine.api.template.TemplateManager
Return the template list for a particular aspect given in input, ordered by rank descendant
getPopularTemplatesByAspect(String, int, String, String) - Method in class org.intermine.api.template.TemplateManager
Return the template list for a particular aspect, ordered by rank descendant for the user/sessionid specified in the input
getPopulatedTemplate(TemplateQuery, Map<String, List<TemplateValue>>) - Static method in class org.intermine.api.template.TemplatePopulator
Given a template and a map of values for editable constraints on each editable node create a copy of the template query with the values filled in.
getPopulationAnnotations() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the count of of each attribute value in the population, e.g.
getPopulationBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
Get the bag's name for reference population
getPopulationCount() - Method in class org.intermine.web.logic.widget.Widget
 
getPopulationIds() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
getPopulationInfo() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
Return a population info instance contanining the population size, N (In our example this is the total number of companies, or possibly the total number of companies that have at least one Department) and the average length of the genes in the whole population.
getPopulationInfo() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getPopulationQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
 
getPopulationTotal() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the number of items in the database (or background population) that were annotated.
getPossibleValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
Values to populate a dropdown for the path if possible values are available.
getPossibleValues(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
Returns a Map of the possible values for editable nodes on a template query.
getPossibleValues(ApiTemplate, String) - Method in class org.intermine.api.template.TemplateSummariser
Returns the possible values that a particular path in a template query can take, for dropdowns on template forms.
getPrecomputedSummarisedInfo(Profile, HttpSession, HttpServletRequest) - Static method in class org.intermine.web.struts.MyMineController
Retrieve the information about precomputed and summarised templates for the given profile, and store it into the request
getPrecomputedTables() - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Get all the precomputed tables in the underlying database.
getPrecomputeQuery(TemplateQuery, List) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.
getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.
getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String, InterMineAPI) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
Get an ObjectStore query to precompute this template - remove editable constraints and add fields to select list if necessary.
getPrecomputer(ObjectStoreInterMineImpl) - Method in class org.intermine.task.PrecomputeTask
Create a ParallelPrecomputer.
getPrecomputeTemplateQueries() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Get the super user's public templates
getPreDefaultBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig
Return a List of BagQuerys for the given type that should be run before the default query
getPreferences() - Method in class org.intermine.api.profile.Profile
Get the object representing the preferences of this user.
getPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager
 
getPreferences(Profile) - Method in class org.intermine.api.profile.ProfileManager
Get the preferences for a profile.
getPrefix() - Method in class org.intermine.pathquery.Node
Gets the value of prefix
getPrefix() - Method in class org.intermine.pathquery.Path
Return a Path object that represents the prefix of this path, ie this Path without the last element.
getPrefix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
A prefix that may be an HTML tag to appear before this part in the title.
getPrefix() - Method in class org.intermine.web.logic.results.InlineList
 
getPreviousLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
getPrimaryKeys(ClassDescriptor) - Static method in class org.intermine.metadata.PrimaryKeyUtil
Retrieve a map from key name to PrimaryKey object.
getPrimaryKeys(ClassDescriptor, Source, ObjectStore) - Static method in class org.intermine.dataloader.DataLoaderHelper
Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor.
getPrintWriterForClient(HttpServletRequest, OutputStream) - Static method in class org.intermine.web.logic.export.http.HttpExportUtil
 
getPriorities(Class<? extends FastPathObject>, String) - Method in class org.intermine.dataloader.PriorityConfig
Returns a List of data source names representing the priority for a given class and fieldname pair.
getProblems() - Method in exception org.intermine.api.query.codegen.InvalidQueryException
 
getProblems() - Method in class org.intermine.metadata.Model
Return a list of problems with the model or an empty list.
getProcessingInstruction() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getProcessingInstruction() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getProcessor() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
getProcessor() - Method in class org.intermine.webservice.server.widget.GraphService
 
getProcessor() - Method in class org.intermine.webservice.server.widget.TableWidgetService
 
getProcessor() - Method in class org.intermine.webservice.server.widget.WidgetService
 
getProductionObjectStore() - Method in class org.intermine.api.profile.ProfileManager
Return the ObjectStore that was passed to the constructor.
getProfile() - Method in class org.intermine.api.bag.operations.BagOperation
 
getProfile() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
getProfile() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the superuser Profile.
getProfile() - Method in class org.intermine.api.search.SearchRepository
Get the profile that this repository belongs to.
getProfile() - Method in class org.intermine.webservice.server.user.DeletionToken
 
getProfile(int) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using an ID
getProfile(String) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username
getProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username and password.
getProfile(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username, password and the classKeys.
getProfile(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Get a user's Profile using a username
getProfile(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns user profile saved in session.
getProfileId() - Method in class org.intermine.api.profile.StorableBag
 
getProfileManager() - Method in interface org.intermine.api.API
 
getProfileManager() - Method in class org.intermine.api.InterMineAPI
 
getProfileManager() - Method in class org.intermine.api.profile.Profile
Return the ProfileManager that was passed to the constructor.
getProfileManager() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the ProfileManager configured in webapp.userprofile.os.alias.
getProfileObjectStoreWriter() - Method in class org.intermine.api.profile.ProfileManager
Return the userprofile ObjectStoreWriter that was passed to the constructor.
getProfileUserName(int) - Method in class org.intermine.api.profile.ProfileManager
Return the name of the user with the given internal DB id.
getProfileUserNames() - Method in class org.intermine.api.profile.ProfileManager
Return a List of the usernames in all of the stored profiles.
getProjectTitle() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getProperties() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the properties accessible for this system.
getProperties() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getProperties() - Static method in class org.intermine.util.PropertiesUtil
Returns all InterMine properties
getPropertiesOrigins(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Gets the origins map from the servlet context.
getPropertiesStartingWith(String) - Static method in class org.intermine.util.PropertiesUtil
Returns all global Properties that begin with str
getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.metadata.Util
Returns all Properties in props that begin with str
getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.util.PropertiesUtil
Returns all Properties in props that begin with str
getProperty() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
Get the constraint index to be put in form when this op is selected.
getProperty(String) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
getProperty(String) - Method in class org.intermine.webservice.server.WebService
Get a configuration property by name.
getProperty(String, String) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Get a configured property for which an accessor does not exist.
getProperty(String, String) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
getPropertyDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
 
getPropertyDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
 
getPropertyName() - Method in class org.intermine.web.struts.EditPropertiesForm
 
getPropertyValue() - Method in class org.intermine.web.struts.EditPropertiesForm
 
getProvider() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
getProxyGetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the proxyGetter Method.
getProxyGetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the proxyGetter for the field name
getProxySetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the proxySetter Method.
getProxySetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the proxySetter for the field name
getPublicId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Returns id of object.
getPublicTagNames(String, String) - Method in class org.intermine.api.profile.TagManager
Get the tags for an object that are visible to all users.
getPublicTagNames(Taggable) - Method in class org.intermine.api.profile.TagManager
Get all the tags that all users have access to.
getPublicTagNames(ClassDescriptor) - Method in class org.intermine.api.profile.TagManager
Get all the tags that all users have access to.
getPValue() - Method in class org.intermine.web.struts.WidgetForm
 
getPValues() - Method in class org.intermine.web.logic.widget.EnrichmentResults
Get the probability of enrichment for each attribute value found in the sample.
getQcb() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Gets the QueryClassBag of this QueryReference.
getQcObject() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Gets the InterMineObject of this QueryReference.
getQcType() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Returns the type of the queryclass of this reference
getQcType() - Method in class org.intermine.objectstore.query.QueryReference
Returns the type of the queryclass of this reference
getQope() - Method in class org.intermine.objectstore.query.PathExpressionField
Returns the QueryObjectPathExpression.
getQualifiedType() - Method in class org.intermine.api.profile.InterMineBag
Get the fully qualified type of this bag
getQualifiedTypeName(String) - Method in class org.intermine.metadata.Model
Return the qualified name of the given unqualified class name.
getQueried(String) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns a Set of values that have been tested for a particular class and fieldname.
getQueries() - Method in class org.intermine.sql.precompute.BestQueryStorer
Gets the set of queries added to this object
getQuery() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getQuery() - Method in class org.intermine.api.results.ExportResultsIterator
 
getQuery() - Method in class org.intermine.api.userprofile.SavedQuery
 
getQuery() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Returns the Query used by this LazyCollection
getQuery() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Returns the Query used by this LazyCollection
getQuery() - Method in class org.intermine.objectstore.query.Results
Get the Query that produced this Results object.
getQuery() - Method in class org.intermine.objectstore.query.ResultsBatches
Get the Query that produced this ResultsBatches object.
getQuery() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the query.
getQuery() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
Get the query.
getQuery() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
Returns the query.
getQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the Query of this Candidate, converting from a String if necessary.
getQuery() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Getter for the stripped query.
getQuery() - Method in class org.intermine.sql.precompute.PrecomputedTable
Gets the Query that is materialised in this PrecomputedTable
getQuery() - Method in class org.intermine.sql.query.SubQuery
Returns the query contained in the subquery.
getQuery() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
Return the Query that was passed to the constructor.
getQuery() - Method in class org.intermine.web.struts.QueryForm
 
getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilder
Returns parsed PathQuery.
getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
For the purposes of exporting into JSON objects the view must be: Ordered by length, such that Company.departments.name precedes Company.departments.employees.name Be constituted so that every class has an attribute on it, root class included, and every reference along the way.
getQuery(boolean, List<String>) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore
 
getQuery(String) - Method in interface org.intermine.api.query.QueryStore
 
getQuery(String, List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
Returns the relevant query.
getQuery(Collection<? extends InterMineObject>) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the Query that will fetch the data represented by this object, given a Collection of objects to fetch it for.
getQuery(Collection<Integer>, boolean) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the Query that will fetch the data represented by this object, given a Collection of objects to fetch it for.
getQuery(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery
Return the Query that was passed to the constructor.
getQuery(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the PathQuery on the session.
getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.query.QueryToListService
Get the pathquery to use for this request.
getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.template.TemplateToListService
 
getQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the PathQuery on the session.
getQuery(PathQuery, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService
Get the Objectstore Query to run to generate the list.
getQueryBuilder() - Method in class org.intermine.web.struts.ImportQueriesForm
Get the queryBuilder field.
getQueryBuilder(String) - Method in class org.intermine.webservice.server.query.AbstractQueryService
Get a path-query builder.
getQueryClass() - Method in class org.intermine.objectstore.query.ContainsConstraint
Returns the QueryClass of the constraint.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the QueryClass of which the field is a member.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryForeignKey
Gets the QueryClass of which this reference is an member.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the QueryClass of which the field is a member.
getQueryClass() - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect
Returns the QueryClass of which the field is a member.
getQueryClass() - Method in class org.intermine.objectstore.query.QueryReference
Gets the QueryClass of which this reference is an member.
getQueryClass() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the QueryClass the query is compare with
getQueryDesc() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
 
getQueryEvaluable() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the QueryEvaluable the query is compared with
getQueryFields(QueryEvaluable) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Descends into QueryExpression and QueryFunction objects to find all instances of QueryField.
getQueryForWildcards(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery
Return a Query to fetch bag contents for wildcards.
getQueryInfo(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Retrieve an entry from the infoCache.
getQueryMap() - Method in class org.intermine.web.struts.ImportQueriesForm
Return a Map from query name to Query object.
getQueryMap(BagManager, Profile) - Method in class org.intermine.web.struts.TemplatesImportForm
Return a Map from template name to Template object.
getQueryName() - Method in class org.intermine.web.struts.SaveQueryForm
Get the query name
getQueryNode() - Method in class org.intermine.objectstore.query.BagConstraint
Get the QueryNode.
getQueryOrderable() - Method in class org.intermine.objectstore.query.OrderDescending
Return the encapsulated QueryOrderable.
getQueryStore() - Method in class org.intermine.api.InterMineAPI
 
getQueryString() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Get the query String NOTE: this will be unvalidated
getQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the String query of this Candidate, converting from Query if necessary.
getQueryString() - Method in class org.intermine.webservice.server.query.QueryUploadService
Get the XML which represents the queries to be saved.
getQueryTime() - Method in class org.intermine.objectstore.intermine.ExtraQueryTime
Returns the total amount of time spent in extra queries, in milliseconds.
getQueryToExecute() - Method in class org.intermine.pathquery.PathQuery
Get the PathQuery that should be executed.
getQueryToExecute() - Method in class org.intermine.template.TemplateQuery
Fetch the PathQuery to execute for this template.
getQueryTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getQueryTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getQueryWithDefaultView(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Used for making a query for a reference or collection.
getQueryXml() - Method in class org.intermine.webservice.server.query.QueryRequestParser
Get query XML from a request.
getRangeConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the range constraint value.
getRangeLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the value of rangeLabel
getRangeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getRangeQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the set of operators valid for range constraints.
getRanges() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getRangeSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getRank(TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker
Return the rank for each public template.It represents a relationship between the templates executions; a template with rank 1 has been executed more than a template with rank 2.
getRank(TemplateManager) - Method in class org.intermine.api.tracker.TrackerDelegate
Return the rank associated to the templates
getRank(TemplateManager, String) - Method in class org.intermine.api.tracker.TemplateTracker
get rank for a specific template
getRank(TemplateManager, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Return the rank associated to a single template
getRatDiseases(String) - Static method in class org.intermine.dwr.AjaxServices
Return list of disease ontology terms associated with list of provided rat genes.
getRawOutput() - Method in class org.intermine.webservice.server.WebService
Get access to the underlying print-writer.
getReader(HttpServletRequest) - Method in class org.intermine.webservice.server.lists.ListUploadService
Get the reader for the identifiers uploaded with this request.
getReference() - Method in class org.intermine.objectstore.query.ContainsConstraint
Returns the QueryReference of the constraint.
getReference(String) - Method in class org.intermine.xml.full.Item
Get a named reference.
getReferencedClassDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor
Returns a ClassDescriptor for the object referenced by this field.
getReferencedClassName() - Method in class org.intermine.metadata.ReferenceDescriptor
Returns the class name of the object referenced by this field.
getReferenceDescriptorByName(String) - Method in class org.intermine.metadata.ClassDescriptor
Gets a ReferenceDescriptor for a field of the given name.
getReferenceDescriptorByName(String, boolean) - Method in class org.intermine.metadata.ClassDescriptor
Gets a ReferenceDescriptor for a field of the given name.
getReferenceDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Gets the descriptors for the external object references in this class.
getReferenceLists() - Method in class org.intermine.webservice.server.lists.ListInput
 
getReferences() - Method in class org.intermine.model.fulldata.Item
 
getReferences() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields
Returns the Set of references
getReferences() - Method in class org.intermine.xml.full.Item
Get all the references.
getRefId() - Method in class org.intermine.model.fulldata.Reference
 
getRefId() - Method in class org.intermine.xml.full.Reference
Get the refId of this field
getRefIds() - Method in class org.intermine.model.fulldata.ReferenceList
 
getRefIds() - Method in class org.intermine.xml.full.ReferenceList
Get the references in this collection.
getRefsAndCollections() - Method in class org.intermine.web.logic.results.ReportObject
Get all the reference and collection fields and values for this object
getRelease() - Static method in class org.intermine.web.filters.ReleaseEtagFilter
 
getReleaseVersion() - Method in class org.intermine.api.mines.LocalMine
 
getReleaseVersion() - Method in interface org.intermine.api.mines.Mine
 
getReleaseVersion() - Method in class org.intermine.api.mines.RemoteMine
 
getReleaseVersion() - Method in class org.intermine.web.registry.model.Instance
 
getRelevantConstraints() - Method in class org.intermine.pathquery.PathQuery
 
getRelevantConstraints() - Method in class org.intermine.template.TemplateQuery
 
getRenamedBags() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Get the mapping from old to new names.
getRenamedClasses() - Method in class org.intermine.api.profile.ModelUpdate
Return a map containing the couple previous class and new class
getRenamedFields() - Method in class org.intermine.api.profile.ModelUpdate
Return a map containing the couple previousClass.previuosField and new field
getRenamedTemplates() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
Get the names of all the templates that failed.
getReplacedFieldExprs() - Method in class org.intermine.web.displayer.ReportDisplayer
Get a list of field names and paths that should be replaced by this displayer - i.e.
getReplacedFieldExprs() - Method in class org.intermine.web.logic.results.ReportObject
Get fields and paths that are replaced by custom report displayers and should not be shown in the report page.
getReplacedFieldNames() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the names of fields this displayer replaces.
getReplacesFields() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the comma separated list of field names that should not be displayed on the report page when this displayer is used.
getReportDisplayer(String) - Method in class org.intermine.web.logic.results.ReportObject
Give us a displayer by a specific name, called by AjaxServices
getReportDisplayerByName(String, String) - Method in class org.intermine.web.displayer.DisplayerManager
Get a specific ReportDisplayer by its name for a given ReportObject type
getReportDisplayerConfigs() - Method in class org.intermine.web.logic.config.WebConfig
Fetch config for the report page displayers.
getReportDisplayers() - Method in class org.intermine.web.logic.results.ReportObject
Get a map from placement (header, summary or a data category) to custom report displayers for that placement.
getReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager
Get a map from placement string (a data category or summary) to displayers for the given type.
getReportObject(HttpSession, String) - Method in class org.intermine.web.struts.ModifyDetails
Get a ReportObject from the session given the object id as a string.
getReportObjects(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Return the ReportObjects Map from the session or create and return it if it doesn't exist.
getReportPageTemplatesForAspect(String, Set<String>) - Method in class org.intermine.api.template.TemplateManager
Get a list of template queries that should appear on report pages for the given type under the specified aspect.
getRequest() - Static method in class org.intermine.objectstore.query.PrefetchManager
Returns a request for a thread to service.
getRequestFileName() - Method in class org.intermine.webservice.server.WebService
If the request has a filename parameter then use that for the fileName, otherwise use the default fileName
getRequiredParameter(String) - Method in class org.intermine.webservice.server.WebService
Get a parameter this service deems to be required.
getResponseType() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getResponseType() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getResponseType() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getResult() - Method in interface org.intermine.api.idresolution.Job
 
getResult() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getResult() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getResultElementRows() - Method in class org.intermine.web.logic.results.InlineResultsTable
Main method used from report to resolve a tablefull of ResultElements
getResultElements(int) - Method in class org.intermine.api.results.WebResults
Return a List containing a ResultElement object for each element in the given row.
getResultElements(int) - Method in interface org.intermine.api.results.WebTable
Return a List containing a ResultElement object for each element given in the given row.
getResultRows(PagedTable, HttpServletRequest) - Method in class org.intermine.web.logic.export.http.HttpExporterBase
 
getResults() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
 
getResults() - Method in class org.intermine.api.searchengine.InterMineResultsContainer
the results
getResults() - Method in interface org.intermine.web.logic.widget.DataSetLdr
Get the Results object
getResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
getResults() - Method in class org.intermine.web.logic.widget.GraphWidget
 
getResults() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
 
getResults() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
getResults() - Method in class org.intermine.web.logic.widget.TableWidget
 
getResults() - Method in class org.intermine.web.logic.widget.Widget
Return the result that represents the data from this widget.
getResults() - Method in class org.intermine.webservice.server.output.MemoryOutput
Returns results added to output
getResultsAsList() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getResultsBatches() - Method in class org.intermine.objectstore.query.Results
Returns the underlying ResultsBatches object that this object is using, in order to create more Results objects (with different settings) from it.
getResultsCount() - Method in class org.intermine.webservice.server.output.MemoryOutput
}
getResultsCount() - Method in class org.intermine.webservice.server.output.Output
 
getResultsCount() - Method in class org.intermine.webservice.server.output.StreamedOutput
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONObjResultProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONResultProcessor
The method a processor must implement to produce a results iterator.
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONRowResultProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONSummaryProcessor
 
getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONTableResultProcessor
 
getResultsKey() - Method in class org.intermine.webservice.server.branding.BrandingService
 
getResultsKey() - Method in class org.intermine.webservice.server.core.JSONService
 
getResultsKey() - Method in class org.intermine.webservice.server.data.DataService
 
getResultsKey() - Method in class org.intermine.webservice.server.FacetListService
 
getResultsKey() - Method in class org.intermine.webservice.server.FacetService
 
getResultsKey() - Method in class org.intermine.webservice.server.fair.BioEntityMarkupService
 
getResultsKey() - Method in class org.intermine.webservice.server.fair.HomePageMarkupService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobResultsService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobStatusService
 
getResultsKey() - Method in class org.intermine.webservice.server.idresolution.ListResolutionService
 
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareCreationService
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
 
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
 
getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService
 
getResultsKey() - Method in class org.intermine.webservice.server.oauth2.CallbackService
 
getResultsKey() - Method in class org.intermine.webservice.server.query.QueryStoreService
 
getResultsKey() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
getResultsKey() - Method in class org.intermine.webservice.server.SchemaListService
 
getResultsKey() - Method in class org.intermine.webservice.server.SessionService
 
getResultsKey() - Method in class org.intermine.webservice.server.SummaryService
 
getResultsKey() - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.LoginService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.ReadPreferencesService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.TokenService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.TokensService
 
getResultsKey() - Method in class org.intermine.webservice.server.user.WhoAmIService
 
getResultsKey() - Method in class org.intermine.webservice.server.VersionService
 
getResultsKey() - Method in class org.intermine.webservice.server.webproperties.WebPropertiesService
 
getResultsSize(String) - Static method in class org.intermine.dwr.AjaxServices
Return the number of rows of results from the query with the given query id.
getResultsTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Given a table identifier, return the cached PagedTable.
getResultsTablesLib() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getResultsWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the (possibly uninitialised) results object used internally by this object, for use by subclass constructors.
getResultTable() - Method in interface org.intermine.web.logic.widget.DataSetLdr
Return the result table that represents the data from this widget.
getResultTable() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
 
getReturnToString() - Method in class org.intermine.web.struts.LoginForm
Return the returnToString set by setReturnToURL().
getReverseAliases() - Method in class org.intermine.objectstore.query.Query
Returns the map of String aliases to QuerySelectables and FromElements
getReverseReferenceDescriptor() - Method in class org.intermine.metadata.ReferenceDescriptor
Gets the field in the referenced object that refers back to this class.
getReverseReferenceFieldName() - Method in class org.intermine.metadata.ReferenceDescriptor
Gets the name of the reverse reference field.
getRight() - Method in class org.intermine.objectstore.query.OverlapConstraint
Returns the right OverlapRange.
getRight() - Method in class org.intermine.sql.query.Constraint
Returns the right argument of the constraint.
getRight() - Method in class org.intermine.sql.query.InListConstraint
Returns the right Set of Constants.
getRight() - Method in class org.intermine.sql.writebatch.Row
Returns right.
getRightArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Get the right argument of the given constraint, will return null if passed a ConstraintSet or a MultipleInBagConstraint.
getRightColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the right column name.
getRightField() - Method in class org.intermine.api.query.range.ConstraintOptions
Defaults to "end".
getRightOp() - Method in class org.intermine.api.query.range.ConstraintOptions
 
getRootClass() - Method in class org.intermine.pathquery.PathQuery
Returns the root path for this query, if the query verifies correctly.
getRootElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getRootElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getRootElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter
 
getRootNode() - Method in class org.intermine.pathquery.LogicExpression
Get the root node.
getRowElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
getRowElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
 
getRowElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter
 
getRowFormatter() - Method in class org.intermine.webservice.server.output.FlatFileFormatter
Get the row formatter
getRows() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the estimated number of rows in the results.
getRows() - Method in class org.intermine.sql.query.ExplainResult
Returns the number of rows estimated by the database for this query.
getRows() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the currently visible rows of the table as a List of Lists of ResultElement objects.
getRows() - Method in class org.intermine.web.tags.table.TableTag
 
getRows() - Method in class org.intermine.webservice.server.core.SubTable
 
getRows(String) - Method in class org.intermine.api.mines.LocalMine
 
getRows(String) - Method in interface org.intermine.api.mines.Mine
Run a path query and get back all the results.
getRows(String) - Method in class org.intermine.api.mines.RemoteMine
 
getRows(PathQuery) - Method in class org.intermine.api.mines.LocalMine
 
getRows(PathQuery) - Method in interface org.intermine.api.mines.Mine
Run a path query and get back all the results.
getRows(PathQuery) - Method in class org.intermine.api.mines.RemoteMine
 
getRowsFromBatch(int, int, int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets a range of rows from within a batch
getRowspan() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Returns the rowspan.
getRowSpan() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Used from JSP in rowspan attr of
getRowsToDelete() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the Set of rows to delete.
getRowsToInsert() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the Set of rows to insert.
getRunner(String, InterMineAPI) - Static method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
getRunningQueryController(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get the QueryMonitor object corresponding to a running query id (qid).
getSampleQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
 
getSampleSize() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
The sample size, n.
getSampleSize() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getSavedBag(String, String) - Method in class org.intermine.api.bag.SharedBagManager
Perform a query to retrieve a bag's backing SavedBag
getSavedBagId() - Method in class org.intermine.api.profile.StorableBag
 
getSavedBags() - Method in class org.intermine.api.profile.Profile
Get the value of savedBags
getSavedBags() - Method in class org.intermine.api.userprofile.UserProfile
 
getSavedBagsByStatus() - Method in class org.intermine.api.profile.Profile
Get the saved bags in a map of "status key" => map of lists
getSavedBagStatus() - Method in class org.intermine.dwr.AjaxServices
This method gets the latest bags from the session (SessionMethods) and returns them in JSON
getSavedQueries() - Method in class org.intermine.api.profile.Profile
Get the value of savedQueries
getSavedQuerys() - Method in class org.intermine.api.userprofile.UserProfile
 
getSavedTemplateQuery() - Method in class org.intermine.api.template.ApiTemplate
Gets the saved template query object.
getSavedTemplateQuerys() - Method in class org.intermine.api.userprofile.UserProfile
 
getSavedTemplates() - Method in class org.intermine.api.profile.Profile
Get the users saved templates
getSchema() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Returns the DatabaseSchema used by this ObjectStore.
getSchemaLocation(HttpServletRequest, String) - Static method in class org.intermine.webservice.server.query.AbstractQueryService
 
getSchemaUrl(String) - Method in class org.intermine.webservice.server.query.AbstractQueryService
 
getScope() - Method in class org.intermine.web.struts.TemplateForm
Get the template scope.
getScore() - Method in class org.intermine.api.searchengine.KeywordSearchResultContainer
score
getScore() - Method in class org.intermine.web.search.KeywordSearchResult
return score
getSearchIndex(String) - Method in class org.intermine.api.search.SearchRepository
Retrieve a search index for a given type of web searchable objects.
getSearchItems() - Method in class org.intermine.api.search.SearchRepository
Returns an unmodifiable view of the the search items observed by this repository.
getSearchRepository() - Method in class org.intermine.api.profile.Profile
Get the SearchRepository for this Profile.
getSearchTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getSearchTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getSecondFieldName() - Method in class org.intermine.objectstore.query.QueryField
Returns the name of the second field.
getSecondLastClassDescriptor() - Method in class org.intermine.pathquery.Path
Returns the second to last ClassDescriptor in the path.
getSection() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getSection(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression
Take a Collection of String variable names, and return the part of the Logic Expression that contains those variables.
getSectionTitle() - Method in class org.intermine.web.logic.config.FieldConfig
Get the section title (if sectionOnRight == true).
getSegment() - Method in class org.intermine.webservice.server.jbrowse.Command
 
getSelect() - Method in class org.intermine.objectstore.query.Query
Gets the SELECT list
getSelect() - Method in interface org.intermine.objectstore.query.Queryable
Returns the SELECT list.
getSelect() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the SELECT list.
getSelect() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the SELECT list.
getSelect() - Method in class org.intermine.sql.query.Query
Gets the list of select fields for this query.
getSelected() - Method in class org.intermine.web.struts.ModifyTemplateForm
Gets the selected templates
getSelected() - Method in class org.intermine.web.struts.WidgetForm
 
getSelectedAsString() - Method in class org.intermine.web.struts.WidgetForm
returns the value of the checkboxes checked by the user on the form.
getSelectedBags() - Method in class org.intermine.web.struts.ModifyBagForm
Gets the selected bags
getSelectedClass() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getSelectedConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
Returns the constraint type selected.
getSelectedElements() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Get a String array of selected bag elements
getSelectedExtraAttribute() - Method in class org.intermine.web.struts.WidgetForm
 
getSelectedExtraValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
If editing an existing LOOKUP constraint return the value selected for the extra constraint field.
getSelectedObjects() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Gets the ids of the selected objects
getSelectedObjects() - Method in class org.intermine.web.struts.SaveBagForm
Gets the selected objects
getSelectedOp() - Method in class org.intermine.web.logic.query.DisplayConstraint
If the bag is selected, return the value setted with the method setSelectedBagOp If editing an existing constraint return the operation used.
getSelectedQueries() - Method in class org.intermine.web.struts.ModifyQueryForm
Gets the selected queries
getSelectedValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
If editing an existing constraint, return the selected value.
getSelectionIds() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getSemanticMarkup(HttpServletRequest) - Method in class org.intermine.web.logic.results.ReportObject
Get the semantic markup to include in the ld+json section
getSequence() - Method in class org.intermine.objectstore.query.Results
Returns the sequence that this Results object was created with
getSequence() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns the sequence that this ResultsBatches object was created with
getSequence(Set<Object>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Return the sequence number representing the state of the ObjectStore.
getSequence(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Returns an object representing the current state of the database, for fail-fast concurrency control.
getSequence(Set<Object>) - Method in interface org.intermine.objectstore.ObjectStore
Return the sequence number representing the state of the ObjectStore.
getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Returns an object representing the current state of the database, for fail-fast concurrency control.
getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return the sequence number representing the state of the ObjectStore.
getSerial() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Gets an ID number which is unique in the database.
getSerial() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets an ID number which is unique in the database.
getSerial() - Method in interface org.intermine.objectstore.ObjectStore
Gets an ID number which is unique in the database.
getSerial() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Gets an ID number which is unique in the database.
getSerial() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Gets an ID number which is unique in the database.
getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets an ID number which is unique in the database, given a Connection.
getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Overrides, in order to store recentSequences.
getSeriesLabels() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getSeriesPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getSeriesValues() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.bg.BGPropertiesServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.RestfulServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.WebServiceServlet
Implement this to route requests.
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.FacetServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.idresolution.ListResolutionServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.AvailableListsServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.JaccardIndexServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListRenameServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListShareServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListSharingInvitationServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListUpgradingServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.query.QueryUploadServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.search.QuickSearchServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.result.TemplateResultServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateToListServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateUploadServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.NewUserServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.PermaTokensServlet
 
getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.WhoAmIServlet
 
getServiceBaseURL() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
getServices() - Method in class org.intermine.webservice.server.ServiceListingHandler
 
getSession() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Get the session
getSession() - Method in class org.intermine.webservice.server.core.SessionlessRequest
 
getSession(boolean) - Method in class org.intermine.webservice.server.core.SessionlessRequest
 
getSessionIdentifier() - Method in class org.intermine.api.tracker.track.TrackAbstract
Return the session id
getSetter() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the setter Method.
getSetter(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Method object that is the setter for the field name
getSharedBags() - Method in class org.intermine.api.profile.Profile
Return the shared bags for the profile.
getSharedBags(Profile) - Method in class org.intermine.api.bag.BagManager
Fetch the shared bags for the given profile.
getSharedBags(Profile) - Method in class org.intermine.api.bag.SharedBagManager
Return a map containing the bags that the user in input has access because shared by someone else
getSharedBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
Fetch bags shared by another user that contain the given id.
getShowIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Used from JSP
getShowImmediately() - Method in class org.intermine.web.displayer.ReportDisplayer
 
getShowImmediately() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Should we display this 'splayer immediately, wo/ waiting for the AJAX call?
getShowInHeader() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getShowInInlineCollection() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the showInInlineCollection flag
getShowInListAnalysisPreviewTable() - Method in class org.intermine.web.logic.config.FieldConfig
 
getShowInQB() - Method in class org.intermine.web.logic.config.FieldConfig
 
getShowInResults() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the showInResults flag
getShowInSummary() - Method in class org.intermine.web.logic.config.FieldConfig
Return the value of the showInSummary flag
getShowLinksToObjects() - Method in class org.intermine.web.logic.config.InlineListConfig
 
getShowLinksToObjects() - Method in class org.intermine.web.logic.results.InlineList
 
getShowOnLeft() - Method in class org.intermine.web.logic.config.Displayer
 
getSimpleClass(Class<? extends FastPathObject>) - Static method in class org.intermine.util.DynamicUtil
Returns the result of decomposeClass if that is a single class, or throws an exception if there are more than one.
getSimpleClass(FastPathObject) - Static method in class org.intermine.util.DynamicUtil
For the given object returns the result of decomposeClass if that is a single class, or throws an exception if there are more than one class.
getSimpleClassName(Class<?>) - Static method in class org.intermine.util.DynamicUtil
Returns the simple class name for the given class or throws an exception if there are more than one.
getSimpleClassName(String) - Static method in class org.intermine.web.uri.InterMineLUI
Given a type, which might not contain capital letters, return the class name as it is defined in the model
getSimpleClassName(FastPathObject) - Static method in class org.intermine.util.DynamicUtil
Returns the simple class name for the given object or throws an exception if there are more than one.
getSimpleName() - Method in class org.intermine.metadata.ClassDescriptor
Returns the simple class name described by this ClassDescriptor.
getSimpleObjectClassDescriptors() - Method in class org.intermine.metadata.Model
Return ClassDescriptors for simple objects only - simple objects are light weight objects without an id and with no inheritance.
getSimplePathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget
Returns the pathquery based on the classkey.
getSingleUseKey() - Method in class org.intermine.api.profile.Profile
Return a single use API key for this profile
getSingleUseKey() - Static method in class org.intermine.dwr.AjaxServices
Return the single use API key for the current profile
getSize() - Method in class org.intermine.api.profile.InterMineBag
 
getSize() - Method in class org.intermine.api.profile.InvalidBag
 
getSize() - Method in class org.intermine.api.profile.StorableBag
Returns the size of the bag.
getSize() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
Returns the current amount of data, in bytes, held in this object.
getSize() - Method in interface org.intermine.sql.writebatch.Table
Returns the current amount of data, in bytes, held in this object.
getSize() - Method in class org.intermine.sql.writebatch.TableBatch
Returns the current amount of data, in bytes, held in this object.
getSize() - Method in class org.intermine.web.logic.results.DisplayField
Get the size of this collection
getSize() - Method in class org.intermine.web.logic.results.InlineList
 
getSize() - Method in class org.intermine.web.logic.widget.PopulationInfo
 
getSize() - Method in class org.intermine.webservice.server.core.Page
 
getSkeleton() - Method in class org.intermine.dataloader.Source
Getter for skeleton.
getSkeletonSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter
Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.
getSkeletonSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Converts a string describing the data source into a Source object suitable for passing to the store method as the skeleton source.
getSolrUrl() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getSome(String...) - Method in class org.intermine.web.security.KeyStorePublicKeySource
 
getSome(String...) - Method in interface org.intermine.web.security.PublicKeySource
Get multiple keys given a set of names.
getSource(Integer, String) - Method in class org.intermine.dataloader.DataTracker
Retrieve the Source for a specified field of an Object stored in the database.
getSource(String) - Method in class org.intermine.dataloader.ObjectDescription
Gets the source associated with the given fieldname.
getSourcePrimaryKeys(Source, Model) - Static method in class org.intermine.dataloader.DataLoaderHelper
Fetch all primary keys for the given source.
getSpecialReferences() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
getSQLString() - Method in class org.intermine.sql.precompute.PrecomputedTable
Get a "CREATE TABLE" SQL statement for this PrecomputedTable.
getSQLString() - Method in class org.intermine.sql.query.AbstractConstraint
Returns a String representation of this AbstractConstraint object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.AbstractTable
Returns a String representation of this AbstractTable object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.AbstractValue
Returns a String representation of this AbstractValue object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Constant
Returns a String representation of this Constant object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Constraint
Returns a String representation of this Constraint object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.ConstraintSet
Returns a String representation of this ConstraintSet object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Field
Returns a String representation of this Field object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Function
Returns a String representation of this Function object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.InListConstraint
Returns a String representation of this InListConstraint object, suitable for forming part of an SQL Query.
getSQLString() - Method in class org.intermine.sql.query.NotConstraint
Returns a String representation of this Constraint object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.OrderDescending
Returns a String representation of this AbstractValue object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.Query
Convert this Query into a SQL String query.
getSQLString() - Method in class org.intermine.sql.query.SelectValue
Returns a String representation of this Field object, suitable for forming part of an SQL SELECT list.
getSQLString() - Method in interface org.intermine.sql.query.SQLStringable
Returns a String representation of this object, suitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.SubQuery
Returns a String representation of this SubQuery object, auitable for forming part of an SQL query.
getSQLString() - Method in class org.intermine.sql.query.SubQueryConstraint
Returns a String representation of this SubQueryConstraint object, suitable for forming part of an SQL Query.
getSQLString() - Method in class org.intermine.sql.query.Table
Returns a String representation of this Table object, suitable for forming part of an SQL query.
getSQLStringForPrecomputedTable(String) - Method in class org.intermine.sql.query.Query
Convert this Query into a SQL String query, without regard to the other members of the the UNION, with an extra field in the SELECT list.
getSQLStringNoUnion() - Method in class org.intermine.sql.query.Query
Convert this Query into a SQL String query, without regard to the other members of the UNION.
getSrc() - Method in class org.intermine.web.logic.config.Displayer
Get the source of this displayer
getStandardIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask
Add indexes for primary keys, indirection tables and 1-N relations to the relevant tables for a given ClassDescriptor
getStart() - Method in interface org.intermine.api.query.range.Range
 
getStart() - Method in class org.intermine.objectstore.query.OverlapRange
Returns the left parameter.
getStart() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns the estimated amount of time taken to produce the first row of the results.
getStart() - Method in class org.intermine.sql.query.ExplainResult
Returns the number of page requests before the first row is returned, estimated by the database for this query.
getStart() - Method in class org.intermine.webservice.server.core.Page
Get the index of the first row that is requested.
getStart() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getStart() - Method in class org.intermine.webservice.server.WebServiceInput
Returns index of first returned result
getStartClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getStartClassDescriptor() - Method in class org.intermine.pathquery.Path
Return the ClassDescriptor of the first element in the path.
getStartClassDisplay() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getStartedAt() - Method in interface org.intermine.api.idresolution.Job
 
getStartedAt() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getStartedAt() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getStartingPoints() - Method in class org.intermine.web.logic.aspects.Aspect
Get a List of starting point class names.
getStartRow() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Get the index of the first row of this page
getState() - Method in class org.intermine.api.profile.InterMineBag
Return the bag state: current, not current, to upgrade
getState() - Method in class org.intermine.api.profile.InvalidBag
 
getState() - Method in class org.intermine.api.profile.StorableBag
Return a string representing the state of this bag (eg.
getState() - Method in class org.intermine.api.userprofile.SavedBag
 
getState(String) - Method in class org.intermine.web.logic.results.WebState
 
getStatementCreatingTable() - Method in class org.intermine.api.tracker.AbstractTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.KeySearchTracker
 
getStatementCreatingTable() - Method in class org.intermine.api.tracker.ListTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.LoginTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.QueryTracker
Generate the sql statement to create the table used by the tracker
getStatementCreatingTable() - Method in class org.intermine.api.tracker.TemplateTracker
Generate the sql statement to create the table used by the tracker
getStates() - Method in class org.intermine.web.logic.results.WebState
 
getStaticPage(String, String) - Static method in class org.intermine.web.logic.WebUtil
Return the contents of the page given by prefixURLString + '/' + path as a String.
getStatus() - Method in interface org.intermine.api.idresolution.Job
 
getStatus() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getStatus() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getStatus() - Method in class org.intermine.objectstore.query.ResultsInfo
Returns an integer describing the type of estimate getRows() returns.
getStatus() - Method in class org.intermine.web.registry.model.Instance
 
getStatusCode() - Method in class org.intermine.web.registry.model.RegistryResponse
 
getString() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
Returns the wrapped String.
getString(String) - Static method in class org.intermine.api.query.codegen.JSStrings
 
getString(String, Object...) - Static method in class org.intermine.api.query.codegen.JSStrings
 
getStrings() - Method in class org.intermine.model.StringConstructor
Returns a Collection containing the Strings that form this object, in the correct order.
getStructure() - Method in class org.intermine.web.logic.query.MetadataNode
Returns the structure of the tree.
getStructure() - Method in class org.intermine.web.logic.TreeNode
Returns the structure of the tree.
getStyle() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Returns element style.
getStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Returns css style class of element.
getSubclass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns the subclass if it exists.
getSubclass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Returns the subclass if it exists.
getSubclass() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Returns the name of the subclass on this path, if there is one.
getSubClassConstraintPaths() - Method in class org.intermine.pathquery.Path
Returns a Map from simplified path string (with dots instead of colons, and no constraints) to constraint class name.
getSubclasses() - Method in class org.intermine.pathquery.PathQuery
Returns the subclass Map for this query, if the query verifies correctly.
getSubclassValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Gets the value of subclassValue
getSubDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Return a Set of ClassDescriptors for all classes that directly extend or implement this class or interface.
getSubject() - Method in class org.intermine.web.struts.ContactForm
 
getSubSequence() - Method in class org.intermine.objectstore.query.ClobAccess
Returns true if this object is a subsequence of a main Clob.
getSubtab(String) - Method in class org.intermine.web.logic.results.WebState
 
getSubtabs() - Method in class org.intermine.web.logic.results.WebState
map of tab --> subtab
getSubTitle() - Method in class org.intermine.web.logic.aspects.Aspect
Get the subtitle
getSubTitles() - Method in class org.intermine.web.logic.config.Type
 
getSubtractLists() - Method in class org.intermine.webservice.server.lists.ListInput
 
getSuffix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
A suffix that may be an HTML tag to appear after this part in the title.
getSummaries() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getSummary() - Method in class org.intermine.api.userprofile.TemplateSummary
 
getSummary(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns a StringBuffer containing summary information.
getSummary(Source) - Method in class org.intermine.dataloader.HintingFetcher
Returns a StringBuffer containing summary information.
getSuperclassDescriptor() - Method in class org.intermine.metadata.ClassDescriptor
Get the super class of this class (may be null).
getSuperclassNames() - Method in class org.intermine.metadata.ClassDescriptor
Return set of superclass class names.
getSuperDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Get a set of ClassDescriptors for the interfaces superclasses that this class implements.
getSuperuser() - Method in class org.intermine.api.profile.Profile
Alias of isSuperUser() for jsp purposes.
getSuperuser() - Method in class org.intermine.api.profile.ProfileManager
Return the super user name set in the properties file
getSuperuser() - Method in class org.intermine.api.userprofile.UserProfile
 
getSuperuserProfile() - Method in class org.intermine.api.profile.ProfileManager
Return the superuser profile set in the properties file
getSuperuserProfile(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Return the super user
getSuperUsers() - Method in class org.intermine.api.profile.ProfileManager
Return a list of users with 'superuser' role
getSuperUsers() - Method in class org.intermine.web.struts.ModifySuperUserForm
Get the super users
getSuperUsersProfile() - Method in class org.intermine.api.profile.ProfileManager
Return a list of profile with 'superuser' role
getSwitchable() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the value on, off, locked depending on the constraint SwitchOffAbility .
getSwitchable() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get the switchoffAbility for a constraint.
getSwitchable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the switchable value (on, off, locked).
getSwitchOff(String) - Method in class org.intermine.web.struts.TemplateForm
Get the SwitchOff ability.
getSwitchOffAbility() - Method in class org.intermine.template.TemplateValue
Returns the SwitchOffAbility.
getSwitchOffAbility(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Gets the sbitch-off-ability of a constraint.
getSystemTemplates() - Method in class org.intermine.api.template.TemplateManager
Return template queries used for converting between types in bag upload and lookup queries, these are Superuser templates that have been tagged with TagNames.IM_CONVERTER.
getTable() - Method in class org.intermine.sql.query.Field
Returns the table of this field.
getTable() - Method in class org.intermine.web.logic.results.DisplayField
Get the inline results table for this collection
getTable() - Method in class org.intermine.web.struts.TableExportForm
Get the table identifier to look up the PagedTable in the servlet context
getTableCount() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
Returns the number of tables in this query.
getTableDefinition() - Static method in class org.intermine.api.bag.SharingInvite
 
getTableDefinition(Database, ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
 
getTableDisplayer() - Method in class org.intermine.web.logic.config.Type
Get the table Displayer
getTableExportConfigs() - Method in class org.intermine.web.logic.config.WebConfig
Return a Map of TableExportConfig.id to TableExportConfig objects.
getTableFieldConfigs() - Method in class org.intermine.web.logic.results.InlineResultsTable
 
getTableFields(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns a Fields object of FieldDescriptors in the given table-mastering ClassDescriptor.
getTableid() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getTableInfo(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Produces metadata for a given table, caching it to save time.
getTableMaster(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the name of the table in which to store a row for the given ClassDescriptor.
getTableName() - Method in class org.intermine.api.tracker.track.KeySearchTrack
 
getTableName() - Method in class org.intermine.api.tracker.track.ListTrack
Return the table name where the track has to be saved
getTableName() - Method in class org.intermine.api.tracker.track.LoginTrack
Return the table name where the track has to be saved
getTableName() - Method in class org.intermine.api.tracker.track.QueryTrack
 
getTableName() - Method in class org.intermine.api.tracker.track.TemplateTrack
Return the table name where the track has to be saved
getTableName() - Method in interface org.intermine.api.tracker.track.Track
Return the table name where the track has to be saved
getTableName(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
Creates a table name for a class descriptor
getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
Returns the approximate number of rows in a table.
getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Returns the approximate number of rows in a table.
getTabLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
Returns link which gives results as lines, where values are tab separated.
getTagById(int) - Method in class org.intermine.api.profile.TagManager
Get Tag by object id.
getTagManager() - Method in interface org.intermine.api.API
 
getTagManager() - Method in class org.intermine.api.InterMineAPI
 
getTagManager() - Method in class org.intermine.api.profile.ProfileManager
Return the TagManager for adding, removing and fetching Tags assigned to templates, bags and classes.
getTagManager() - Method in class org.intermine.api.profile.TagManagerFactory
 
getTagName() - Method in class org.intermine.api.search.TaggingEvent
 
getTagName() - Method in class org.intermine.api.userprofile.Tag
 
getTags() - Method in class org.intermine.api.userprofile.UserProfile
 
getTags() - Method in class org.intermine.webservice.server.lists.ListInput
 
getTags(String) - Static method in class org.intermine.dwr.AjaxServices
Returns all tags of specified tag type together with prefixes of these tags.
getTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
Return a List of Tags that match all the arguments.
getTags(ApiTemplate, Profile) - Method in class org.intermine.api.template.TemplateManager
For a (public or private) template, return all the tags.
getTagsByName(String, Profile, String) - Method in class org.intermine.api.profile.TagManager
Return all the tags with the given tag name, optionally filtered by tag-type.
getTagsByType(String) - Method in class org.intermine.api.profile.TagManager
Return all tags of given type.
getTagsForBag(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Get a list of tags for a given bag.
getTagType() - Method in class org.intermine.api.profile.StorableBag
 
getTagType() - Method in interface org.intermine.api.profile.Taggable
Poly-Morphic Constant.
getTagType() - Method in class org.intermine.api.template.ApiTemplate
 
getTargetType() - Method in class org.intermine.api.bag.AdditionalConverter
 
getTemplate() - Method in class org.intermine.api.userprofile.TemplateSummary
 
getTemplate(String) - Method in class org.intermine.api.profile.Profile
get a template
getTemplate(Profile, String, String) - Method in class org.intermine.api.template.TemplateManager
Fetch a template with the scope provided, possible values are defined in Scope class.
getTemplateButton() - Method in class org.intermine.web.struts.ModifyTemplateForm
 
getTemplateLabel() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the template label.
getTemplateManager() - Method in interface org.intermine.api.API
 
getTemplateManager() - Method in class org.intermine.api.InterMineAPI
 
getTemplateManager() - Static method in class org.intermine.api.query.PathQueryAPI
Returns the TemplateManager for access to global and user template queries.
getTemplateName() - Method in class org.intermine.api.tracker.track.TemplateTrack
Return the template name
getTemplateQuery() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getTemplates() - Method in class org.intermine.web.search.KeywordSearchResult
templates associated with this class
getTemplateSummariser() - Method in interface org.intermine.api.API
 
getTemplateSummariser() - Method in class org.intermine.api.InterMineAPI
 
getTemplateTracker() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the tracker template
getTemplateTracksPercentage(String) - Method in class org.intermine.dwr.TrackAjaxServices
 
getTemplateTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
 
getTemporaryListName() - Method in class org.intermine.webservice.server.lists.ListInput
 
getTestCount() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
The test count represents the number of tests that will be performed.
getTestCount() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
 
getText() - Method in class org.intermine.web.logic.config.HeaderConfigLink
 
getText() - Method in class org.intermine.web.logic.TreeNode
Get the text that was passed to the constructor
getText() - Method in class org.intermine.web.struts.BuildBagForm
Get the text string
getTextToFind() - Method in class org.intermine.web.struts.FindInListForm
 
getTickleCount() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out how many times tickle has been called.
getTileName() - Method in class org.intermine.web.logic.aspects.Aspect
Get the name of tile/page to embed in the centre of the data set homepage
getTime() - Method in class org.intermine.sql.query.DummyExplainResult
Returns an estimate of the time it will take to complete the query.
getTime() - Method in class org.intermine.sql.query.ExplainResult
Returns an estimate of the time it will take to complete the query.
getTimeLimit() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Returns the time limit.
getTimestamp() - Method in class org.intermine.api.tracker.track.TrackAbstract
Return the timestamp of the event
getTitle() - Method in class org.intermine.api.bag.AdditionalConverter
 
getTitle() - Method in class org.intermine.api.profile.InterMineBag
The user-friendly title for this object.
getTitle() - Method in class org.intermine.api.profile.InvalidBag
 
getTitle() - Method in interface org.intermine.api.search.WebSearchable
The user-friendly title for this object.
getTitle() - Method in class org.intermine.pathquery.PathQuery
Gets the title for this query.
getTitle() - Method in class org.intermine.template.TemplateQuery
 
getTitle() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return the last class in the path and fieldname as the title for the constraint.
getTitle() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getTitle() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
Get the title
getTitle() - Method in class org.intermine.web.logic.widget.Widget
Get the widget title
getTitle() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
title of the widget
getTitle() - Method in class org.intermine.web.struts.TemplateSettingsForm
Return the title
getTitleMain() - Method in class org.intermine.web.logic.results.ReportObject
Used by JSP
getTitles() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
 
getTitleSub() - Method in class org.intermine.web.logic.results.ReportObject
Used by JSP
getToggledElements() - Static method in class org.intermine.dwr.AjaxServices
This method gets a map of ids of elements that were in the past (during session) toggled and returns them in JSON
getToggledElements() - Method in class org.intermine.web.logic.results.WebState
Gets map of ids of elements that were in the past (during session) toggled - if they are opened or closed.
getToken() - Method in class org.intermine.api.bag.SharingInvite
 
getToken() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
getToken() - Method in class org.intermine.api.userprofile.PermanentToken
 
getToken() - Method in class org.intermine.web.struts.PasswordResetForm
Gets the value of token.
getToken() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService
 
getTokenUrl() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
 
getTokenUrl() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
 
getTokenUrl() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
 
getTopDownLevelTraversal() - Method in class org.intermine.metadata.Model
Return the classes in the model in level order from shallowest to deepest, the order of nodes at any given level is undefined.
getTotalHits() - Method in class org.intermine.api.searchengine.KeywordSearchResults
 
getTracker(String) - Method in class org.intermine.api.tracker.TrackerDelegate
Return the tracker specified in input
getTracker(String, Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.factory.TrackerFactory
Return the tracker instantiated with the reflection
getTrackerDelegate() - Method in interface org.intermine.api.API
 
getTrackerDelegate() - Method in class org.intermine.api.InterMineAPI
 
getTrackers() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the trackers saved in the TrackerManager
getTrackTableName() - Method in class org.intermine.api.tracker.AbstractTracker
Return the table's name associated to the tracker
getTrail() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Get the trail URL parameter for this trail element.
getTranslator() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Returns the Translator associated with the underlying ObjectStoreTranslatingImpl.
getTranslator() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Return the Translator that was passed to the constructor.
getTwitter() - Method in class org.intermine.web.registry.model.Instance
 
getType() - Method in class org.intermine.api.bag.BagQueryUpgrade
 
getType() - Method in class org.intermine.api.beans.ObjectDetails
 
getType() - Method in interface org.intermine.api.idresolution.Job
 
getType() - Method in interface org.intermine.api.idresolution.JobInput
 
getType() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getType() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getType() - Method in class org.intermine.api.profile.InterMineBag
Get the type of this bag (a class from InterMine model)
getType() - Method in class org.intermine.api.profile.InvalidBag
 
getType() - Method in class org.intermine.api.profile.StorableBag
Get the unqualified name of class that the objects in this bag represent.
getType() - Method in class org.intermine.api.results.Column
Return the type of this Column
getType() - Method in interface org.intermine.api.results.ResultCell
 
getType() - Method in class org.intermine.api.results.ResultElement
Get the type
getType() - Method in class org.intermine.api.searchengine.KeywordSearchFacetData
type of facet
getType() - Method in class org.intermine.api.tracker.track.ListTrack
Return the class type of items contained into the list
getType() - Method in class org.intermine.api.userprofile.SavedBag
 
getType() - Method in class org.intermine.api.userprofile.Tag
 
getType() - Method in class org.intermine.dataloader.Source
 
getType() - Method in class org.intermine.metadata.AttributeDescriptor
Get the type of the attribute - either name of primitive or fully qualified class name.
getType() - Method in class org.intermine.metadata.ClassDescriptor
Returns the Class described by this ClassDescriptor.
getType() - Method in class org.intermine.metadata.TypeUtil.FieldInfo
Returns the type of the field.
getType() - Method in class org.intermine.objectstore.query.Clob
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.ObjectStoreBag
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.OrderDescending
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.PathExpressionField
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryCast
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryClass
Gets the Java class represented by this QueryClass
getType() - Method in class org.intermine.objectstore.query.QueryClassBag
Gets the Java class represented by this QueryClassBag.
getType() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryCollectionReference
Gets the Java class of this QueryReference.
getType() - Method in class org.intermine.objectstore.query.QueryExpression
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryField
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryForeignKey
Gets the Java class of this QueryReference.
getType() - Method in class org.intermine.objectstore.query.QueryFunction
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryObjectReference
Gets the Java class of this QueryReference.
getType() - Method in interface org.intermine.objectstore.query.QueryOrderable
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryReference
Gets the Java class of this QueryReference.
getType() - Method in interface org.intermine.objectstore.query.QuerySelectable
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.QueryValue
Get Java type represented by this item.
getType() - Method in class org.intermine.objectstore.query.WidthBucketFunction
Get Java type represented by this item.
getType() - Method in class org.intermine.pathquery.Node
Gets the value of type
getType() - Method in class org.intermine.pathquery.PathConstraintSubclass
Returns the class that the constraint is constraining to.
getType() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getType() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns the type of the value represented by this path, as a string.
getType() - Method in class org.intermine.web.logic.results.ReportObject
Get the unqualified class name for the report object.
getType() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getType() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getType() - Method in class org.intermine.web.search.KeywordSearchResult
returns the name of the class for this object (category)
getType() - Method in class org.intermine.web.struts.BuildBagForm
Get the bag type
getType() - Method in class org.intermine.web.struts.CSVExportForm
Return the export type: "tab", etc.
getType() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
Return whether or not this trail element refers to a table.
getType() - Method in class org.intermine.web.struts.TableExportForm
Return the export type: "tab", etc.
getType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Returns type of tag.
getType() - Method in class org.intermine.webservice.server.core.TableCell
 
getType() - Method in class org.intermine.webservice.server.lists.ListInput
 
getType() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
 
getType(String) - Method in class org.intermine.webservice.server.jbrowse.Command
 
getType(FieldDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
Return the java type of a particular field.
getType(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
A static method to get the type of this constraint if it is a sub-class constraint, or otherwise return null.
getTypeByName(String) - Static method in class org.intermine.metadata.TypeUtil
Returns the Class for a given name (promoting primitives to their container class) and returning null if the name does not refer to any known class.
getTypeClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getTypeClsString() - Method in class org.intermine.api.results.Column
Get the column type unqualified as a String
getTypeForColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the class from the data model for the data displayed in indexed column.
getTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Get the comma separated unqualified class names for which this displayer should be displayed.
getTypes() - Method in class org.intermine.web.logic.config.WebConfig
Get a map from fully qualified class name to the Type config for that class
getUid() - Method in interface org.intermine.api.idresolution.Job
 
getUid() - Method in class org.intermine.api.idresolution.ResolutionJob
 
getUid() - Method in class org.intermine.api.idresolution.UpgradeJob
 
getUnformatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue
Get the unformatted version that is just the field value.
getUnion() - Method in class org.intermine.sql.query.Query
Returns the List of queries in the UNION set of this query.
getUniqueInteger(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Return a unique integer from a SEQUENCE in the database.
getUniqueItemId(String) - Method in class org.intermine.dataconversion.DataConverter
List of unique identifiers and their refIds.
getUnqualifiedClassName() - Method in class org.intermine.web.logic.config.Type
 
getUnqualifiedName() - Method in class org.intermine.metadata.ClassDescriptor
Returns unqualified name of class described by this ClassDescriptor.
getUnresolved() - Method in class org.intermine.api.bag.BagQueryResult
Deprecated.
Use getUnresolvedIdentifiers
getUnresolvedIdentifiers() - Method in class org.intermine.api.bag.BagQueryResult
Get all the unresolved identifiers.
getUpdatedPathQuery() - Method in class org.intermine.api.profile.PathQueryUpdate
Return a new pathquery updated to the new model
getUrl() - Method in class org.intermine.api.mines.LocalMine
 
getUrl() - Method in interface org.intermine.api.mines.Mine
 
getUrl() - Method in class org.intermine.api.mines.RemoteMine
 
getUrl() - Method in class org.intermine.web.logic.aspects.AspectSource
Get the URL back to source website.
getUrl() - Method in class org.intermine.web.logic.config.HeaderConfigLink
 
getUrl() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
getUrl() - Method in class org.intermine.web.registry.model.Instance
 
getURL() - Method in class org.intermine.sql.Database
Gets the URL from this database
getUrlField() - Method in class org.intermine.api.bag.AdditionalConverter
 
getUseBagConstraint(String) - Method in class org.intermine.web.struts.TemplateForm
Get the value of useBagConstraint for given constraint key.
getUseJoin() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
getUser() - Method in class org.intermine.sql.Database
Gets the username for this Database
getUserAndGlobalTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager
Fetch all user and global templates in a single map for the given user.
getUserBag(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch a user bag by name.
getUserBags(Profile) - Method in class org.intermine.api.bag.BagManager
Fetch bags for the given profile.
getUserBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
Fetch user bags that contain the given id.
getUserBagsWithTag(Profile, String) - Method in class org.intermine.api.bag.BagManager
Fetch bags from given protocol with a particular tag assigned to them.
getUserBagsWithTags(Profile, List<String>) - Method in class org.intermine.api.bag.BagManager
Give me profile bags matching a set of tags
getUserId() - Method in class org.intermine.api.profile.Profile
Get the value of userId
getUserLogin() - Method in class org.intermine.api.tracker.TrackerDelegate
Return the number of access for each user
getUserLogin(Connection) - Method in class org.intermine.api.tracker.LoginTracker
Return the number of access for each user
getUsername() - Method in class org.intermine.api.profile.Profile
Get the value of username
getUsername() - Method in class org.intermine.api.userprofile.UserProfile
 
getUsername() - Method in class org.intermine.api.util.AnonProfile
 
getUsername() - Method in class org.intermine.web.struts.CreateAccountForm
 
getUsername() - Method in class org.intermine.web.struts.LoginForm
Gets the value of username The user name is always returned in LOWER CASE.
getUsername() - Method in class org.intermine.web.struts.RequestPasswordForm
Gets the value of username
getUserName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
The name of the user logged in when this info was generated
getUserName() - Method in class org.intermine.api.tracker.track.TrackAbstract
Return the user name
getUserName() - Method in class org.intermine.webservice.server.WebServiceInput
 
getUsernameForToken(String) - Method in class org.intermine.api.profile.ProfileManager
Returns the username associated with the given token, if the token is valid.
getUserOrGlobalTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager
Fetch a user or global template by name.
getUserProfile() - Method in class org.intermine.api.InterMineAPI
 
getUserProfile() - Method in class org.intermine.api.userprofile.PermanentToken
 
getUserProfile() - Method in class org.intermine.api.userprofile.SavedBag
 
getUserProfile() - Method in class org.intermine.api.userprofile.SavedQuery
 
getUserProfile() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
getUserProfile() - Method in class org.intermine.api.userprofile.Tag
 
getUserProfile(Integer) - Method in class org.intermine.api.profile.ProfileManager
Perform a query to retrieve a user's backing UserProfile
getUserProfile(String) - Method in class org.intermine.api.profile.ProfileManager
Perform a query to retrieve a user's backing UserProfile
getUserProfileWriter() - Method in class org.intermine.api.profile.InterMineBag
 
getUserProfileWriter() - Method in class org.intermine.api.profile.InvalidBag
 
getUserProfileWriter() - Method in class org.intermine.api.profile.StorableBag
Get a reference to a connection to the database where user data is persisted.
getUsersSharingBag(String) - Method in class org.intermine.dwr.AjaxServices
Return the list of users who have access to this bag because it has been shared with them.
getUsersSharingBag(String, String) - Method in class org.intermine.api.bag.BagManager
Return the users sharing the list given in input, not the owner
getUsersWithAccessToBag(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager
Return the users this bag is shared with.
getUserTagNames(String, String) - Method in class org.intermine.api.profile.TagManager
Deprecated.
It is better to use the typed methods instead.
getUserTagNames(String, Profile) - Method in class org.intermine.api.profile.TagManager
Returns names of tags of specified user and tag type.
getUserTags(String) - Method in class org.intermine.api.profile.TagManager
Returns tags of specified user.
getUserTags(Profile) - Method in class org.intermine.api.profile.TagManager
Returns tags of specified user.
getUserTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager
Fetch a user template by name.
getUserToken() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
A token for the user.
getUserWithUniqueMapping(String, String) - Method in class org.intermine.api.profile.PreferencesManager
 
getUUID() - Method in class org.intermine.webservice.server.user.DeletionToken
 
getV() - Method in class org.intermine.web.registry.model.Instance
 
getValidGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager
Return a map from template name to template query containing superuser templates that are tagged as public and are valid for the current data model.
getValidOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
Given the path being constrained return the valid constraint operations.
getValidRangeTargets() - Static method in class org.intermine.api.query.MainHelper
 
getValue() - Method in class org.intermine.api.profile.BagValue
 
getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Returns the value of the entry.
getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
Returns the value of the entry.
getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowValue
Returns the value of the entry.
getValue() - Method in class org.intermine.api.searchengine.KeywordSearchFacet
selected value
getValue() - Method in class org.intermine.api.searchengine.ObjectValueContainer
value
getValue() - Method in class org.intermine.model.fulldata.Attribute
 
getValue() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
Returns the value.
getValue() - Method in class org.intermine.objectstore.query.QueryCast
Returns the QueryEvaluable that is the actual value.
getValue() - Method in class org.intermine.objectstore.query.QueryValue
Returns the object that is the actual value.
getValue() - Method in class org.intermine.objectstore.query.UnknownTypeValue
Returns the value.
getValue() - Method in class org.intermine.pathquery.PathConstraintAttribute
Returns the value that the constraint is constraining to.
getValue() - Method in class org.intermine.pathquery.PathConstraintLookup
Returns the lookup value for this constraint.
getValue() - Method in class org.intermine.sql.query.OrderDescending
Returns the value.
getValue() - Method in class org.intermine.sql.query.SelectValue
Gets the AbstractValue from this object.
getValue() - Method in class org.intermine.template.TemplateValue
Returns value.
getValue() - Method in class org.intermine.web.logic.config.InlineListObject
Fetch the column value, ie "Zerknullt" for Synonyms of a Gene
getValue() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Get a string representation of the constraint value to be displayed.
getValue() - Method in class org.intermine.web.logic.results.ReportObjectField
Get field value
getValue() - Method in class org.intermine.web.logic.template.ConstraintInput
Returns constraint value.
getValue() - Method in class org.intermine.webservice.server.core.Pair
 
getValue() - Method in class org.intermine.xml.full.Attribute
Get the value of this field
getValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
A static method for accessing values without having to handle the subclasses manually.
getValueHasDisplayer() - Method in class org.intermine.web.logic.results.ReportObjectField
Does the field have a custom displayer defined for the value?
getValueMap() - Method in class org.intermine.sql.precompute.PrecomputedTable
Gets a Map from AbstractValue to SelectValue for the Query in this PrecomputedTable.
getValues() - Static method in class org.intermine.metadata.ConstraintOp
Get the the internal list of ConstraintOps (Only for use in webapp)
getValues() - Method in class org.intermine.pathquery.PathConstraintMultiValue
Returns the value collection that the constraint is constraining to.
getValues() - Method in class org.intermine.template.TemplateValue
 
getValues(String) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns a Set of values that were in the database for a particular class and fieldname.
getValues(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
Get the values for a constraint.
getValuesFromInput(TemplateQuery, TemplateResultInput) - Static method in class org.intermine.web.logic.template.Templates
Creates a map from input to be used later to populate the template.
getVariableNames() - Method in class org.intermine.pathquery.LogicExpression
Get the Set of variable names.
getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets the verboseQueryLog configuration option.
getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Gets the verboseQueryLog configuration option.
getVersion() - Method in class org.intermine.api.profile.ProfileManager
Returns the version number of the data format in the database for this ProfileManager.
getVersion() - Method in class org.intermine.metadata.Model
 
getVersion() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns the database format version.
getVersion() - Method in class org.intermine.sql.Database
Get the version number of the database as a string.
getView() - Method in class org.intermine.pathquery.PathQuery
Returns the current view list.
getView() - Method in class org.intermine.web.struts.TemplateForm
Get the selected alternative view name.
getViewPaths() - Method in class org.intermine.api.results.ExportResultsIterator
 
getViews() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getVisibleColumnCount() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return the number of visible columns.
getVisibleIndexes() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Returns indexes of columns, that should be displayed.
getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator
Returns warnings occurred during parsing xml.
getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
Returns warning occurred during parsing xml.
getWebConfig() - Static method in class org.intermine.web.context.InterMineContext
 
getWebConfig() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
getWebConfig(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
 
getWebConfig(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
 
getWebProperties() - Static method in class org.intermine.web.context.InterMineContext
 
getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the web properties.
getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.struts.InterMineAction
Get the web proprties.
getWebProperties(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Returns the web properties.
getWebResultsExecutor(Profile) - Method in interface org.intermine.api.API
 
getWebResultsExecutor(Profile) - Method in class org.intermine.api.InterMineAPI
 
getWebSearchableMap(String) - Method in class org.intermine.api.search.GlobalRepository
Get a map from name -> object for all the websearchables of the given type.
getWebSearchableMap(String) - Method in class org.intermine.api.search.SearchRepository
Get a map from name -> object for all the websearchables of the given type.
getWebSearchablesByType(String) - Method in class org.intermine.api.profile.Profile
Return a WebSearchable Map for the given type.
getWebState(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Get WebState object that is used for saving state of webapp GUI.
getWebTable() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
getWhere() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getWhere() - Method in class org.intermine.sql.query.Query
Gets the Set of constraints in the where clause of this query.
getWhereBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
getWhichInput() - Method in class org.intermine.web.struts.BuildBagForm
Get the method the user used to upload the bag.
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions, String, String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions, String, String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions, String, String) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
 
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions, String, String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions, String, String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
getWidgetid() - Method in class org.intermine.web.struts.WidgetForm
 
getWidgetId() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
Get the name or id of the widget
getWidgets() - Method in class org.intermine.web.logic.config.Type
 
getWidgets() - Method in class org.intermine.web.logic.config.WebConfig
 
getWidgetTitle() - Method in class org.intermine.web.struts.WidgetForm
used on results page for description: "results for widget XYZ"
getWidgetTotal() - Method in interface org.intermine.web.logic.widget.DataSetLdr
This method is used to calculate the 'not analysed' total displayed on each widget
getWidgetTotal() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
 
getWidgetTotal() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
getWidgetType(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
 
getWidth() - Method in class org.intermine.sql.query.ExplainResult
Returns the width of the data returned by the database for this query.
getWidth() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
getWildCards() - Method in interface org.intermine.api.idresolution.JobInput
 
getWildCards() - Method in class org.intermine.web.logic.bag.WebJobInput
 
getWithinOptions() - Method in class org.intermine.api.query.range.AbstractHelper
 
getWorkingTemplates() - Method in class org.intermine.api.template.TemplateManager
Fetch all global templates that are valid.
getWorkingTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager
Fetch all user and global templates that are valid.
getWriter() - Method in class org.intermine.webservice.server.output.StreamedOutput
Returns associated writer
getWrittenResultsCount() - Method in interface org.intermine.web.logic.export.Exporter
 
getWrittenResultsCount() - Method in class org.intermine.web.logic.export.ExporterImpl
getXml() - Method in class org.intermine.web.struts.ImportTagsForm
Get the xml.
getXml() - Method in class org.intermine.web.struts.ImportXMLForm
Get the xml.
getXml() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Gets xml query string.
GLOBAL - Static variable in class org.intermine.api.search.Scope
Global scope for public bags, templates, etc.
GLOBAL_BAGS - Static variable in class org.intermine.api.search.SearchTarget
The search target for global bags
GLOBAL_CACHE - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
GLOBAL_SEARCH_REPOSITORY - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
GLOBAL_SEGMENT - Static variable in class org.intermine.webservice.server.jbrowse.Segment
global segment
GLOBAL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
The search target for global templates
GlobalRepository - Class in org.intermine.api.search
A representation of an object that knows how to index global objects, and also how to respond to changes to those objects.
GlobalRepository(Profile) - Constructor for class org.intermine.api.search.GlobalRepository
Build a new global search repository and register it with the list of global repositories available.
GLOBALS - Static variable in class org.intermine.api.search.SearchRepository
 
goFaster() - Method in class org.intermine.api.results.ExportResultsIterator
Switches on the goFaster mode in the objectstore for this query.
goFaster() - Method in class org.intermine.api.results.WebResults
Calls ObjectStore.goFaster() if this object wraps a Results object from an ObjectStoreInterMineImpl.
goFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Makes a certain Query go faster, using extra resources.
goFasterCacheMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
goFasterCountMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
goFasterMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
goFasterWithConnection(Query, Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Makes a certain Query go faster, using extra resources.
GORNULL - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that the left is greater than the right, or the left is null.
GORNULL - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
gornull_constraint() - Method in class org.intermine.sql.query.SqlParser
 
GotoWebSearchableAction - Class in org.intermine.web.struts
Action handles search.
GotoWebSearchableAction() - Constructor for class org.intermine.web.struts.GotoWebSearchableAction
 
grant(Database, String, String) - Static method in class org.intermine.sql.DatabaseUtil
Grant permission on all tables for given user on specified database.
grantPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
Grant permission to the given identity, creating a profile for this identity if it is not already available.
GrantTask - Class in org.intermine.task
Task to grant permissions on all tables in a database to a given user.
GrantTask() - Constructor for class org.intermine.task.GrantTask
 
GRAPH_CACHE - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
GraphJSONProcessor - Class in org.intermine.webservice.server.widget
A widget result processor that produces chart results in JSON.
GraphService - Class in org.intermine.webservice.server.widget
 
GraphService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.GraphService
 
GraphWidget - Class in org.intermine.web.logic.widget
 
GraphWidget(GraphWidgetConfig, InterMineBag, ObjectStore, WidgetOptions, String) - Constructor for class org.intermine.web.logic.widget.GraphWidget
 
GraphWidget.DivNumberFormat - Class in org.intermine.web.logic.widget
class used to format the p-values on the graph
GraphWidgetActionType - Enum in org.intermine.web.logic.widget
Enumeration for possible actions when create the query for graph widgets.
GraphWidgetConfig - Class in org.intermine.web.logic.widget.config
Configuration object describing details of a graph displayer
GraphWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
GraphWidgetLoader - Class in org.intermine.web.logic.widget
The class that does the actual querying for results.
GraphWidgetLoader(InterMineBag, ObjectStore, GraphWidgetConfig, String, String) - Constructor for class org.intermine.web.logic.widget.GraphWidgetLoader
Constructor.
GraphWidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet running WidgetsService.
GraphWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.GraphWidgetsServlet
 
GraphXMLProcessor - Class in org.intermine.webservice.server.widget
A processor for returning results from graph widgets in XML.
GraphXMLProcessor() - Constructor for class org.intermine.webservice.server.widget.GraphXMLProcessor
Constructor, obvs
GREATER - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being greater than another AbstractValue.
GREATER_THAN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is greater than the second
GREATER_THAN_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is greater than or equal to the second
greaterOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare this value of this AbstractValue with another to see if it is more or equal.
greaterThan(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be greater than a value.
greaterThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare this value of this AbstractValue with another to see if it is more.
greaterThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be greater than or equal to a value.
GREATEST - Static variable in class org.intermine.objectstore.query.QueryExpression
Return the greatest value from two expressions, e.g.
GREATEST - Static variable in class org.intermine.sql.query.Function
GREATEST(x, y) - takes two operands
group_clause() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
group_clause() - Method in class org.intermine.sql.query.SqlParser
 
group_clause(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
GROUP_CLAUSE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
GROUP_CLAUSE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
groupBy - Variable in class org.intermine.sql.query.Query
 
groupByClass(Collection<E>, boolean) - Static method in class org.intermine.util.CollectionUtil
Sorts objects in the given collection into different types by Class.
GT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
GT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 

H

handleCreation(CreationEvent) - Method in class org.intermine.api.search.GlobalRepository
 
handleCreation(CreationEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the creation of a web searchable object.
handleCreation(CreationEvent) - Method in class org.intermine.api.search.UserRepository
 
handleDeletion(DeletionEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the deletion of a web searchable object.
handleDeletion(DeletionEvent) - Method in class org.intermine.api.search.UserRepository
 
handleHeaderAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
 
handleHeaderAttributes(Map<String, Object>, StringBuilder) - Method in class org.intermine.webservice.server.output.XMLFormatter
Serialise the headers to the current string builder.
handleMassTagging() - Method in class org.intermine.api.search.GlobalRepository
 
handleMassTagging() - Method in class org.intermine.api.search.SearchRepository
Respond to the fact that multiple tags have been added and that we do not know what they are.
handleMassTagging() - Method in class org.intermine.api.search.UserRepository
 
handleMessages(BagQueryResult, HttpSession, Properties, String, String) - Static method in class org.intermine.web.struts.DisplayLookupMessageHandler
Generates and saves messages for bag lookup
handlePropertyChange(PropertyChangeEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the change in the properties of a web searchable object.
handlePropertyChange(PropertyChangeEvent) - Method in class org.intermine.api.search.UserRepository
 
handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.GlobalRepository
 
handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the addition of a tag to a web searchable object.
handleTagAddition(TaggingEvent) - Method in class org.intermine.api.search.UserRepository
 
handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.GlobalRepository
 
handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.SearchRepository
Respond in some way to the removal of a tag from a web searchable object.
handleTagRemoval(TaggingEvent) - Method in class org.intermine.api.search.UserRepository
 
hasAllTags(Taggable) - Method in class org.intermine.api.search.TagFilter
Check to see if this taggable item has all the tags it is meant to.
hasAttribute(String) - Method in class org.intermine.xml.full.Item
Return true if named attribute exists.
hasAutocompleter(String, String) - Method in class org.intermine.web.autocompletion.AutoCompleter
checks if an autocompletion exists
hasCallback() - Method in class org.intermine.webservice.server.WebService
Determine whether a callback was supplied to this request.
hasClassDescriptor(String) - Method in class org.intermine.metadata.Model
Return true if named ClassDescriptor is found in the model.
hasCollection(String) - Method in class org.intermine.xml.full.Item
Return true if named collection exists.
HasFromList - Interface in org.intermine.objectstore.query
Interface to define the types of things that can have from elements added to them.
hashCode() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
hashCode() - Method in class org.intermine.api.bag.SharingInvite
 
hashCode() - Method in class org.intermine.api.beans.ObjectDetails
 
hashCode() - Method in class org.intermine.api.beans.PartnerLink
 
hashCode() - Method in class org.intermine.api.idresolution.ResolutionJob
 
hashCode() - Method in class org.intermine.api.mines.ObjectRequest
 
hashCode() - Method in class org.intermine.api.mines.RemoteMine
 
hashCode() - Method in class org.intermine.api.profile.BagValue
 
hashCode() - Method in class org.intermine.api.profile.SavedQuery
Hash code.
hashCode() - Method in class org.intermine.api.results.Column
hashCode() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
hashCode() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
hashCode() - Method in class org.intermine.api.results.ResultElement
hashCode() - Method in class org.intermine.api.template.ApiTemplate
 
hashCode() - Method in class org.intermine.api.userprofile.PermanentToken
 
hashCode() - Method in class org.intermine.api.userprofile.SavedBag
 
hashCode() - Method in class org.intermine.api.userprofile.SavedQuery
 
hashCode() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
hashCode() - Method in class org.intermine.api.userprofile.Tag
 
hashCode() - Method in class org.intermine.api.userprofile.TemplateSummary
 
hashCode() - Method in class org.intermine.api.userprofile.UserProfile
 
hashCode() - Method in class org.intermine.metadata.AttributeDescriptor
hashCode() - Method in class org.intermine.metadata.ClassDescriptor
hashCode() - Method in class org.intermine.metadata.CollectionDescriptor
hashCode() - Method in class org.intermine.metadata.Model
hashCode() - Method in class org.intermine.metadata.PrimaryKey
hashCode() - Method in class org.intermine.metadata.ReferenceDescriptor
hashCode() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
hashCode() - Method in class org.intermine.model.fulldata.Item
 
hashCode() - Method in class org.intermine.objectstore.query.BagConstraint
hashCode() - Method in class org.intermine.objectstore.query.ClassConstraint
Get the hashCode for this object
hashCode() - Method in class org.intermine.objectstore.query.Clob
Override Object#hashCode.
hashCode() - Method in class org.intermine.objectstore.query.ConstraintSet
Get the hashCode for this object overrides Object.hashCode().
hashCode() - Method in class org.intermine.objectstore.query.ContainsConstraint
Get the hashCode for this object, overrides Object.hashCode()
hashCode() - Method in class org.intermine.objectstore.query.iql.IqlQuery
hashCode() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBag
Override Object#hashCode.
hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
hashCode() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
hashCode() - Method in class org.intermine.objectstore.query.OverlapConstraint
hashCode() - Method in class org.intermine.objectstore.query.PathExpressionField
hashCode() - Method in class org.intermine.objectstore.query.QueryCast
hashCode() - Method in class org.intermine.objectstore.query.QueryField
Returns a hash code for this object.
hashCode() - Method in class org.intermine.objectstore.query.QueryValue
Overrides Object.
hashCode() - Method in class org.intermine.objectstore.query.Results
 
hashCode() - Method in class org.intermine.objectstore.query.ResultsInfo
hashCode() - Method in class org.intermine.objectstore.query.SimpleConstraint
Get the hashCode for this object overrides Object.hashCode()
hashCode() - Method in class org.intermine.objectstore.query.SubqueryConstraint
Get the hashCode for this object overrides Object.hashCode()
hashCode() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
Get the hashCode for this object overrides Object.hashCode()
hashCode() - Method in class org.intermine.pathquery.LogicExpression
hashCode() - Method in class org.intermine.pathquery.Node
hashCode() - Method in class org.intermine.pathquery.OrderElement
hashCode() - Method in class org.intermine.pathquery.Path
hashCode() - Method in class org.intermine.pathquery.PathQuery
 
hashCode() - Method in class org.intermine.sql.precompute.PrecomputedTable
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.AbstractConstraint
Overrides Object.hashcode();
hashCode() - Method in class org.intermine.sql.query.AbstractTable
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.AbstractValue
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Constant
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Constraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.ConstraintSet
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.ExplainResult
hashCode() - Method in class org.intermine.sql.query.Field
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Function
Overrides Object.hashcode.
hashCode() - Method in class org.intermine.sql.query.InListConstraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.NotConstraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.OrderDescending
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.query.Query
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.SelectValue
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.SubQuery
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.SubQueryConstraint
Overrides Object.hashCode().
hashCode() - Method in class org.intermine.sql.query.Table
Overrides Object.hashcode().
hashCode() - Method in class org.intermine.sql.writebatch.Row
hashCode() - Method in class org.intermine.template.TemplateQuery
 
hashCode() - Method in class org.intermine.util.AlwaysMap
hashCode() - Method in class org.intermine.util.IdentityMap
hashCode() - Method in class org.intermine.util.ReferenceMap
hashCode() - Method in class org.intermine.web.logic.config.Displayer
hashCode() - Method in class org.intermine.web.logic.config.FieldConfig
hashCode() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
 
hashCode() - Method in class org.intermine.web.logic.config.TableExportConfig
hashCode() - Method in class org.intermine.web.logic.config.Type
hashCode() - Method in class org.intermine.web.logic.config.WebConfig
hashCode() - Method in class org.intermine.web.logic.template.ConstraintInput
 
hashCode() - Method in class org.intermine.web.logic.TreeNode
hashCode() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
hashCode() - Method in class org.intermine.webservice.server.core.Either
 
hashCode() - Method in class org.intermine.webservice.server.core.Either.Left
 
hashCode() - Method in class org.intermine.webservice.server.core.Either.Right
 
hashCode() - Method in class org.intermine.webservice.server.jbrowse.Command
 
hashCode() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
hashCode() - Method in class org.intermine.webservice.server.JWTBuilder
 
hashCode() - Method in class org.intermine.xml.full.Attribute
hashCode() - Method in class org.intermine.xml.full.Item
hashCode() - Method in class org.intermine.xml.full.Reference
hashCode() - Method in class org.intermine.xml.full.ReferenceList
hashCode(Object) - Static method in class org.intermine.metadata.Util
Return a zero hashCode if the object is null, otherwise return the real hashCode
hashCodeNoUnion() - Method in class org.intermine.sql.query.Query
Returns a partial hashcode, ignoring other queries in the union.
hasHelperForType(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
 
hashPassword(String) - Static method in class org.intermine.util.PasswordHasher
Converts a password into a hashed password, with a salt.
hasIssues() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
 
hasKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
For a given classreturn true if it has any identifying fields.
hasNext() - Method in class org.intermine.api.results.ExportResultsIterator
hasNext() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
hasNext() - Method in class org.intermine.util.CombinedIterator
hasNext() - Method in class org.intermine.util.ObjectPipe
hasNext() - Method in class org.intermine.util.SynchronisedIterator
hasNext() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.FilteringResultIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
hasNext() - Method in class org.intermine.webservice.server.output.JSONRowIterator
 
hasNext() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator
 
hasProblems() - Method in class org.intermine.metadata.Model
Return true if there are problems with the model despite it's successful creation.
hasProfile(String) - Method in class org.intermine.api.profile.ProfileManager
Check whether a user already has a Profile
hasReference(String) - Method in class org.intermine.xml.full.Item
Return true if named reference exists.
hasSeries() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
hasTag(String, Taggable) - Method in class org.intermine.api.profile.TagManager
Test whether a particular taggable thing has been tagged with a particular tag.
hasTag(String, Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
Test whether a particular taggable thing has been tagged with a particular tag, by a particular user.
hasValidPath(Object, String, InterMineAPI) - Static method in class org.intermine.web.logic.WebUtil
Check whether the runtime type of an object supports a particular path.
having - Variable in class org.intermine.sql.query.Query
 
having_clause() - Method in class org.intermine.sql.query.SqlParser
 
having_clause(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
HAVING_CLAUSE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
HeaderConfigLink - Class in org.intermine.web.logic.config
Will store a link configured through HeaderConfig (WebConfig) and used on report page header
HeaderConfigLink() - Constructor for class org.intermine.web.logic.config.HeaderConfigLink
 
HeaderConfigTitle - Class in org.intermine.web.logic.config
Configuration of an object (Type) header when displayed on report
HeaderConfigTitle() - Constructor for class org.intermine.web.logic.config.HeaderConfigTitle
 
HeaderConfigTitle.TitlePart - Class in org.intermine.web.logic.config
Holder for a path that appears in the title and any prefix and suffix values if they have been configured.
HeaderFilter - Class in org.intermine.web.filters
A Filter that modifies response headers of outgoing pages.
HeaderFilter() - Constructor for class org.intermine.web.filters.HeaderFilter
 
HeartbeatAction - Class in org.intermine.web.struts
Takes a parameter "type" with value "webapp" or "query" and prints "OK" to the client if everything is ok, otherwise something else.
HeartbeatAction() - Constructor for class org.intermine.web.struts.HeartbeatAction
 
HIDDEN - Static variable in class org.intermine.web.logic.Constants
The preference set if the user does not want to be found
hideColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't hide columns any more
HintingFetcher - Class in org.intermine.dataloader
Class providing EquivalentObjectFetcher functionality that makes use of hints to improve performance.
HintingFetcher(BaseEquivalentObjectFetcher) - Constructor for class org.intermine.dataloader.HintingFetcher
Constructor
HOLM_BONFERRONI - org.intermine.web.logic.widget.ErrorCorrection.Strategy
The Holm-Bonferroni error correction strategy
HomePageMarkupService - Class in org.intermine.webservice.server.fair
Serve markup to be added to the home page
HomePageMarkupService(InterMineAPI) - Constructor for class org.intermine.webservice.server.fair.HomePageMarkupService
Constructor
HTML - org.intermine.webservice.server.Format
The HTML format
HtmlHeadController - Class in org.intermine.web.struts
Controller for the html head tile.
HtmlHeadController() - Constructor for class org.intermine.web.struts.HtmlHeadController
 
htmlId - Variable in class org.intermine.api.results.ResultElement
 
HtmlListFormatter - Class in org.intermine.webservice.server.lists
A formatter that represents lists as HTML.
HtmlListFormatter() - Constructor for class org.intermine.webservice.server.lists.HtmlListFormatter
 
HTMLOutput - Class in org.intermine.webservice.server.output
HTMLOutput extends is similar to MemoryOutput, only difference is, that it prints out errors immediately to output.
HTMLOutput(PrintWriter) - Constructor for class org.intermine.webservice.server.output.HTMLOutput
Constructor.
HTMLTableFormatter - Class in org.intermine.webservice.server.output
A formatter that presents query results as HTML.
HTMLTableFormatter() - Constructor for class org.intermine.webservice.server.output.HTMLTableFormatter
 
HTMLWidget - Class in org.intermine.web.logic.widget
Represents a widget with no data, it just diplays the "content" string.
HTMLWidget(WidgetConfig) - Constructor for class org.intermine.web.logic.widget.HTMLWidget
 
HTMLWidgetConfig - Class in org.intermine.web.logic.widget.config
dummy widget to output html widget
HTMLWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.HTMLWidgetConfig
 
HttpClient - Class in org.intermine.web.util
Very simple http client that downloads data.
HttpClient() - Constructor for class org.intermine.web.util.HttpClient
 
HttpExporterBase - Class in org.intermine.web.logic.export.http
Abstract class with functionality common for all classes implementing TableHttpExporter interface like getting result from paged table.
HttpExporterBase() - Constructor for class org.intermine.web.logic.export.http.HttpExporterBase
 
HttpExportUtil - Class in org.intermine.web.logic.export.http
Util for export.
HttpRequester - Class in org.intermine.api.mines
A mine requester that makes HTTP requests.
HttpRequester() - Constructor for class org.intermine.api.mines.HttpRequester
Create an object that will make HTTP requests
HUNDRED - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
hyperLinkNote(String) - Static method in class org.intermine.task.AcceptanceTestTask
Return a hyperlinked version of the given note.

I

id - Variable in class org.intermine.api.userprofile.PermanentToken
 
id - Variable in class org.intermine.api.userprofile.SavedBag
 
id - Variable in class org.intermine.api.userprofile.SavedQuery
 
id - Variable in class org.intermine.api.userprofile.SavedTemplateQuery
 
id - Variable in class org.intermine.api.userprofile.Tag
 
id - Variable in class org.intermine.api.userprofile.TemplateSummary
 
id - Variable in class org.intermine.api.userprofile.UserProfile
 
id - Variable in class org.intermine.model.fulldata.Item
 
ID - org.intermine.api.profile.TagMapper.Field
The identifier of the tagged object.
ID_ONLY - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
IDs only
identifier - Variable in class org.intermine.model.fulldata.Item
 
IDENTIFIER - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
IDENTIFIER - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
IDENTIFIER - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
IDENTIFIER_CONSTRAINT - Static variable in class org.intermine.api.config.Constants
constrain by object identifier
IDENTIFIERS - org.intermine.api.tracker.util.ListBuildMode
identifiers in list
identifierToId(String) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Turn an item identifier into an object id.
IdentityMap<E> - Class in org.intermine.util
This is a dumb implementation of a Map.
idMap - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
idMap - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
idMapOps - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
IdResolutionService - Class in org.intermine.webservice.server.idresolution
 
IdResolutionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.IdResolutionService
Default constructor.
IdResolutionServlet - Class in org.intermine.webservice.server.idresolution
Route requests for ID resolution.
IdResolutionServlet() - Constructor for class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
IDResolver - Class in org.intermine.api.idresolution
 
ids - Variable in class org.intermine.web.logic.widget.Widget
 
ids - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
ids - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
idToIdentifier(Integer) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Turn an object id into an item identifier.
idToNamespace - Variable in class org.intermine.dataconversion.ItemToObjectTranslator
 
IdUpgrader - Interface in org.intermine.api.bag
Bag object id upgrader - find old objects in a new ObjectStore.
ignore - Variable in class org.intermine.web.filters.SetCharacterEncodingFilter
Should a character encoding specified by the client be ignored?
ignore - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
ignoreDuplicates - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
ignoreDuplicates - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
ignoreDuplicates - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
ignoreNames - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
im - Variable in class org.intermine.web.displayer.ReportDisplayer
 
im - Variable in class org.intermine.web.logic.bag.BagConverter
 
im - Variable in class org.intermine.webservice.server.WebService
The configuration object.
IM_ASPECT_MISC - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects by Miscellaneous aspect
IM_ASPECT_PREFIX - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects by some aspect
IM_CONVERTER - Static variable in class org.intermine.api.tag.TagNames
String used to tag converter templates in the webapp.
IM_FAVOURITE - Static variable in class org.intermine.api.tag.TagNames
String used to tag favourite objects
IM_HIDDEN - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects that should be hidden at jsp page
IM_PREFIX - Static variable in class org.intermine.api.tag.TagNames
Prefix common for all InterMine internal tags
IM_PUBLIC - Static variable in class org.intermine.api.tag.TagNames
Tag for pubic things (bags, templates).
IM_REPORT - Static variable in class org.intermine.api.tag.TagNames
String used to tag templates that should appear on report pages.
IM_SEARCH_RESULTS - Static variable in class org.intermine.api.tag.TagNames
templates to be displayed on search results page
IM_SUMMARY - Static variable in class org.intermine.api.tag.TagNames
String used to tag objects to appear in the summary section of the report page
IM_WIDGET - Static variable in class org.intermine.api.tag.TagNames
bag with background population for specific widget
immutable - Variable in class org.intermine.objectstore.query.Results
 
imObj - Variable in class org.intermine.api.results.ResultElement
 
implementations - Variable in class org.intermine.model.fulldata.Item
 
IMPLIED_BY - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes one constraint as being implied by another constraint.
IMPLIES - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes one constraint as implying another constraint.
ImportQueriesAction - Class in org.intermine.web.struts
Imports query in XML format and forward user to the query builder.
ImportQueriesAction() - Constructor for class org.intermine.web.struts.ImportQueriesAction
 
ImportQueriesForm - Class in org.intermine.web.struts
Form bean representing query import form.
ImportQueriesForm() - Constructor for class org.intermine.web.struts.ImportQueriesForm
 
ImportTagsAction - Class in org.intermine.web.struts
Import tags.
ImportTagsAction() - Constructor for class org.intermine.web.struts.ImportTagsAction
 
ImportTagsForm - Class in org.intermine.web.struts
Form bean representing tags import form.
ImportTagsForm() - Constructor for class org.intermine.web.struts.ImportTagsForm
Creates a new instance of ImportTagsForm.
ImportXMLForm - Class in org.intermine.web.struts
Form bean representing a generic import form.
ImportXMLForm() - Constructor for class org.intermine.web.struts.ImportXMLForm
Construct a form.
in(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be IN a named bag.
IN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is IN the second
INCOMPARABLE - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being incomparable to another AbstractValue.
IncompatibleTypes - Exception in org.intermine.api.bag.operations
 
IncompatibleTypes(MetaDataException) - Constructor for exception org.intermine.api.bag.operations.IncompatibleTypes
 
IncompatibleTypesException - Exception in org.intermine.api.bag
Exception thrown when given bags are of incompatible types, has methods to set and fetch the types.
IncompatibleTypesException(String) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException
Constructs an IncompatibleBagTypesException with the specified detail message.
IncompatibleTypesException(String, Throwable) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException
Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.
IncompatibleTypesException(Throwable) - Constructor for exception org.intermine.api.bag.IncompatibleTypesException
Constructs an IncompatibleBagTypesException with the specified nested throwable.
incrementHintCount(String) - Method in class org.intermine.web.logic.results.WebState
Increment the number of times a hint has been displayed.
indefiniteArticle(String) - Static method in class org.intermine.metadata.StringUtil
Return 'a' or 'an' according to first letter of the given article.
INDENT - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
INDENT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
INDENT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
INDENT - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
INDENT - Static variable in class org.intermine.codegen.JavaModelOutput
 
INDENT - Static variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
INDENT2 - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
INDENT3 - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
indentXmlSimple(String) - Static method in class org.intermine.util.XmlUtil
Apply some indentiation to some XML.
INDEPENDENT - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being independent.
index - Variable in class org.intermine.api.results.Column
 
INDEX_OF - Static variable in class org.intermine.objectstore.query.QueryExpression
Position of specified string in other specified string
indexes - Variable in class org.intermine.api.search.SearchRepository
 
IndexHandler - Interface in org.intermine.api.searchengine
Interface for handling indexes.
indirections - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
IndirectionTableBatch - Class in org.intermine.sql.writebatch
A class representing all changes to be made to an SQL indirection table.
IndirectionTableBatch(String, String) - Constructor for class org.intermine.sql.writebatch.IndirectionTableBatch
Constructor for this class.
IndirectionTableBatch(String, String, Set<Row>) - Constructor for class org.intermine.sql.writebatch.IndirectionTableBatch
Constructor for dodgy temp table deleting stuff
info - Variable in class org.intermine.objectstore.query.ResultsBatches
 
informUserOfNewSharedBag(String, Profile, InterMineBag) - Method in class org.intermine.util.Emailer
Send a 'sharing list' message
inIds(String, Collection<Integer>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be IN a collection of ids.
init() - Method in class org.intermine.objectstore.query.ClobAccess
Initialises the state of this object.
init() - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
 
init() - Method in class org.intermine.webservice.server.core.RestfulServlet
 
init() - Method in class org.intermine.webservice.server.lists.ListInput
Initialise this structure
init(FilterConfig) - Method in class org.intermine.web.filters.ExpiresHeaderFilter
Initialise this Filter.
init(FilterConfig) - Method in class org.intermine.web.filters.HeaderFilter
Initialise this Filter.
init(FilterConfig) - Method in class org.intermine.web.filters.PermanentURLFilter
Initialise this Filter.
init(FilterConfig) - Method in class org.intermine.web.filters.ReleaseEtagFilter
 
init(FilterConfig) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Place this filter into service.
init(FilterConfig) - Method in class org.intermine.webservice.server.filter.RequestSubClassFilter
 
init(ServletConfig) - Method in class org.intermine.web.logic.login.OpenIDAuthenticator
 
init(ServletConfig) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
init(ActionServlet, ModuleConfig) - Method in class org.intermine.web.struts.InitialiserPlugin
Init method called at Servlet initialisation
initialise() - Method in class org.intermine.web.struts.BagUploadConfirmForm
Initialise the form.
initialise() - Method in class org.intermine.web.struts.ChangeTableSizeForm
Initialiser
initialise() - Method in class org.intermine.web.struts.CSVExportForm
Initialiser
initialise() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyBagForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyQueryForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifySuperUserForm
Initialiser
initialise() - Method in class org.intermine.web.struts.ModifyTemplateForm
Initialiser
initialise() - Method in class org.intermine.web.struts.SaveBagForm
Initialiser
initialise() - Method in class org.intermine.web.struts.TableExportForm
Initialiser
initialise() - Method in class org.intermine.web.struts.TriageBagForm
 
initialise() - Method in class org.intermine.web.struts.WidgetForm
Initialiser
initialise(InterMineAPI, Properties, WebConfig, ResourceOpener) - Static method in class org.intermine.web.context.InterMineContext
Set up the Context with everything it needs.
initialised - Variable in class org.intermine.objectstore.query.ResultsBatches
 
initialiseDelendumAccumulator(Set<String>, ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService
Initialise the accumulator that builds up the list of temporary lists to delete.
INITIALISER_KEY_ERROR - Static variable in class org.intermine.web.logic.Constants
Key for the initialiser error
InitialiserPlugin - Class in org.intermine.web.struts
Initialiser for the InterMine web application.
InitialiserPlugin() - Constructor for class org.intermine.web.struts.InitialiserPlugin
 
initSession(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Initialise a new session.
initState() - Method in class org.intermine.webservice.server.jbrowse.Config
 
initState() - Method in class org.intermine.webservice.server.jbrowse.Names
 
initState() - Method in class org.intermine.webservice.server.model.ModelService
 
initState() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
initState() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
initState() - Method in class org.intermine.webservice.server.VersionService
 
initState() - Method in class org.intermine.webservice.server.WebService
Subclasses can put initialisation here.
initUserProfileResources(ObjectStoreWriter) - Method in class org.intermine.api.InterMineAPI
Initialise parts of this object that require connection to a user-profile object store.
INLINE_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants
The name of the property to look up to find the maximum size of an inline table.
InlineList - Class in org.intermine.web.logic.results
 
InlineList(Set<Object>, String, Boolean, String, Integer) - Constructor for class org.intermine.web.logic.results.InlineList
Set a set ;) of Objects by turning them into InterMineObjects and then InlineListObjects
InlineListConfig - Class in org.intermine.web.logic.config
Represents an inline list to be shown on a Report page
InlineListConfig() - Constructor for class org.intermine.web.logic.config.InlineListConfig
 
InlineListObject - Class in org.intermine.web.logic.config
An individual InterMineObject wrapped in an InlineList Set
InlineListObject(InterMineObject, Object, Object) - Constructor for class org.intermine.web.logic.config.InlineListObject
Initialize
InlineResultsTable - Class in org.intermine.web.logic.results
An inline table created from a Collection This table has one object per row
InlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>) - Constructor for class org.intermine.web.logic.results.InlineResultsTable
Construct a new InlineResultsTable object
InlineResultsTable(Collection<?>, Model, WebConfig, Map<String, List<FieldDescriptor>>, int, boolean, List<Class<?>>, String, FieldDescriptor) - Constructor for class org.intermine.web.logic.results.InlineResultsTable
Construct with parent type and a field descriptor.
InlineResultsTableRow - Class in org.intermine.web.logic.results
Provides a wrapper for a row of InlineTableResultElement
InlineResultsTableRow() - Constructor for class org.intermine.web.logic.results.InlineResultsTableRow
 
InlineTableResultElement - Class in org.intermine.web.logic.results
ResultElement used in an InlineResultsTable
InlineTableResultElement(FastPathObject, Path, FieldConfig, Boolean) - Constructor for class org.intermine.web.logic.results.InlineTableResultElement
Instantiate ResultElement while saving its FieldConfig
InlineTagEditorController - Class in org.intermine.web.struts
Controller for the inline tag editing tile
InlineTagEditorController() - Constructor for class org.intermine.web.struts.InlineTagEditorController
 
inlist_constraint() - Method in class org.intermine.sql.query.SqlParser
 
inlist_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
INLIST_CONSTRAINT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
InListConstraint - Class in org.intermine.sql.query
A representation of a constraint where an AbstractValue is IN a list of constants.
InListConstraint(AbstractValue) - Constructor for class org.intermine.sql.query.InListConstraint
Constructor for InListConstraint object.
INNER - org.intermine.pathquery.OuterJoinStatus
 
inputModelFile - Variable in class org.intermine.task.ModelMergerTask
 
INSIDE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
instance() - Static method in class org.intermine.webservice.server.widget.EnrichmentJSONProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.EnrichmentXMLProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.FlatFileWidgetResultProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.FlatWidgetProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.GraphJSONProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.JSONWidgetProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.TableJSONProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.TableXMLProcessor
 
instance() - Static method in class org.intermine.webservice.server.widget.XMLWidgetProcessor
 
Instance - Class in org.intermine.web.registry.model
Pojo class to map the intermine instance retrieved from the registry
Instance() - Constructor for class org.intermine.web.registry.model.Instance
 
INSTANCE - Static variable in class org.intermine.pathquery.PathQueryBinding
A single instance of this class
INSTANCE - Static variable in class org.intermine.template.xml.TemplateQueryBinding
A single instance of this class
INSTANCE_INFO - Static variable in class org.intermine.web.logic.Constants
The key under which basic instance info (from the registry) are stored
instances - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
instances - Static variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
instantiate(String) - Static method in class org.intermine.metadata.TypeUtil
Deprecated.
This method is named incorrectly - use getTypeByName instead.
instantiate(String) - Static method in class org.intermine.metadata.Util
Returns the Class for a given name (promoting primitives to their container class)
instantiateObject(String, String) - Static method in class org.intermine.util.DynamicUtil
Create an outline business object from a class name and a list of interface names
INT_BAG_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the table that holds the integer ObjectStoreBag elements.
integer - org.intermine.sql.DatabaseUtil.Type
integer
INTEGER - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
INTEGER - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
integrationWriter - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
integrationWriter - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
IntegrationWriter - Interface in org.intermine.dataloader
Define methods needed to deal with integration when writing to an ObjectStore.
IntegrationWriterAbstractImpl - Class in org.intermine.dataloader
Abstract implementation of ObjectStoreIntegrationWriter.
IntegrationWriterAbstractImpl(ObjectStoreWriter) - Constructor for class org.intermine.dataloader.IntegrationWriterAbstractImpl
Constructs a new instance of an IntegrationWriter
IntegrationWriterDataTrackingImpl - Class in org.intermine.dataloader
Priority-based implementation of IntegrationWriter.
IntegrationWriterDataTrackingImpl(ObjectStoreWriter, DataTracker) - Constructor for class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Constructs a new instance of IntegrationWriterDataTrackingImpl.
IntegrationWriterDataTrackingImpl(ObjectStoreWriter, DataTracker, Set<Class<?>>) - Constructor for class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Constructs a new instance of IntegrationWriterDataTrackingImpl.
IntegrationWriterFactory - Class in org.intermine.dataloader
Produce IntegrationWriters
intercept(Object, Method, Object[], MethodProxy) - Method in class org.intermine.util.DynamicBean
Intercept all method calls, and operate on Map.
IntermediateRepresentation() - Constructor for class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
 
INTERMINE_API - Static variable in class org.intermine.web.logic.Constants
Key for the InterMine API object
INTERMINE_VERSION - Static variable in class org.intermine.web.logic.Constants
Current version of the InterMine code
InterMineAction - Class in org.intermine.web.struts
An InterMine specific version of Action.
InterMineAction() - Constructor for class org.intermine.web.struts.InterMineAction
 
InterMineAPI - Class in org.intermine.api
InterMineAPI provides access to manager objects for the main parts of an InterMine application: the production ObjectStore, the userprofile (via ProfileManager), template queries, bags and tags.
InterMineAPI() - Constructor for class org.intermine.api.InterMineAPI
Protected no-argument constructor only used for building test implementations of this class.
InterMineAPI(ObjectStore, ObjectStoreWriter, ClassKeys, BagQueryConfig, ObjectStoreSummary, TrackerDelegate, LinkRedirectManager) - Constructor for class org.intermine.api.InterMineAPI
Construct an InterMine API object.
InterMineBag - Class in org.intermine.api.profile
An object that represents a bag of objects in our database for the webapp.
InterMineBag(String, String, String, Date, BagState, ObjectStore, Integer, ObjectStoreWriter, List<String>) - Constructor for class org.intermine.api.profile.InterMineBag
Constructs a new InterMineIdBag, and saves it in the UserProfile database.
InterMineBag(String, String, String, Date, BagState, ObjectStore, ObjectStoreWriter, List<String>) - Constructor for class org.intermine.api.profile.InterMineBag
Constructs a new InterMineBag, and saves it in the UserProfile database.
InterMineBag(ObjectStore, Integer, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InterMineBag
Loads an InterMineBag from the UserProfile database.
InterMineBag(ObjectStore, Integer, ObjectStoreWriter, boolean) - Constructor for class org.intermine.api.profile.InterMineBag
Loads an InterMineBag from the UserProfile database.
InterMineBagBinding - Class in org.intermine.api.xml
Parse InterMineIdBags in XML format
InterMineBagBinding() - Constructor for class org.intermine.api.xml.InterMineBagBinding
 
InterMineBagHandler - Class in org.intermine.api.xml
A handler for turning XML bags data into an InterMineIdBag.
InterMineBagHandler(ObjectStoreWriter, ObjectStoreWriter, Map<String, InterMineBag>, Map<String, InvalidBag>, Map<String, Set<BagValue>>) - Constructor for class org.intermine.api.xml.InterMineBagHandler
Create a new InterMineBagHandler object.
InterMineBagHandler(ObjectStoreWriter, ObjectStoreWriter, Map<String, InterMineBag>, Map<String, InvalidBag>, Map<String, Set<BagValue>>, Integer) - Constructor for class org.intermine.api.xml.InterMineBagHandler
Create a new InterMineBagHandler object.
InterMineContext - Class in org.intermine.web.context
A context object that doesn't require the session.
InterMineDispatchAction - Class in org.intermine.web.struts
An InterMine specific version of DispatchAction.
InterMineDispatchAction() - Constructor for class org.intermine.web.struts.InterMineDispatchAction
 
InterMineException - Exception in org.intermine
An Exception that may be thrown by client facing parts of InterMine code.
InterMineException() - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException
InterMineException(String) - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException with the specified detail message.
InterMineException(String, Throwable) - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException with the specified detail message and nested throwable.
InterMineException(Throwable) - Constructor for exception org.intermine.InterMineException
Constructs an InterMineException with the specified nested throwable.
InterMineExceptionHandler - Class in org.intermine.web.struts
InterMine implementation of the Struts ExceptionHandler
InterMineExceptionHandler() - Constructor for class org.intermine.web.struts.InterMineExceptionHandler
 
InterMineFastPathObject - Interface in org.intermine.model
A root interface for all objects that can be stored in a InterMine database.
InterMineLinkGenerator - Class in org.intermine.web.util
Helper class for intermine links generated on report and list pages
InterMineLinkGenerator - Interface in org.intermine.web.displayer
Helper class for intermine links generated on report and list pages
InterMineLinkGenerator() - Constructor for class org.intermine.web.util.InterMineLinkGenerator
 
InterMineLookupDispatchAction - Class in org.intermine.web.struts
An InterMine specific version of LookupDispatchAction.
InterMineLookupDispatchAction() - Constructor for class org.intermine.web.struts.InterMineLookupDispatchAction
 
InterMineLUI - Class in org.intermine.web.uri
Class to represent the InterMine Local Unique Identifier InterMineLUI schema: className:identifier where the identifier is the id provided by the data source provider, in some cases, adapted with a prefix e.g.RGD:62030 Some examples: humanmine.org/humanmine/protein:P31946-> InterMineLUI=protein:P31946 humanmine.org/humanmine/gene:RGD:62030-> InterMineLUI=gene:RGD:62030
InterMineLUI(String) - Constructor for class org.intermine.web.uri.InterMineLUI
Constructor.
InterMineLUI(String, String) - Constructor for class org.intermine.web.uri.InterMineLUI
Constructor.
InterMineLUIConverter - Class in org.intermine.web.uri
This class converts an intermineID into a InterMineLUI or a InterMineLUI into an intermineID.
InterMineLUIConverter() - Constructor for class org.intermine.web.uri.InterMineLUIConverter
Constructor
InterMineLUIConverter(Profile) - Constructor for class org.intermine.web.uri.InterMineLUIConverter
Constructor
InterMineModelParser - Class in org.intermine.metadata
Parse InterMine metadata XML to produce an InterMine Model
InterMineModelParser() - Constructor for class org.intermine.metadata.InterMineModelParser
 
InterMineObject - Interface in org.intermine.model
A root interface for all objects that can be stored in a InterMine database.
InterMineRequestProcessor - Class in org.intermine.web.struts
A RequestProcessor that sends you back to the start if your session isn't valid.
InterMineRequestProcessor() - Constructor for class org.intermine.web.struts.InterMineRequestProcessor
 
InterMineResultsContainer - Class in org.intermine.api.searchengine
container to hold results for a reference query and associated iterator
InterMineResultsContainer(Results) - Constructor for class org.intermine.api.searchengine.InterMineResultsContainer
create container and set iterator
InternalBagOperationException - Exception in org.intermine.api.bag.operations
Exceptions that are the fault of underlying infrastructure, and not the way the classes themselves were used.
InternalBagOperationException() - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
Constructor
InternalBagOperationException(String) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
 
InternalBagOperationException(String, Throwable) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
 
InternalBagOperationException(Throwable) - Constructor for exception org.intermine.api.bag.operations.InternalBagOperationException
 
internalCompare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet
Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member fields and tables.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Internal service method for getObjectById.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Internal service method for getObjectById.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Internal service method for getObjectById.
internalGetObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Internal service method for getObjectById.
internalGetObjectByIdWithConnection(Connection, Integer, Class<?>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Gets an object by id given a Connection.
interpretFormat(String) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Figure out which format the user wants.
intersect(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
Create a bag that is the INTERSECTION of all the bags provided, if the intersection is the empty set then don't create the new bag.
INTERSECT - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical intersection.
INTERSECT - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing an INTERSECTION operation
Intersection - Class in org.intermine.api.bag.operations
 
Intersection(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.Intersection
 
IntHelper - Class in org.intermine.api.query.range
 
IntHelper() - Constructor for class org.intermine.api.query.range.IntHelper
 
IntPresentSet - Class in org.intermine.util
This is a set of ints.
IntPresentSet() - Constructor for class org.intermine.util.IntPresentSet
Constructor for this class.
IntToIntMap - Class in org.intermine.util
This is a map that maps from int to int.
IntToIntMap() - Constructor for class org.intermine.util.IntToIntMap
Constructor for this class.
INVALID_NAME_MSG - Static variable in class org.intermine.api.profile.TagManager
What we tell users when they give us an invalid tag name
INVALID_NAME_MSG - Static variable in class org.intermine.api.util.NameUtil
error message for bad names.
INVALID_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
invalidate() - Method in class org.intermine.api.profile.InterMineBag
Declare that this bag is invalid, and return its InvalidBag representation.
invalidateBagTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Remove a cached bag table from the session.
invalidateCache() - Method in class org.intermine.api.template.TemplateManager
Empty cache of global valid templates when these change.
invalidateObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Removes an entry from the objectstore getObjectById cache.
invalidateObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Removes an entry from the objectstore getObjectById cache.
invalidateObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Removes an entry from the objectstore getObjectById cache.
invalidateObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Removes an entry from the objectstore getObjectById cache.
invalidateTemplateCacheIfRequired() - Method in class org.intermine.api.profile.Profile
When a template or tag is updated, invalidate cache so it can be refreshed
InvalidBag - Class in org.intermine.api.profile
A class representing a bag that is invalid because it does not conform to the current model.
InvalidBag(String, String, String, Date, ObjectStore, Integer, Integer, ObjectStoreBag, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag
Constructor.
InvalidBag(String, String, String, Date, ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag
Minimal constructor.
InvalidBag(SavedBag, Integer, ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.InvalidBag
Constructor callable by the ProfileManager.
InvalidPermanentURLException - Exception in org.intermine.web.uri
Thrown to indicate that the http request is not a permanent URL The valid patters is: domain/context/classname:identifier (e.g.
InvalidPermanentURLException() - Constructor for exception org.intermine.web.uri.InvalidPermanentURLException
 
InvalidQueryException - Exception in org.intermine.api.query.codegen
A class representing a failure to generate the code for a query because the query is invalid.
InvalidQueryException(String) - Constructor for exception org.intermine.api.query.codegen.InvalidQueryException
Construct an exception with a single problem.
InvalidQueryException(Collection<? extends String>) - Constructor for exception org.intermine.api.query.codegen.InvalidQueryException
Construct an exception with a list of problems.
InvitationAction - Class in org.intermine.web.struts
Action that processes invitations.
InvitationAction() - Constructor for class org.intermine.web.struts.InvitationAction
 
InvitationForm - Class in org.intermine.web.struts
A form that contains the information for requests that invite users to share resources.
InvitationForm() - Constructor for class org.intermine.web.struts.InvitationForm
 
InvitationHandler - Class in org.intermine.api.bag
 
InvitationHandler() - Constructor for class org.intermine.api.bag.InvitationHandler
 
inviteToShare(InterMineBag, String) - Static method in class org.intermine.api.bag.SharedBagManager
Generate an invitation to share a bag.
invokeConstructor(ClobAccess) - Method in class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory
Method to return a new instance of the subclass of ClobAccess that this object represents.
iql_statement() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
IQL_STATEMENT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
IqlLexer - Class in org.intermine.objectstore.query.iql
 
IqlLexer(InputBuffer) - Constructor for class org.intermine.objectstore.query.iql.IqlLexer
 
IqlLexer(LexerSharedInputState) - Constructor for class org.intermine.objectstore.query.iql.IqlLexer
 
IqlLexer(InputStream) - Constructor for class org.intermine.objectstore.query.iql.IqlLexer
 
IqlLexer(Reader) - Constructor for class org.intermine.objectstore.query.iql.IqlLexer
 
IqlParser - Class in org.intermine.objectstore.query.iql
 
IqlParser(ParserSharedInputState) - Constructor for class org.intermine.objectstore.query.iql.IqlParser
 
IqlParser(TokenBuffer) - Constructor for class org.intermine.objectstore.query.iql.IqlParser
 
IqlParser(TokenBuffer, int) - Constructor for class org.intermine.objectstore.query.iql.IqlParser
 
IqlParser(TokenStream) - Constructor for class org.intermine.objectstore.query.iql.IqlParser
 
IqlParser(TokenStream, int) - Constructor for class org.intermine.objectstore.query.iql.IqlParser
 
IqlQuery - Class in org.intermine.objectstore.query.iql
OQL representation of an object-based Query
IqlQuery() - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
No-arg constructor (for deserialization)
IqlQuery(String, String) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
Construct an IQL query from a String.
IqlQuery(String, String, List<?>) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
Construct an IQL query from a String.
IqlQuery(Query) - Constructor for class org.intermine.objectstore.query.iql.IqlQuery
Construct an IQL query from a Query object.
IqlQueryParser - Class in org.intermine.objectstore.query.iql
Parser for the InterMine dialect of OQL (IQL)
IqlTokenTypes - Interface in org.intermine.objectstore.query.iql
 
IS_EMPTY - Static variable in class org.intermine.metadata.ConstraintOp
Synonym for IS NULL
IS_NOT_EMPTY - Static variable in class org.intermine.metadata.ConstraintOp
Synonym for IS NOT NULL
IS_NOT_NULL - Static variable in class org.intermine.metadata.ConstraintOp
Require that the argument is not null
IS_NULL - Static variable in class org.intermine.metadata.ConstraintOp
Require that the argument is null
IS_SUPERUSER - Static variable in class org.intermine.web.logic.Constants
Session attribute equals Boolean.TRUE when logged in user is superuser.
ISA - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument be of the type named by the right argument
isAggregate() - Method in class org.intermine.sql.query.AbstractValue
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.Constant
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.Field
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.Function
Returns true if this value is an aggregate function.
isAggregate() - Method in class org.intermine.sql.query.OrderDescending
Returns true if this value is an aggregate function.
isAllRowsSelected() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return true if a whole column is selected either by selecting the whole column checkbox or by selecting each row individually.
isAnyBagInState(Profile, BagState) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the given state
isAnyBagInStates(Profile, Set<BagState>) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in at least one of the given states
isAnyBagNotCurrent(Profile) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the 'not_current' state.
isAnyBagNotCurrentOrUpgrading(Profile) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the 'not_current' state or 'upgrading'.
isAnyBagToUpgrade(Profile) - Method in class org.intermine.api.bag.BagManager
Return true if there is at least one user bag for the given profile in the 'to_upgrade' state.
isAnyBagUnresolvable() - Method in class org.intermine.webservice.server.core.ListManager
Return true if there is at least one bag in the 'to_upgrade' state.
isApplicable() - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Return true if the correction coefficient is applicable
isAspectTag(String) - Static method in class org.intermine.api.tag.AspectTagUtil
 
isAssignableFrom(Class<?>, Class<?>) - Static method in class org.intermine.util.DynamicUtil
Returns true if sup is a superclass of sub (or the same), taking into account dynamic classes.
isAssociatedWith(Constraint, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the constraint is associated with the given FromElement.
isAssociatedWithNothing(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the given constraint is associated with no particular FromElement.
isAttribute() - Method in class org.intermine.metadata.FieldDescriptor
Is this FieldDescriptor an attribute?
isAttribute() - Method in class org.intermine.pathquery.Node
Gets the value of attribute
isAttribute() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns true if the path represents an attribute (rather than a class, reference, or collection).
isAuthenticated() - Method in class org.intermine.webservice.server.WebService
 
isBagConstraint() - Method in class org.intermine.template.TemplateValue
Return true if this constraint value is a bag.
isBagSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a bag has been selected.
isBagValuesEmpty(Connection) - Static method in class org.intermine.sql.DatabaseUtil
Verify if 'bagvalues' table is empty
isBoolean() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing having the attribute type boolean or Boolean
isCancelled() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out whether the query was cancelled.
isCancelledWithError() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out whether an error occured while trying to run the query.
isCellValidForPath(ResultElement, Path) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Test whether a result element matches the type of its path.
isCollection() - Method in class org.intermine.metadata.FieldDescriptor
Is this FieldDescriptor a collection?
isCollection() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns true if the reference is a collection.
isCollection() - Method in class org.intermine.pathquery.Node
Gets the value of collection
isCollection() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns true if the path represents a collection.
isCompleted() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Find out whether the query has completed.
isComputeTotalCount() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Returns true if should be displayed total count of all available results.
isConsistentType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
 
isCountRequest(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
 
isCrossReference(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the Constraint is a cross-reference between two QueryClasses.
isCurrent() - Method in class org.intermine.api.profile.InterMineBag
Return true if the status bag is current, otherwise false (status is not current or to upgrade)
isDebugOutput() - Method in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
 
isDeleteTracks() - Method in class org.intermine.web.struts.TemplatesImportForm
Get the deleteTracks flag.
isDirty() - Method in class org.intermine.dataloader.ObjectDescription
Returns whether this ObjectDescription is dirty.
isDisabled() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the constraint is disabled, false if it is enabled or locked.
isDistinct() - Method in class org.intermine.objectstore.query.Query
Get the value of the distinct property
isDistinct() - Method in class org.intermine.sql.query.Query
Gets the current distinct status of this query.
isDuplicates - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
isEditable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Get the editable flag (when building a template).
isEditable(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns whether a constraint is editable.
isEditableInTemplate() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing template constraint and that constraint is editable.
isEditableInTemplate() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Returns true if the constraint is part of a template query and the constraint is editable in that template.
isEdited() - Method in class org.intermine.template.TemplateQuery
Returns true if the TemplateQuery has been edited by the user and is therefore saved only in the query history.
isEmpty() - Method in class org.intermine.objectstore.query.Results
isEmpty() - Method in class org.intermine.pathquery.PathQuery
Returns true if the query has no features yet.
isEmpty() - Method in class org.intermine.util.AlwaysMap
isEmpty() - Method in class org.intermine.util.IdentityMap
isEmpty() - Method in class org.intermine.util.PseudoSet
isEmpty() - Method in class org.intermine.util.ReferenceMap
isEmpty() - Method in class org.intermine.web.logic.results.DisplayField
Return true if the collection is empty or reference null.
isEmpty(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Returns true is there are no rows in the results.
isEmptySelection() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return true if and only if nothing is selected
isEnabled() - Static method in class org.intermine.web.fair.SemanticMarkupFormatter
Return true if markup are enabled (disabled by default)
isEnabled() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the constraint is enabled, false if it is disabled or locked.
isErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
Return true if exists blocking errors
isExplain() - Method in class org.intermine.sql.query.Query
Gets the current explain status of this query.
isExtraConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if this is a LOOKUP constraint and an extra constraint should be available.
isFetchFromInterMineObject() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if ProxyReferences can be fetched from the InterMineObject table.
isFilterConstraint(WidgetConfig, PathConstraint) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
 
isFirstPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Check if were are on the first page
isFlatMode(Class<?>) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if the ObjectStore needs to run in flat mode for this Class - if notXml is missing and the InterMineObject table is missing (or if the class is not a subclass of InterMineObject).
isForcedInnerJoin() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Return true if this path is forced to be an inner join because it is involved in a loop constraint.
isGeneratedClassAvailable(String) - Method in class org.intermine.metadata.Model
 
isGeneratedClassesAvailable() - Method in class org.intermine.metadata.Model
 
isGzip() - Method in class org.intermine.webservice.server.WebService
 
isInputFieldDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the input field can be displayed, method for use in JSP
isInRole(String) - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
True if the permission granted includes access to this role.
isInstance(Object, Class<?>) - Static method in class org.intermine.util.DynamicUtil
Returns true if obj is an instance of clazz, taking into account dynamic classes.
isInstanceOf(FastPathObject, String) - Static method in class org.intermine.metadata.TypeUtil
Return true if and only if the object is an instance of the class given by the className.
isInterface() - Method in class org.intermine.metadata.ClassDescriptor
True if this class is an interface.
isInTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Check whether the ObjectStore is performing a transaction, delegate to internal ObjectStoreWriter.
isInTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Check whether the ObjectStoreWriter is performing a transaction
isInTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
Check whether the ObjectStoreWriter is performing a transaction
isInTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Finds if we are in a transaction.
isInvalidTemplate(WebSearchable) - Static method in class org.intermine.api.search.SearchResults
Check if a websearchable is an invalid template.
isIsProduction() - Method in class org.intermine.web.registry.model.Instance
 
isIssues() - Method in class org.intermine.web.struts.DisplayLookupMessageHandler
Check if there are any identifiers that didn't match.
isJsonP(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Work out if this a JSON-P request.
isKeyField() - Method in interface org.intermine.api.results.ResultCell
 
isKeyField() - Method in class org.intermine.api.results.ResultElement
Return true if this object represents a field that is an identifying field (according to ClassKeyHelper.isKeyField())
isKeyField() - Method in class org.intermine.webservice.server.core.TableCell
 
isKeyField(Map<String, List<FieldDescriptor>>, String, String) - Static method in class org.intermine.api.config.ClassKeyHelper
For a given class/field return true if it is an 'identifying' field.
isLastPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Check if we are on the last page
isLeaf() - Method in class org.intermine.web.logic.TreeNode
Is this node a leaf?
isLegalColumnName(String) - Static method in class org.intermine.sql.DatabaseUtil
Check that a column name provided to us is a legal column name, to prevent SQL injection.
isListConstraint(PathConstraint) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
 
isListPathSet() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
isLocal() - Method in class org.intermine.api.profile.Profile
Returns true if this is a local account, and not, for example, an OpenID account.
isLocked() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the constraint is locked, it should'n be enabled or disabled.
isLocked() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Return true if this path is locked because it is involved in a loop constraint.
isLoggedIn() - Method in class org.intermine.api.profile.Profile
Return true if and only if the user is logged is (and the Profile will be written to the userprofile).
isLoggedIn() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
isLoggedIn() - Method in class org.intermine.api.util.AnonProfile
 
isLookup() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if this constraint should be a LOOKUP, true if constraining a class (ref/col) instead of an attribute and that class has class keys defined.
isLoopSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a loop value has been selected.
isMissingNotXml() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if NotXML should be omitted from all tables except the InterMineObject table, and the InterMineObject table is present.
isMultiConnection() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in interface org.intermine.objectstore.ObjectStore
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultiConnection() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Return whether or not this ObjectStore gives a performance improvement when multiple simultaneous are made.
isMultipleValue() - Method in class org.intermine.template.TemplateValue
 
isMultiValuesDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the multi-select containing the possibleValue can be displayed, method for use in JSP
isMultiValueSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a multivalue has been selected.
isNextEnabled() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
isNotNull(String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be not null.
ISNOTNULL - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
ISNT - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument be of the type named by the right argument
isNull(String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be null.
ISNULL - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
isNullSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and 'has a value' or 'has no value' has been selected.
isNumeric() - Method in class org.intermine.metadata.AttributeDescriptor
Returns true if the type of the attribute is some kind of number.
ISO_DATE_FORMAT - Static variable in class org.intermine.pathquery.ConstraintValueParser
A date format for ISO dates.
ISO8601DateFormat - Class in org.intermine.webservice.server.core
A date formatter for the ISO8601 date format.
ISO8601DateFormat() - Constructor for class org.intermine.webservice.server.core.ISO8601DateFormat
Constructor.
isObjectConstraint() - Method in class org.intermine.template.TemplateValue
Return true if this constraint value is on InterMineObject
isOfType(String) - Method in class org.intermine.api.profile.InterMineBag
Test whether the given type can be added to this bag, type can be a qualified or un-qualified string.
isOnlyAttribute() - Method in class org.intermine.pathquery.Path
Return true if the Path does not contain references or collections
isOpen() - Method in class org.intermine.web.logic.TreeNode
Is this node expanded?
isOpenByDefault() - Method in class org.intermine.web.logic.config.FieldConfig
Get whether this field should be uncollapsed if sectionOnRight is true.
isOptional(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns whether a constraint is optional.
isOuterJoin() - Method in class org.intermine.pathquery.Node
Returns true if this should be an outer join.
isOverwriting() - Method in class org.intermine.web.struts.ImportTagsForm
Get the overwrite flag.
isOverwriting() - Method in class org.intermine.web.struts.TemplatesImportForm
Get the overwrite flag.
isPathCompletelyInner(String) - Method in class org.intermine.pathquery.PathQuery
Returns true if a path string is in the root outer join group of this query.
isPathContainingSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
Check to see if the path contains a subclass.
isPossibleValuesDisplayed() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if the drop-down containing the possibleValues can be displayed, method for use in JSP
isPrecomputed(Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Checks if a query is precomputed or not for the given type
isPrecomputedWithConnection(Connection, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Checks if a query is precomputed or not for the given type and connection
isPrimitive() - Method in class org.intermine.metadata.AttributeDescriptor
Returns true if the type of the attribute is a primitive type (rather than object).
isPrimitive() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Return true if the end element of the path is an attribute and the attribute is a primitive type.
isProfileCached(String) - Method in class org.intermine.api.profile.ProfileManager
Check if the profile, whose username is given in input, has been cached by the profile cache
isPublic() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Returns whether this query is publicly accessible.
isPublic(InterMineBag) - Method in class org.intermine.api.bag.BagManager
Return true if the bag is public.
isRangeSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and a range has been entered.
isReference() - Method in class org.intermine.metadata.FieldDescriptor
Is this FieldDescriptor a reference?
isReference() - Method in class org.intermine.pathquery.Node
Gets the value of reference
isReference() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns true if the path represents a reference.
isRelatedTo(Constraint, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the constraint is associated with the given FromElement.
isRelatedToNothing(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Returns true if the given constraint is related to no FromElement.
isRequired(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Returns whether a constraint is required.
isReservedWord(String) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Returns true if the given String is an IQL reserved word.
isReverseReference() - Method in class org.intermine.web.logic.query.MetadataNode
Returns true if this path is a reverse reference back onto the previous node.
isRO() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
isRootPath() - Method in class org.intermine.pathquery.Path
Return true if this path represents just the starting class, e.g.
isRW() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
 
isSectionOnRight() - Method in class org.intermine.web.logic.config.FieldConfig
Whether this field should be rendered in its own section on the right side of the page.
isSelectable() - Method in class org.intermine.api.results.Column
Gets the value of selectable
isSelected() - Method in class org.intermine.web.logic.query.MetadataNode
Get the value of selected
isSelected() - Method in class org.intermine.web.logic.TreeNode
Is this node selected?
isSelected(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Return true if the correction coefficient is selected
isShowExtraConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
isSingleBatch() - Method in class org.intermine.api.results.WebResults
Returns true if the results are known to be contained in a single batch.
isSingleBatch() - Method in interface org.intermine.api.results.WebTable
Returns true if the results are known to be contained in a single batch.
isSingleBatch() - Method in class org.intermine.objectstore.query.Results
Returns true if the results are known to fit entirely within the first batch.
isSingleBatch() - Method in class org.intermine.objectstore.query.ResultsBatches
Returns true if the results are known to fit entirely within the first batch.
isSingleton() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Returns true if the SELECT list is empty or if singleton results are requested.
isSizeEstimate() - Method in class org.intermine.api.results.WebResults
Check whether the result of getEstimatedSize() is an estimate
isSizeEstimate() - Method in interface org.intermine.api.results.WebTable
Check whether the result of getEstimatedSize() is an estimate
isSizeEstimate() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Check whether the result of getSize is an estimate
ISSUE_KEYS - Static variable in class org.intermine.api.bag.BagQueryResult
keys of the map in a set
IssueResult(String, String, List) - Constructor for class org.intermine.api.bag.BagQueryResult.IssueResult
 
issueToken(Profile, int) - Method in class org.intermine.webservice.server.JWTBuilder
Issue a new token for the given profile.
IssueTokenTask - Class in org.intermine.web.task
A task that will issue a signed JWT token for the current configuration.
IssueTokenTask() - Constructor for class org.intermine.web.task.IssueTokenTask
 
isSummarised(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
Returns true if the given template has been summarised.
isSuperuser() - Method in class org.intermine.api.profile.Profile
Return true if and only if the user logged is superuser
isSuperuser() - Method in class org.intermine.api.util.AnonProfile
 
isSuperUser - Variable in class org.intermine.api.profile.Profile
 
isSuperUser(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Return true if and only if the current user if the superuser.
isToUpgrade() - Method in class org.intermine.api.profile.InterMineBag
Return true if the status bag is to_upgrade, otherwise false
isTreatColNames() - Method in class org.intermine.web.tags.table.TableTag
 
isTruncated() - Method in class org.intermine.metadata.StringUtil.LineWrappedString
Returns whether the String had to be truncated.
isTruncated(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
Returns true if a query using the given table-mastering ClassDescriptor would require a constraint on the className field.
isUncompressed() - Method in class org.intermine.webservice.server.WebService
 
isUpdated - Variable in class org.intermine.api.profile.PathQueryUpdate
 
isUpdated() - Method in class org.intermine.api.profile.PathQueryUpdate
Return true if the pathquery has been updated
isValid() - Method in class org.intermine.pathquery.PathQuery
Returns true if the query verifies correctly.
isValid(String, String, String, UserProfile) - Method in interface org.intermine.api.profile.TagChecker
Returns true if and only the given arguments are valid fields for a tag of this type.
isValidEditableConstraintType() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
Return true if this type of constraint can be set as editable in a template query - i.e.
isValidName(String) - Static method in class org.intermine.api.util.NameUtil
Verifies names (bags, queries, etc) only contain A-Z, a-z, 0-9, underscores and dashes.
isValidName(String, boolean) - Static method in class org.intermine.api.util.NameUtil
Verifies names (bags, queries, etc) only contain A-Z, a-z, 0-9, underscores and dashes.
isValidRange() - Method in class org.intermine.web.logic.query.DisplayConstraint
 
isValidTagName(String) - Static method in class org.intermine.api.profile.TagManager
TODO this should use the same validation method the other classes use Verifies that tag name can only contain A-Z, a-z, 0-9, '_', '-', ' ', ':', '.'
isValueSelected() - Method in class org.intermine.web.logic.query.DisplayConstraint
Return true if editing an existing constraint and an attribute value or LOOKUP constraint was selected.
isVerbose() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Returns true if the optimiser will print out stuff.
isVersionAtLeast(String) - Method in class org.intermine.sql.Database
Return true if the database version is at least as high as the test number given, taking into account major and minor versions.
isVisible() - Method in class org.intermine.api.results.Column
Gets the value of visible
isWindowsClient(HttpServletRequest) - Static method in class org.intermine.web.logic.RequestUtil
 
isWithinLimit(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
Check that this requester is within their limit.
isZip() - Method in class org.intermine.webservice.server.WebService
 
item - Variable in class org.intermine.model.fulldata.Attribute
 
item - Variable in class org.intermine.model.fulldata.Reference
 
item - Variable in class org.intermine.model.fulldata.ReferenceList
 
Item - Class in org.intermine.model.fulldata
 
Item - Class in org.intermine.xml.full
Representation of an object
Item() - Constructor for class org.intermine.model.fulldata.Item
 
Item() - Constructor for class org.intermine.xml.full.Item
Construct an item.
Item(String, String, String) - Constructor for class org.intermine.xml.full.Item
Construct an item with no Model.
Item(Model, String, String, String) - Constructor for class org.intermine.xml.full.Item
Construct an item.
ItemFactory - Class in org.intermine.xml.full
ItemFactory class
ItemFactory() - Constructor for class org.intermine.xml.full.ItemFactory
Create an ItemFactory that isn't specific to a particular model.
ItemFactory(Model) - Constructor for class org.intermine.xml.full.ItemFactory
Create an ItemFactory specific to a particular model.
ItemFactory(Model, String) - Constructor for class org.intermine.xml.full.ItemFactory
Create an ItemFactory specific to a particular model.
ItemHelper - Class in org.intermine.xml.full
Class providing Item utility methods
ItemToObjectTranslator - Class in org.intermine.dataconversion
Translator that translates fulldata Items to business objects
ItemToObjectTranslator(Model, ObjectStore) - Constructor for class org.intermine.dataconversion.ItemToObjectTranslator
Constructor
ItemWriter - Interface in org.intermine.dataconversion
Stores Items in something - an objectstore or otherwise.
iter - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
 
iterator - Variable in class org.intermine.util.SynchronisedIterator
 
iterator() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
iterator() - Method in class org.intermine.api.results.WebResults
 
iterator() - Method in class org.intermine.api.search.SearchResults
 
iterator() - Method in class org.intermine.objectstore.proxy.ProxyCollection
iterator() - Method in class org.intermine.objectstore.query.Results
iterator() - Method in class org.intermine.util.ConsistentSet
Return an iterator for the elements in the Set.
iterator() - Method in class org.intermine.util.IteratorIterable
Returns the iterator.
iterator() - Method in class org.intermine.util.PseudoSet
iterator() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
iteratorFrom(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
iteratorFrom(int) - Method in class org.intermine.api.results.WebResults
 
iteratorFrom(int) - Method in class org.intermine.objectstore.query.Results
Returns an iterator over the List, starting from the given position.
IteratorIterable<T> - Class in org.intermine.util
This is an Iterable that returns a given Iterator.
IteratorIterable(Iterator<T>) - Constructor for class org.intermine.util.IteratorIterable
Constructs an Iterable from an Iterator.
iteratorIterator - Variable in class org.intermine.util.CombinedIterator
 

J

JaccardIndexService - Class in org.intermine.webservice.server.lists
A service to compare the given list to all other available lists using the Jaccard Index
JaccardIndexService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.JaccardIndexService
Constructor
JaccardIndexServlet - Class in org.intermine.webservice.server.lists
 
JaccardIndexServlet() - Constructor for class org.intermine.webservice.server.lists.JaccardIndexServlet
 
javaiseClassName(String) - Static method in class org.intermine.metadata.TypeUtil
Filter a URI fragment to remove illegal characters
javaisePackageName(String) - Static method in class org.intermine.metadata.TypeUtil
Filter a string to remove illegal characters and join the rest in lower case.
JavaModelOutput - Class in org.intermine.codegen
Maps InterMine metadata to Java source files
JavaModelOutput(Model, File) - Constructor for class org.intermine.codegen.JavaModelOutput
Constructor.
Job - Interface in org.intermine.api.idresolution
 
Job(String, Query, Collection<? extends QueryNode>, boolean, String) - Constructor for class org.intermine.objectstore.intermine.ParallelPrecomputer.Job
Constructor - takes the same arguments as ObjectStoreInterMineImpl.precompute().
Job.JobStatus - Enum in org.intermine.api.idresolution
 
JobInput - Interface in org.intermine.api.idresolution
 
JobJanitor - Class in org.intermine.webservice.server.idresolution
Wake up once a minute and evict old completed jobs.
JobJanitor() - Constructor for class org.intermine.webservice.server.idresolution.JobJanitor
 
JobRemovalService - Class in org.intermine.webservice.server.idresolution
 
JobRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.JobRemovalService
 
JobResultsService - Class in org.intermine.webservice.server.idresolution
 
JobResultsService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.idresolution.JobResultsService
Construct a jobs service handler.
JobStatusService - Class in org.intermine.webservice.server.idresolution
 
JobStatusService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.idresolution.JobStatusService
Construct a handler for this request.
join(Collection<?>, String) - Static method in class org.intermine.metadata.StringUtil
Returns a String formed by the delimited results of calling toString over a collection.
join(Collection<?>, String) - Static method in class org.intermine.metadata.Util
Returns a String formed by the delimited results of calling toString over a collection.
joinType - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
JSON - org.intermine.api.mines.ContentType
The JSON content type
JSON - org.intermine.web.struts.oauth2.ResponseType
This provider responds with JSON
JSON - org.intermine.webservice.server.Format
Vanilla-JSON
JSON_FORMATS - Static variable in enum org.intermine.webservice.server.Format
The JSON formats: JSON, OBJECTS, TABLE, ROWS
JSONCountFormatter - Class in org.intermine.webservice.server.output
A formatter that presents count results as JSON.
JSONCountFormatter() - Constructor for class org.intermine.webservice.server.output.JSONCountFormatter
 
JSONDataTableRowIterator - Class in org.intermine.webservice.server.output
 
JSONDataTableRowIterator(ExportResultsIterator) - Constructor for class org.intermine.webservice.server.output.JSONDataTableRowIterator
Constructor
JSONDataTableRowResultProcessor - Class in org.intermine.webservice.server.output
A result processor for result rows.
JSONDataTableRowResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor
Constructor.
JSONFormatter - Class in org.intermine.webservice.server.output
Base class for formatters that process JSON data.
JSONFormatter() - Constructor for class org.intermine.webservice.server.output.JSONFormatter
Constructor
JSONFormattingException - Exception in org.intermine.webservice.server.output
 
JSONFormattingException(String) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException
 
JSONFormattingException(String, Throwable) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException
 
JSONFormattingException(Throwable) - Constructor for exception org.intermine.webservice.server.output.JSONFormattingException
 
JSONListFormatter - Class in org.intermine.webservice.server.lists
 
JSONListFormatter(InterMineAPI, Profile, boolean) - Constructor for class org.intermine.webservice.server.lists.JSONListFormatter
Construct a list formatter.
JSONObjectFormatter - Class in org.intermine.webservice.server.output
 
JSONObjectFormatter() - Constructor for class org.intermine.webservice.server.output.JSONObjectFormatter
Constructor
JSONObjResultProcessor - Class in org.intermine.webservice.server.output
 
JSONObjResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONObjResultProcessor
Constructor.
JSONQueryHandler - Class in org.intermine.pathquery
Handle parsing JSON queries and template queries
JSONResultFormatter - Class in org.intermine.webservice.server.output
 
JSONResultFormatter() - Constructor for class org.intermine.webservice.server.output.JSONResultFormatter
 
JSONResultProcessor - Class in org.intermine.webservice.server.output
An class that defines the basic methods for processing JSON results.
JSONResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONResultProcessor
Constructor.
JSONResultsIterator - Class in org.intermine.webservice.server.output
A class to to produce a sequence of JSONObjects from a set of database rows.
JSONResultsIterator(ExportResultsIterator) - Constructor for class org.intermine.webservice.server.output.JSONResultsIterator
Constructor.
JSONRowFormatter - Class in org.intermine.webservice.server.output
 
JSONRowFormatter() - Constructor for class org.intermine.webservice.server.output.JSONRowFormatter
Constructor
JSONRowIterator - Class in org.intermine.webservice.server.output
 
JSONRowIterator(ExportResultsIterator, InterMineAPI) - Constructor for class org.intermine.webservice.server.output.JSONRowIterator
Constructor
JSONRowResultProcessor - Class in org.intermine.webservice.server.output
A result processor for result rows.
JSONRowResultProcessor(InterMineAPI) - Constructor for class org.intermine.webservice.server.output.JSONRowResultProcessor
Constructor.
JSONRowResultProcessor(InterMineAPI, JSONRowResultProcessor.Verbosity) - Constructor for class org.intermine.webservice.server.output.JSONRowResultProcessor
Construct a row result processor.
JSONRowResultProcessor.Verbosity - Enum in org.intermine.webservice.server.output
 
JSONService - Class in org.intermine.webservice.server.core
A Service that has specialisations for supplying JSON.
JSONService(InterMineAPI) - Constructor for class org.intermine.webservice.server.core.JSONService
Constructor
JSONSummaryProcessor - Class in org.intermine.webservice.server.output
A processor for summary results in JSON format.
JSONSummaryProcessor() - Constructor for class org.intermine.webservice.server.output.JSONSummaryProcessor
 
JSONTableFormatter - Class in org.intermine.webservice.server.output
 
JSONTableFormatter() - Constructor for class org.intermine.webservice.server.output.JSONTableFormatter
Constructor.
JSONTableResultProcessor - Class in org.intermine.webservice.server.output
 
JSONTableResultProcessor() - Constructor for class org.intermine.webservice.server.output.JSONTableResultProcessor
Constructor.
JSONUserFormatter - Class in org.intermine.webservice.server.user
A formatter that knows how to format a user in JSON
JSONUserFormatter(Profile) - Constructor for class org.intermine.webservice.server.user.JSONUserFormatter
Construct a user formatter.
JSONWidgetProcessor - Class in org.intermine.webservice.server.widget
 
JSStrings - Class in org.intermine.api.query.codegen
 
JWTBuilder - Class in org.intermine.webservice.server
A class that encapsulates the logic required to generate JWT tokens for users.
JWTBuilder(PrivateKey, String) - Constructor for class org.intermine.webservice.server.JWTBuilder
Constructor
JWTBuilder(JWTBuilder.Algorithm, PrivateKey, String) - Constructor for class org.intermine.webservice.server.JWTBuilder
Constructor
JWTBuilder.Algorithm - Enum in org.intermine.webservice.server
The signing algorithms this builder supports.
JWTVerifier - Class in org.intermine.webservice.server
A class to encapsulate the logic for verifying identity claims as represented as JWTs (JSON Web Tokens).
JWTVerifier(PublicKeySource, Properties) - Constructor for class org.intermine.webservice.server.JWTVerifier
Construct a verifier.
JWTVerifier.Verification - Class in org.intermine.webservice.server
The result of a successful verification.
JWTVerifier.VerificationError - Exception in org.intermine.webservice.server
An error that declares that something has gone wrong when trying to verify a JWT.

K

KEY_CALLBACK - Static variable in class org.intermine.webservice.server.output.JSONFormatter
The key for the callback
KEY_COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.HTMLTableFormatter
The key for setting headers
KEY_COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the title.
KEY_COUNT - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the count.
KEY_CURRENT_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attribute for the current page
KEY_DEFINITIONS - Static variable in class org.intermine.metadata.Util
Name of the key under which to store the serialized version of the key definitions
KEY_DEFINITIONS - Static variable in class org.intermine.modelproduction.MetadataManager
Name of the key under which to store the serialized version of the key definitions
KEY_DESCRIPTION - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the description.
KEY_EXPORT_CSV_URL - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the CSV export URL.
KEY_EXPORT_TSV_URL - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the TSV export URL.
KEY_HEADER_OBJS - Static variable in class org.intermine.webservice.server.output.JSONFormatter
Things that should go into the header
KEY_INTRO - Static variable in class org.intermine.webservice.server.output.JSONFormatter
the key for the result object.
KEY_KV_PAIRS - Static variable in class org.intermine.webservice.server.output.JSONFormatter
A map of optional key value pairs that should go in the header of the object.
KEY_MODEL_NAME - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter
The key for the model name
KEY_NEXT_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the next page
KEY_OUTRO - Static variable in class org.intermine.webservice.server.output.JSONFormatter
The way to wrap up after the result.
KEY_PREVIOUS_PAGE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the previous page
KEY_QUOTE - Static variable in class org.intermine.webservice.server.output.JSONFormatter
Whether we should quote the result item.
KEY_ROOT_CLASS - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter
The key for the root class
KEY_TIME - Static variable in class org.intermine.webservice.server.output.JSONFormatter
The key for the execution time
KEY_TITLE - Static variable in class org.intermine.webservice.server.output.JSONTableFormatter
The key for setting the header attributes for the title.
KEY_VIEWS - Static variable in class org.intermine.webservice.server.output.JSONResultFormatter
The key for the views
KeyDecoder - Interface in org.intermine.web.security
Classes that can decode public keys from strings.
keyField - Variable in class org.intermine.api.results.ResultElement
boolean protected as we need to determine if the element is a key field from JSP
KeyFormatException - Exception in org.intermine.api.query
 
KeyFormatException(String, NumberFormatException) - Constructor for exception org.intermine.api.query.KeyFormatException
 
KEYLESS_CLASSES_MAP - Static variable in class org.intermine.web.logic.Constants
Key for a Map from class name to Boolean.TRUE for all classes in the model that do not have any class keys.
KeySearchTrack - Class in org.intermine.api.tracker.track
 
KeySearchTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.KeySearchTrack
 
KeySearchTracker - Class in org.intermine.api.tracker
 
KeySearchTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.KeySearchTracker
Build a search tracker
keySet() - Method in class org.intermine.util.AlwaysMap
keySet() - Method in class org.intermine.util.IdentityMap
keySet() - Method in class org.intermine.util.ReferenceMap
KeySigner - Class in org.intermine.web.security
Issue certificates for keys we trust.
KeySigner(PrivateKey, String, int, String) - Constructor for class org.intermine.web.security.KeySigner
Build a new signer.
KeySigner.SigningException - Exception in org.intermine.web.security
Errors thrown when signing certificates.
KeySourceException - Exception in org.intermine.web.security
Errors encountered when using a PublicKeySource
KeySourceException(Throwable) - Constructor for exception org.intermine.web.security.KeySourceException
An error caused by another error
KeyStoreBuilder - Class in org.intermine.web.security
Build a key store from some options and possibly a keystore file.
KeyStoreBuilder(Properties, ResourceOpener) - Constructor for class org.intermine.web.security.KeyStoreBuilder
Construct a new KeyStoreBuilder.
KeyStorePublicKeySource - Class in org.intermine.web.security
A public key store that reads keys from a key store.
KeyStorePublicKeySource(KeyStore) - Constructor for class org.intermine.web.security.KeyStorePublicKeySource
Build a key source that reads them from a key store.
KeyStoreTask - Class in org.intermine.web.task
Base task for tasks that require a key store.
KeyStoreTask() - Constructor for class org.intermine.web.task.KeyStoreTask
 
KeywordSearchFacet<E> - Class in org.intermine.api.searchengine
container for one faceting field, the current faceting value and the list of possible items
KeywordSearchFacet(String, String, String, List<E>) - Constructor for class org.intermine.api.searchengine.KeywordSearchFacet
constructor
KeywordSearchFacetData - Class in org.intermine.api.searchengine
container class for a facet field and its settings
KeywordSearchFacetData(String[], String, KeywordSearchFacetType) - Constructor for class org.intermine.api.searchengine.KeywordSearchFacetData
constructor
KeywordSearchFacetData(String, String, KeywordSearchFacetType) - Constructor for class org.intermine.api.searchengine.KeywordSearchFacetData
convenience constructor for single field
KeywordSearchFacetType - Enum in org.intermine.api.searchengine
type of faceting to use see http://snaprojects.jira.com/wiki/display/BOBO/Create+a+Browse+Index
KeywordSearchHandler - Interface in org.intermine.api.searchengine
Interface for handling indexes.
KeywordSearchPropertiesManager - Class in org.intermine.api.searchengine
A manager class to handle all the configuration properties from keyword_search.properties file
KeywordSearchResult - Class in org.intermine.web.search
Container for a single result row from the keyword search
KeywordSearchResult(WebConfig, InterMineObject, Map<String, List<FieldDescriptor>>, ClassDescriptor, float, Map<String, TemplateQuery>, String) - Constructor for class org.intermine.web.search.KeywordSearchResult
create the container object - automatically reads fields and saves the results in members
KeywordSearchResultContainer<E> - Class in org.intermine.api.searchengine
Container for individual Keyword Search Result The document type has been given as generic type.
KeywordSearchResultContainer(E, InterMineObject, float) - Constructor for class org.intermine.api.searchengine.KeywordSearchResultContainer
constructor
KeywordSearchResults - Class in org.intermine.api.searchengine
A class that wraps both a collection of hits and a collection of facets.
KeywordSearchResults(Collection<KeywordSearchResultContainer>, Collection<KeywordSearchFacet>, int) - Constructor for class org.intermine.api.searchengine.KeywordSearchResults
 
KeywordSearchResultsController - Class in org.intermine.web.struts
Controller for keyword search.
KeywordSearchResultsController() - Constructor for class org.intermine.web.struts.KeywordSearchResultsController
 

L

LabelsSummaryAction - Class in org.intermine.web.struts
An action that presents how all the labels configured for classes and their top-level fields appear.
LabelsSummaryAction() - Constructor for class org.intermine.web.struts.LabelsSummaryAction
 
labourer - Variable in class org.intermine.webservice.server.output.FlatFileFormatter
 
LargeObjectInputStream(Connection, LargeObject) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
Constructor.
LargeObjectInputStream(Connection, LargeObject, boolean) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
Constructor.
LargeObjectOutputStream(Connection, LargeObject) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
Constructs a new object.
LargeObjectOutputStream(Connection, LargeObject, boolean) - Constructor for class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
Constructs a new object.
last(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Change to the last results page
lastBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
lastGet - Variable in class org.intermine.objectstore.query.Results
 
lastPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the last page
lastSource - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
lastTickle - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout
Time of last call to tickle.
LAYOUT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Layout parameter name.
Lazy - Interface in org.intermine.objectstore.proxy
Class which uses an ObjectStore to perform lazy fetching of data
LazyCollection<E> - Interface in org.intermine.objectstore.proxy
Class which uses an ObjectStore to perform lazy fetching of data
lazyList() - Method in class org.intermine.webservice.server.core.JSONService
 
lazyList() - Method in class org.intermine.webservice.server.data.DataService
 
lcm(int, int) - Static method in class org.intermine.metadata.Util
Takes two integers, and returns the lowest common multiple.
LE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LEAF_DESCRIPTORS_MAP - Static variable in class org.intermine.web.logic.Constants
Servlet attribute.
LEAST - Static variable in class org.intermine.objectstore.query.QueryExpression
Return the lowest value from two expressions, e.g.
LEAST - Static variable in class org.intermine.sql.query.Function
LEAST(x, y) - takes two operands
left - Variable in class org.intermine.objectstore.query.OverlapConstraint
 
left - Variable in class org.intermine.sql.query.Constraint
 
left - Variable in class org.intermine.sql.query.InListConstraint
 
left - Variable in class org.intermine.sql.query.SubQueryConstraint
 
Left(A) - Constructor for class org.intermine.webservice.server.core.Either.Left
Construct a left.
LEFT_BRACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
LEFT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always false.
LEFT_FALSE_RIGHT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always false, and the right is always true.
LEFT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always true.
LEFT_TRUE_RIGHT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the left is always true, and the right is always false.
length - Variable in class org.intermine.objectstore.query.ClobAccess
 
length() - Method in class org.intermine.model.StringConstructor
length() - Method in class org.intermine.objectstore.query.ClobAccess
Returns the length of this character sequence.
length() - Method in class org.intermine.objectstore.query.PendingClob
Returns the length of this character sequence.
LESS - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being less than another AbstractValue.
LESS_THAN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is less than the second
LESS_THAN_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is less than or equal to the second
lessOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another to see if it is less or equal.
lessThan(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be less than a value.
lessThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another to see if it is less.
lessThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be less than or equal to a value.
level - Variable in class org.intermine.api.userprofile.PermanentToken
 
like(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be LIKE a value.
LIKE - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that left should be pattern-matched against right.
limit - Variable in class org.intermine.sql.query.Query
 
limit_clause() - Method in class org.intermine.sql.query.SqlParser
 
limit_clause(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
LIMIT_CLAUSE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LIMIT_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Name of size parameter that determines number of returned results.
limitedContext - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
LimitedMap<K,​V> - Class in org.intermine.api.util
A caching map that drops its eldest entries if the map grows beyond a certain size.
LimitedMap(int) - Constructor for class org.intermine.api.util.LimitedMap
 
LimitOffsetQuery - Class in org.intermine.sql.precompute
A class specifically for use with the OptimiserCache, designed to split a SQL string into its functional part, and the limit and offset.
LimitOffsetQuery(String) - Constructor for class org.intermine.sql.precompute.LimitOffsetQuery
Creates a new LimitOffsetQuery object from this query string.
LineWrappedString(String, boolean) - Constructor for class org.intermine.metadata.StringUtil.LineWrappedString
Constructor.
linkedHashMapAdd(LinkedHashMap<K, V>, K, K, V) - Static method in class org.intermine.util.CollectionUtil
Return a copy of the given map with the object inserted at the given index.
LinkGeneratorBase - Class in org.intermine.webservice.server
Base class for link generators.
LinkGeneratorBase() - Constructor for class org.intermine.webservice.server.LinkGeneratorBase
Empty constructor.
LinkRedirectManager - Class in org.intermine.api
Class to manage external links.
LinkRedirectManager(Properties) - Constructor for class org.intermine.api.LinkRedirectManager
Constructor
linkRedirector - Variable in class org.intermine.api.InterMineAPI
 
list(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadQueryAction
Load a query using given list
list(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction
Load a template from template name passed as parameter.
LIST_DESCRIPTION_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService
 
LIST_ID_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService
 
LIST_NAME_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService
 
LIST_SEPARATOR - Static variable in class org.intermine.webservice.server.lists.ListInput
The separator used between lists when passed joined together.
LIST_SIZE_KEY - Static variable in class org.intermine.webservice.server.lists.AbstractListService
 
LIST_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks lists
LIST_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks lists
LIST_TYPE_KEY - Static variable in class org.intermine.webservice.server.lists.ListMakerService
 
ListAppendService - Class in org.intermine.webservice.server.lists
 
ListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListAppendService
 
ListBuildMode - Enum in org.intermine.api.tracker.util
 
ListCreationInput - Class in org.intermine.webservice.server.lists
Class representing the input to a list creation request.
ListCreationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListCreationInput
Constructor.
ListDeletionService - Class in org.intermine.webservice.server.lists
A service for deleting lists from the user-profile database.
ListDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListDeletionService
Constructor.
ListDifferenceService - Class in org.intermine.webservice.server.lists
A service for performing a symmetric difference operation on a collection of lists.
ListDifferenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListDifferenceService
Constructor
ListFormatter - Interface in org.intermine.webservice.server.lists
The common interface for formatters that know how to format lists.
ListFunctions - Class in org.intermine.webservice.server.core
Similar to Apache CollectionUtils - but with Generics.
ListInput - Class in org.intermine.webservice.server.lists
Class representing input to a list service request.
ListInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListInput
Parse the values from the request, and validate them.
ListIntersectionService - Class in org.intermine.webservice.server.lists
A service that intersects one or more lists.
ListIntersectionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListIntersectionService
 
listLeft - Variable in class org.intermine.web.struts.ModifyBagForm
 
ListMaker<T> - Interface in org.intermine.webservice.server.lists
The type of things that can make lists.
ListMakerService - Class in org.intermine.webservice.server.lists
A base class for all list services that create lists.
ListMakerService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListMakerService
Constructor.
ListManager - Class in org.intermine.webservice.server.core
Manager of public lists used by web service.
ListManager(InterMineAPI, Profile) - Constructor for class org.intermine.webservice.server.core.ListManager
ListManager constructor.
ListOperationService - Class in org.intermine.webservice.server.lists
A base class for services that perform operations on lists.
ListOperationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListOperationService
Constructor.
listRelatedConstraints(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Return a List of Constraint objects that relate to the given FromElement.
ListRenameInput - Class in org.intermine.webservice.server.lists
Class for encapsulating the input to a list rename request.
ListRenameInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.ListRenameInput
Constructor.
ListRenameService - Class in org.intermine.webservice.server.lists
A service for renaming lists.
ListRenameService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListRenameService
Constructor.
ListRenameServlet - Class in org.intermine.webservice.server.lists
 
ListRenameServlet() - Constructor for class org.intermine.webservice.server.lists.ListRenameServlet
 
ListResolutionService - Class in org.intermine.webservice.server.idresolution
 
ListResolutionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.idresolution.ListResolutionService
Default constructor.
ListResolutionServlet - Class in org.intermine.webservice.server.idresolution
Route requests for list resolution.
ListResolutionServlet() - Constructor for class org.intermine.webservice.server.idresolution.ListResolutionServlet
 
listRight - Variable in class org.intermine.web.struts.ModifyBagForm
 
LISTS_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The lists to operate on
listsButton - Variable in class org.intermine.web.struts.ModifyBagForm
 
ListServiceUtils - Class in org.intermine.webservice.server.lists
Utility functions for dealing with list requests.
ListShareCreationService - Class in org.intermine.webservice.server.lists
 
ListShareCreationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareCreationService
 
ListShareDeletionService - Class in org.intermine.webservice.server.lists
 
ListShareDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareDeletionService
 
ListShareDetailsService - Class in org.intermine.webservice.server.lists
 
ListShareDetailsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListShareDetailsService
 
ListShareServlet - Class in org.intermine.webservice.server.lists
 
ListShareServlet() - Constructor for class org.intermine.webservice.server.lists.ListShareServlet
 
ListSharingInvitationAcceptanceService - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationAcceptanceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
 
ListSharingInvitationDeletionService - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationDeletionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationDeletionService
Construct a service handler.
ListSharingInvitationDetailsService - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationDetailsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
 
ListSharingInvitationService - Class in org.intermine.webservice.server.lists
Invite a user to share a list.
ListSharingInvitationService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationService
 
ListSharingInvitationServlet - Class in org.intermine.webservice.server.lists
 
ListSharingInvitationServlet() - Constructor for class org.intermine.webservice.server.lists.ListSharingInvitationServlet
 
ListsRequestParser - Class in org.intermine.webservice.server.lists
Request processor for ListsService that process request, validates it and returns parsed input as a parameter object.
ListsRequestParser(HttpServletRequest) - Constructor for class org.intermine.webservice.server.lists.ListsRequestParser
ListsRequestProcessor constructor.
ListsService - Class in org.intermine.webservice.server.lists
Web service that returns all public lists (bags) that contain object with specified id.
ListsService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListsService
Constructor
ListsServiceInput - Class in org.intermine.webservice.server.lists
ListsServiceInput is parameter object representing parameters for ListService web service.
ListsServiceInput() - Constructor for class org.intermine.webservice.server.lists.ListsServiceInput
 
ListSubtractionService - Class in org.intermine.webservice.server.lists
A service for subtracting one group of lists from another group of lists to produce a new list.
ListSubtractionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListSubtractionService
Constructor
ListTagAddingService - Class in org.intermine.webservice.server.lists
A service for adding tags to a list.
ListTagAddingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagAddingService
Constructor.
ListTagRemovalService - Class in org.intermine.webservice.server.lists
A service for removing tags from a list.
ListTagRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagRemovalService
Constructor.
ListTagsController - Class in org.intermine.web.struts
Controller for tag display tile on the lists page
ListTagsController() - Constructor for class org.intermine.web.struts.ListTagsController
 
ListTagService - Class in org.intermine.webservice.server.lists
A service for getting the tags of a list.
ListTagService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListTagService
Constructor.
ListTrack - Class in org.intermine.api.tracker.track
Class to represent the track for the lists objects.
ListTrack(String, int, ListBuildMode, ListTrackerEvent) - Constructor for class org.intermine.api.tracker.track.ListTrack
 
ListTrack(String, int, ListBuildMode, ListTrackerEvent, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.ListTrack
 
LISTTRACK - Static variable in class org.intermine.api.tracker.xml.ListTrackBinding
label for XML
ListTrackBinding - Class in org.intermine.api.tracker.xml
 
ListTracker - Class in org.intermine.api.tracker
 
ListTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.ListTracker
Build a list tracker
ListTrackerEvent - Enum in org.intermine.api.tracker.util
 
LISTTRACKS - Static variable in class org.intermine.api.tracker.xml.ListTrackBinding
label for XML
ListUnionService - Class in org.intermine.webservice.server.lists
A class for exposing creating unions of lists as a resource.
ListUnionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUnionService
Constructor.
ListUpdateService - Class in org.intermine.webservice.server.lists
A service for updating list descriptions.
ListUpdateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUpdateService
Constructor.
ListUpgradingService - Class in org.intermine.webservice.server.lists
A service for upgrading lists after a new build.
ListUpgradingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUpgradingService
Constructor.
ListUpgradingServlet - Class in org.intermine.webservice.server.lists
 
ListUpgradingServlet() - Constructor for class org.intermine.webservice.server.lists.ListUpgradingServlet
 
ListUploadService - Class in org.intermine.webservice.server.lists
A class to create a new list with via a set of identifiers uploaded by a user.
ListUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.lists.ListUploadService
Constructor
LITERAL_all - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_all - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_allbutintersect - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_and - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_and - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
LITERAL_and - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_as - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_as - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_avg - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_avg - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_bag - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_bags - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_bigint - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_boolean - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_by - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_by - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_ceil - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_coalesce - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_contain - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_contains - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_count - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_count - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_desc - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_desc - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_distinct - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_distinct - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_does - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_double - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_except - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_exist - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_exists - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_explain - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_explain - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_false - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_false - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_floor - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_for - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_from - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_from - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_greatest - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_greatest - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_group - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_group - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_having - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_in - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_in - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_indexof - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_integer - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_intersect - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_is - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_least - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_least - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_like - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_like - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_limit - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_limit - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_lower - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_lower - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_max - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_max - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_min - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_min - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_not - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_not - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_null - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_null - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_numeric - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_offset - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_or - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_or - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
LITERAL_or - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_order - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_order - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_precision - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_real - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_select - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_select - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_singleton - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_smallint - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_stddev - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_stddev - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_strpos - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_substr - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_substr - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_sum - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_sum - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_text - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_true - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_true - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_union - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_union - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_upper - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_upper - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
LITERAL_where - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LITERAL_where - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
load(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
Load a query.
LoadBagValuesTask - Class in org.intermine.web.task
Task to load bagvalues table in the userprofile database.
LoadBagValuesTask() - Constructor for class org.intermine.web.task.LoadBagValuesTask
 
loadClassKeyDefinitions() - Static method in class org.intermine.modelproduction.MetadataManager
Load the class key / key field definitions.
LoadDefaultTemplatesTask - Class in org.intermine.web.task
Load template queries form an XML file into a given user profile.
LoadDefaultTemplatesTask() - Constructor for class org.intermine.web.task.LoadDefaultTemplatesTask
 
loadHelpers(Properties) - Static method in class org.intermine.api.query.MainHelper
 
loadHelpers(Properties) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
 
LOADING - Static variable in class org.intermine.objectstore.query.PrefetchManager
 
loadKeyDefinitions(String) - Static method in class org.intermine.metadata.Util
Load the key definitions file for the named model from the classpath
loadKeyDefinitions(String) - Static method in class org.intermine.modelproduction.MetadataManager
Load the key definitions file for the named model from the classpath
loadModel(String) - Static method in class org.intermine.metadata.ModelFactory
Load a named model from the classpath
loadProperties(String) - Static method in class org.intermine.metadata.Util
Load a specified properties file
loadProperties(String) - Static method in class org.intermine.util.PropertiesUtil
Load a specified properties resource
loadQuery(PathQuery, HttpSession, HttpServletResponse) - Static method in class org.intermine.web.logic.session.SessionMethods
Load a query into the session, cloning to avoid modifying the original
LoadQueryAction - Class in org.intermine.web.struts
Implementation of Action that sets the current Query for the session from some random XML the user has passed in, and maybe executes it.
LoadQueryAction() - Constructor for class org.intermine.web.struts.LoadQueryAction
 
LoadTemplateAction - Class in org.intermine.web.struts
Implementation of Action that runs a template
LoadTemplateAction() - Constructor for class org.intermine.web.struts.LoadTemplateAction
 
localAccount - Variable in class org.intermine.api.userprofile.UserProfile
 
LocalMine - Class in org.intermine.api.mines
A mine that refers to the local application instance.
LocalMine(InterMineAPI, Properties) - Constructor for class org.intermine.api.mines.LocalMine
Construct a mine that refers to the local application instance.
lock - Static variable in class org.intermine.sql.logging.QueryLogger
 
LOCKED - org.intermine.template.SwitchOffAbility
template constraint can't be edited by the user
log - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
log(Query, Writer) - Static method in class org.intermine.sql.logging.QueryLogger
Allows a Query to be logged
LOG - Static variable in class org.intermine.api.bag.operations.BagOperation
 
LOG - Static variable in class org.intermine.api.profile.InterMineBag
 
LOG - Static variable in class org.intermine.api.profile.InvalidBag
 
LOG - Static variable in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
 
LOG - Static variable in class org.intermine.api.results.WebResults
 
LOG - Static variable in class org.intermine.dwr.AjaxServices
 
LOG - Static variable in class org.intermine.dwr.TrackAjaxServices
 
LOG - Static variable in class org.intermine.pathquery.Path
 
LOG - Static variable in class org.intermine.task.DynamicAttributeTask
 
LOG - Static variable in class org.intermine.task.FileConverterTask
 
LOG - Static variable in class org.intermine.web.displayer.DisplayerManager
 
LOG - Static variable in class org.intermine.web.logic.export.http.StandardHttpExporter
 
LOG - Static variable in class org.intermine.web.logic.export.ResultElementConverter
 
LOG - Static variable in class org.intermine.web.logic.results.DisplayField
 
LOG - Static variable in class org.intermine.web.logic.results.InlineResultsTable
 
LOG - Static variable in class org.intermine.web.logic.session.SessionMethods
 
LOG - Static variable in class org.intermine.web.logic.WebUtil
 
LOG - Static variable in class org.intermine.web.struts.ContactAction
 
LOG - Static variable in class org.intermine.web.struts.CreateTemplateAction
 
LOG - Static variable in class org.intermine.web.struts.ExportQueryAction
 
LOG - Static variable in class org.intermine.web.struts.HtmlHeadController
 
LOG - Static variable in class org.intermine.web.struts.InterMineExceptionHandler
 
LOG - Static variable in class org.intermine.web.struts.ObjectTrailController
 
LOG - Static variable in class org.intermine.web.struts.ObjectViewController
 
LOG - Static variable in class org.intermine.web.struts.PollQueryAction
 
LOG - Static variable in class org.intermine.web.struts.QueryBuilderChange
 
LOG - Static variable in class org.intermine.web.struts.QueryBuilderController
 
LOG - Static variable in class org.intermine.web.struts.RequestPasswordAction
 
LOG - Static variable in class org.intermine.web.struts.SaveBagAction
 
LOG - Static variable in class org.intermine.web.struts.SaveFromIdsToBagAction
 
LOG - Static variable in class org.intermine.web.struts.SaveQueryAction
 
LOG - Static variable in class org.intermine.web.struts.SummariseTemplatesAction
 
LOG - Static variable in class org.intermine.web.struts.TableExportAction
 
LOG - Static variable in class org.intermine.web.struts.TemplatesExportAction
 
LOG - Static variable in class org.intermine.web.struts.WebserviceCodeGenAction
 
LOG - Static variable in class org.intermine.webservice.server.query.CodeService
 
logBeforeExecute - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logError(String) - Method in class org.intermine.web.task.KeyStoreTask
Log a message to standard error.
logEverything - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logExampleQueryUse(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Log load of an example query.
logExplains - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
LogicExpression - Class in org.intermine.pathquery
In memory representation of constraint logic expression.
LogicExpression(String) - Constructor for class org.intermine.pathquery.LogicExpression
Create a new instance of LogicExpression parsing the given expression.
LogicExpression.And - Class in org.intermine.pathquery
An AND operator node.
LogicExpression.Node - Class in org.intermine.pathquery
Node of parse tree.
LogicExpression.Operator - Class in org.intermine.pathquery
An operator node.
LogicExpression.Or - Class in org.intermine.pathquery
An OR operator node.
LogicExpression.Variable - Class in org.intermine.pathquery
A variable node.
LogicLexer - Class in org.intermine.pathquery
 
LogicLexer(InputBuffer) - Constructor for class org.intermine.pathquery.LogicLexer
 
LogicLexer(LexerSharedInputState) - Constructor for class org.intermine.pathquery.LogicLexer
 
LogicLexer(InputStream) - Constructor for class org.intermine.pathquery.LogicLexer
 
LogicLexer(Reader) - Constructor for class org.intermine.pathquery.LogicLexer
 
LogicParser - Class in org.intermine.pathquery
 
LogicParser(ParserSharedInputState) - Constructor for class org.intermine.pathquery.LogicParser
 
LogicParser(TokenBuffer) - Constructor for class org.intermine.pathquery.LogicParser
 
LogicParser(TokenBuffer, int) - Constructor for class org.intermine.pathquery.LogicParser
 
LogicParser(TokenStream) - Constructor for class org.intermine.pathquery.LogicParser
 
LogicParser(TokenStream, int) - Constructor for class org.intermine.pathquery.LogicParser
 
LogicTokenTypes - Interface in org.intermine.pathquery
 
LOGIN_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks lists
LOGIN_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks logins
LoginAction - Class in org.intermine.web.struts
Action to handle button presses on the main tile
LoginAction() - Constructor for class org.intermine.web.struts.LoginAction
 
LoginController - Class in org.intermine.web.struts
Controller for the login page.
LoginController() - Constructor for class org.intermine.web.struts.LoginController
 
LoginForm - Class in org.intermine.web.struts
The main form, using for editing constraints
LoginForm() - Constructor for class org.intermine.web.struts.LoginForm
 
LoginHandler - Class in org.intermine.web.logic.profile
 
LoginHandler() - Constructor for class org.intermine.web.logic.profile.LoginHandler
 
LoginService - Class in org.intermine.webservice.server.user
Login service which authenticates an existing user, given username and password and attaches the anonymously created lists to it.
LoginService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.LoginService
Constructor
LoginServlet - Class in org.intermine.webservice.server.user
Runs the login service
LoginServlet() - Constructor for class org.intermine.webservice.server.user.LoginServlet
 
LoginTrack - Class in org.intermine.api.tracker.track
 
LoginTrack(String, Timestamp) - Constructor for class org.intermine.api.tracker.track.LoginTrack
 
LOGINTRACK - Static variable in class org.intermine.api.tracker.xml.LoginTrackBinding
label for XML
LoginTrackBinding - Class in org.intermine.api.tracker.xml
 
LoginTracker - Class in org.intermine.api.tracker
Class for tracking when the users log into their accounts.
LoginTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.LoginTracker
Build a login tracker
LOGINTRACKS - Static variable in class org.intermine.api.tracker.xml.LoginTrackBinding
label for XML
logMessage(String) - Method in class org.intermine.web.task.KeyStoreTask
Log a message to standard out.
LogoutAction - Class in org.intermine.web.struts
Action that invalidates the user session effectively logging the user out of intermine.
LogoutAction() - Constructor for class org.intermine.web.struts.LogoutAction
 
LogoutService - Class in org.intermine.webservice.server.user
Logout service which invalidates the token assigned to the user logging out It requires token authentication
LogoutService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.LogoutService
Constructor
LogoutServlet - Class in org.intermine.webservice.server.user
Runs the logout service
LogoutServlet() - Constructor for class org.intermine.webservice.server.user.LogoutServlet
 
logQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Before running a query via web services, add to query history and add a track
logTableBatch - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logTableConnection - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logTableName - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
logTemplateQueryUse(HttpSession, String, String) - Static method in class org.intermine.web.logic.session.SessionMethods
Log use of a template query.
lookup(String, int) - Method in class org.intermine.sql.precompute.OptimiserCache
Attempts to find a match in the cache for an original query.
lookup(String, String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path with the LOOKUP operator.
LOOKUP - Static variable in class org.intermine.metadata.ConstraintOp
Special operation indicating a bag upload step should be used, for the webapp only.
LOOKUP_CONSTRAINT - Static variable in class org.intermine.api.config.Constants
LOOKUP constraint
LOOKUP_MSG - Static variable in class org.intermine.web.logic.Constants
Session attribute that holds message when a lookup constraint has been used
lookupCategory(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Returns a Map from original SQL to PrecomputedTable for a given category in the manager.
lookupOs - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
lookupSql(String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Returns a PrecomputedTable object if one exists in the manager with the given original SQL string.
lookupSql(String, String) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Returns a PrecomputedTable object if one exists in the manager with the given category and original SQL string.
LookupTokeniser - Class in org.intermine.api.query
Class for tokenising identifier input.
LOOP_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
LOOP_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
loopQueryOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
loopQueryValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
LOWER - Static variable in class org.intermine.objectstore.query.QueryExpression
Lower case version of the given string
LOWER - Static variable in class org.intermine.sql.query.Function
LOWER operator - takes one operand
LT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
LT - Static variable in class org.intermine.sql.query.Constraint
An operation for this constraint indicating that left is less than right.
LT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 

M

M_N_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A M:N relationship.
MailAction - Interface in org.intermine.web.context
The type of objects that can send themselves with an Emailer.
MailDaemon - Class in org.intermine.web.context
An runnable that will send emails delivered over a concurrent queue.
MailDaemon(ArrayBlockingQueue<MailAction>, Emailer) - Constructor for class org.intermine.web.context.MailDaemon
Create a MailDaemon
mailinglist - Variable in class org.intermine.web.struts.CreateAccountForm
 
MailUtils - Class in org.intermine.util
Mail utilities for the webapp.
main(String[]) - Static method in class org.intermine.sql.query.Query
A testing method - converts the argument into a Query object, and then converts it back to a String again.
main(String[]) - Static method in class org.intermine.web.commandline.PerformanceTester
.
MAIN - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
The first part of a page title.
MainHelper - Class in org.intermine.api.query
Helper methods for main controller and main action
MainHelper.RangeConfig - Class in org.intermine.api.query
 
MainHelper.SummaryConfig - Class in org.intermine.api.query
Controls access to configuration information on which fields should be summarised as a count of occurrences.
makeForward(ActionMapping, HttpServletRequest, PagedTable) - Method in class org.intermine.web.struts.ChangeTableAction
Create a forward with parameters setting start item and page size.
makeItem() - Method in class org.intermine.xml.full.ItemFactory
Make an empty Item with a unique identifier.
makeItem(String) - Method in class org.intermine.xml.full.ItemFactory
Make an empty Item with the given identifier.
makeItem(String, String, String) - Method in class org.intermine.xml.full.ItemFactory
Construct an item from an identifier, a class name and the names of implemented classes
makeItem(FastPathObject) - Method in class org.intermine.xml.full.ItemFactory
Convert an Object to Item format.
makeItemForClass(String) - Method in class org.intermine.xml.full.ItemFactory
Construct an item from a class name.
makeItemImpl(FastPathObject, Set<String>) - Method in class org.intermine.xml.full.ItemFactory
Convert an Object to Item format, writing the fields provided in includeFields.
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.jbrowse.Config
 
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.jbrowse.Names
 
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
makeJSONOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.WebService
Make the default JSON output given the HttpResponse's PrintWriter.
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListAppendService
 
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListMakerService
Make the list requested by the user.
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListOperationService
 
makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.webservice.server.lists.ListUploadService
 
makeList(T, String, Profile, Set<String>) - Method in interface org.intermine.webservice.server.lists.ListMaker
Make the list requested by the user.
makeMultiTypeConstraint(Model, QueryNode, PathConstraintMultitype) - Static method in class org.intermine.api.query.MainHelper
Construct a new multi-type constraint.
makeNodes(String, Model, boolean, PathQuery, WebConfig, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary) - Static method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper
Given a path, render a set of metadata Nodes to the relevant depth
makeNodes(ClassDescriptor, Set<String>, int, Map<?, ?>, List<String>, boolean) - Method in class org.intermine.web.struts.TreeController
Produce a list of tree nodes for a class and its children, marking as 'open' and recursing on any that appear on the openClasses list.
makePath(String) - Method in class org.intermine.pathquery.PathQuery
Produces a Path object from the given path String, using subclass information from the query.
makePathQueryForBag(InterMineBag, WebConfig, Model) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Create a PathQuery to get the contents of an InterMineBag
makePathQueryForCollection(WebConfig, ObjectStore, InterMineObject, String, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Create a PathQuery to get results for a collection of items from an InterMineObject
makeQuery(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor
Make the Lower-level Query object to run from the the higher level PathQuery one.
makeQuery(PathQuery) - Method in class org.intermine.api.query.QueryExecutor
Make an InterMine Query object from a PathQuery.
makeQuery(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Creates an IQL query from a PathQuery.
makeQuery(PathQuery, Map<String, BagQueryResult>, Map<String, QuerySelectable>) - Method in class org.intermine.api.query.WebResultsExecutor
Creates an IQL query from a PathQuery.
makeQuery(PathQuery, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner, Map<String, BagQueryResult>) - Static method in class org.intermine.api.query.MainHelper
Converts a PathQuery object into an ObjectStore Query object, and optionally populates a Map from String path in the PathQuery to the object in the Query that represents it.
makeQueryDateConstraint(QueryField, PathConstraintAttribute) - Static method in class org.intermine.api.query.MainHelper
Make a SimpleConstraint for the given Date Constraint.
makeRangeConstraint(ConstraintOp, Range, ConstraintOptions, QueryField, QueryField, QueryClass) - Method in class org.intermine.api.query.range.AbstractHelper
Construct a constraint for an individual range, to be combined as per the ConstraintOptions.
makeRangeConstraint(Queryable, QueryNode, PathConstraintRange) - Static method in class org.intermine.api.query.MainHelper
 
makeSegment(String, Integer, Integer) - Static method in class org.intermine.webservice.server.jbrowse.Segment
 
makeSelectedNodes(String, String, Model, boolean, PathQuery, WebConfig, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary) - Static method in class org.intermine.web.logic.querybuilder.ModelBrowserHelper
Finds the collection of MetadataNode objects that the model browser needs to display.
makeSql(PathQuery) - Method in class org.intermine.api.query.PathQueryExecutor
Get the SQl that will be run on the database.
makeSql(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Creates an SQL query from a PathQuery.
makeSummaryQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
 
makeSummaryQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Creates a query that returns the summary for a column in a PathQuery.
makeSummaryQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Creates a query that returns the summary for a column in a PathQuery, applying a filter at the database level.
makeSummaryQuery(PathQuery, String, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner) - Static method in class org.intermine.api.query.MainHelper
Generate a query from a PathQuery, to summarise a particular column of results.
makeSummaryQuery(PathQuery, String, Map<String, InterMineBag>, Map<String, QuerySelectable>, BagQueryRunner, boolean) - Static method in class org.intermine.api.query.MainHelper
Generate a query from a PathQuery, to summarise a particular column of results.
makeSummaryQuery(PathQuery, Map<String, InterMineBag>, Map<String, QuerySelectable>, String, ObjectStore, Map<String, List<FieldDescriptor>>, BagQueryConfig, ProfileManager, boolean) - Static method in class org.intermine.api.query.MainHelper
Generate a query from a PathQuery, to summarise a particular column of results.
makeWithDifferentBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Returns a new ResultsBatches object with a different batch size with some of the data already filled in.
makeXMLOutput(PrintWriter) - Method in class org.intermine.webservice.server.widget.GraphService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.model.ModelService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.QueryUploadService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.search.QuickSearch
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.SingleTemplateService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.template.SystemTemplatesService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.user.DeregistrationService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.WebService
Make the XML output given the HttpResponse's PrintWriter.
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
 
makeXMLOutput(PrintWriter, String) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
 
mALIAS(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
manager - Variable in class org.intermine.api.profile.Profile
 
map(Iterable<T>, Function<T, R>) - Static method in class org.intermine.webservice.server.core.ListFunctions
Transform a collection of things into a list of other things.
map(List<Tag>) - Method in class org.intermine.api.profile.TagMapper
Safely transform a list of tags into a list of string, preserving type information.
MAP_TEMPLATE - Static variable in class org.intermine.api.config.Constants
template to run to get map of values associated with this mine gene.organism --> gene.homologue.organism
MapListener<K,​V> - Interface in org.intermine.webservice.server.jbrowse
 
mappingExists(String, String) - Method in class org.intermine.api.profile.PreferencesManager
 
MappingUtil - Class in org.intermine.util
Useful utilities to do with mappings.
MappingUtilChecker<T> - Interface in org.intermine.util
Interface providing the capability to check partial mappings for validity for the MappingUtil.
marshal(Collection<FastPathObject>, Writer) - Method in class org.intermine.util.XmlBinding
Marshal a collection of objects to an XML file.
marshal(InterMineBag) - Method in class org.intermine.api.xml.InterMineBagBinding
Convert an InterMine bag to XML
marshal(InterMineBag, XMLStreamWriter) - Static method in class org.intermine.api.xml.InterMineBagBinding
Convert a InterMineIdBag to XML and write XML to given writer.
marshal(Profile) - Method in class org.intermine.api.xml.SharedBagBinding
Convert the shared bags to XML
marshal(ProfileManager, XMLStreamWriter) - Static method in class org.intermine.api.xml.ProfileManagerBinding
Convert the contents of a ProfileManager to XML and write the XML to the given writer.
marshal(Profile, XMLStreamWriter) - Static method in class org.intermine.api.xml.SharedBagBinding
Convert the bags shared to the profile given in input and write XML to given writer.
marshal(Profile, ObjectStore, XMLStreamWriter, boolean, boolean, boolean, boolean, boolean, boolean, int, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.xml.ProfileBinding
Convert a Profile to XML and write XML to given writer.
marshal(Profile, ObjectStore, XMLStreamWriter, int, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.xml.ProfileBinding
Convert a Profile to XML and write XML to given writer.
marshal(SavedQuery, int) - Static method in class org.intermine.api.xml.SavedQueryBinding
Convert a TemplateQuery to XML
marshal(SavedQuery, XMLStreamWriter, int) - Static method in class org.intermine.api.xml.SavedQueryBinding
Convert a SavedQuery to XML and write XML to given writer.
marshal(Tag, XMLStreamWriter) - Static method in class org.intermine.api.xml.TagBinding
Convert a Tag to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.ListTrackBinding
Convert a ListTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.LoginTrackBinding
Convert a LoginTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.QueryTrackBinding
Convert a QueryTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.SearchTrackBinding
Convert a SearchTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.TemplateTrackBinding
Convert a TemplateTrack to XML and write XML to given writer.
marshal(ObjectStore, XMLStreamWriter) - Static method in class org.intermine.api.tracker.xml.TrackManagerBinding
Convert all tracks to XML and write XML to given writer.
marshal(PathQuery, String, String, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Convert a PathQuery to XML.
marshal(PathQuery, String, String, XMLStreamWriter, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Marshal to an XMLStreamWriter.
marshal(TemplateQuery, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Convert a TemplateQuery to XML
marshal(TemplateQuery, XMLStreamWriter, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Convert a TemplateQuery to XML and write XML to given writer.
MassTaggingEvent - Class in org.intermine.api.search
A representation of a notification that multiple tags have been added to a profile, and that we do not (indeed cannot) know what they all are.
MassTaggingEvent() - Constructor for class org.intermine.api.search.MassTaggingEvent
 
mASTERISK(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mASTERISK(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mAT_SIGN(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mAT_SIGN(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
MATCHES - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments match
matchesAreIssues() - Method in class org.intermine.api.bag.BagQuery
Return the flag passed to the constructor.
max - Variable in class org.intermine.objectstore.query.ResultsInfo
 
MAX - Static variable in class org.intermine.objectstore.query.QueryFunction
Maximum value of a number of rows
MAX - Static variable in class org.intermine.sql.query.Function
MAX(v) aggregate function - takes one operand.
MAX_BAG_INLINE_SIZE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
The maximum size a bag in a BagConstraint can be before we consider using a temporary table instead.
MAX_CODE - Static variable in class org.intermine.pathquery.PathQuery
The highest code value a constraint may be assigned.
MAX_CONSTRAINTS - Static variable in class org.intermine.pathquery.PathQuery
The maximum number of coded constraints a PathQuery may hold.
MAX_LINESETS - Static variable in class org.intermine.sql.precompute.OptimiserCache
Maximum number of cache linesets in the cache.
MAX_NOT_LOGGED_BAG_SIZE - Static variable in class org.intermine.web.logic.Constants
Maximum size a bag should have if the user is not logged in (to save memory)
MAX_ROWS - Static variable in class org.intermine.task.RunIqlQueryTask
 
maxLimit - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxOffset - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxP - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
maxQueryParseTime - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxSize - Variable in class org.intermine.objectstore.query.ResultsBatches
 
maxSummaryValues - Variable in class org.intermine.api.template.TemplateSummariser
 
maxTime - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
maxValues - Variable in class org.intermine.objectstore.ObjectStoreSummary
 
mCLOSE_PAREN(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mCLOSE_PAREN(boolean) - Method in class org.intermine.pathquery.LogicLexer
 
mCLOSE_PAREN(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mCOLONTYPE(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mCOLONTYPE(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mCOMMA(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mCOMMA(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mDIVIDE(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mDIVIDE(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mDOT(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mDOT(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
MemoryOutput - Class in org.intermine.webservice.server.output
Implementation of Output that saves data to memory.
MemoryOutput() - Constructor for class org.intermine.webservice.server.output.MemoryOutput
Constructor
MemoryQueryStore - Class in org.intermine.api.query
An in-memory implementation of a query store.
MemoryQueryStore(int) - Constructor for class org.intermine.api.query.MemoryQueryStore
 
mEQ(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mEQ(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
merge(PrecomputedTable, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Finds all the possible uses of a given precomputed table in the query, and returns them as a Set of new Queries.
mergeAttributes(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the attributes of a target model class descriptor original with the attributes present in class descriptor merge.
mergeClass(ClassDescriptor, ClassDescriptor, Model, Set<ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the attributes, collections and references from ClassDescriptor merge into the ClassDescriptor original.
mergeCollections(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the collections of a target model class descriptor original with the collections present in class descriptor merge.
mergeGroupBy(PrecomputedTable, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Tries to match a PrecomputedTable with a GROUP BY clause to this query.
mergeModel(Model, Set<ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
'Merges' the information from the set of ClassDescriptors classes into the model target.
mergeModelFromFiles(File, List<String>, ModelParser) - Static method in class org.intermine.modelproduction.ModelFileMerger
Merges a model from a core model file and a list of additions files.
mergeMultiple(Set<PrecomputedTable>, Query, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Iteratively calls merge on query with all the PrecomputedTables in a Set, returning the results in a Map from the PrecomputedTable to the Set that merge returns.
mergeProfiles(Profile, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
Merge two profiles together.
mergeReferences(ClassDescriptor, ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
Merge the references of a target model class descriptor original with the references present in class descriptor merge.
mESCAPED_STRING(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
message - Variable in class org.intermine.api.userprofile.PermanentToken
 
MessageFormat - Enum in org.intermine.web.struts.oauth2
 
MESSAGES - Static variable in class org.intermine.web.logic.Constants
Session attribute that temporarily holds a Vector of messages that will be displayed by the errorMessages.jsp on the next page viewed by the user and then removed (allows message after redirect).
METADATA_TABLE - Static variable in class org.intermine.modelproduction.MetadataManager
Name of the metadata table (created by TorqueModelOutput)
MetaDataException - Exception in org.intermine.metadata
An Exception that may be thrown if metadata is in an invalid state.
MetaDataException() - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException
MetaDataException(String) - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException with the specified detail message.
MetaDataException(String, Throwable) - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException with the specified detail message and nested throwable.
MetaDataException(Throwable) - Constructor for exception org.intermine.metadata.MetaDataException
Constructs an MetaDataException with the specified nested throwable.
MetadataManager - Class in org.intermine.modelproduction
Class to handle persistence of an intermine objectstore's metadata to the objectstore's database
MetadataManager.LargeObjectInputStream - Class in org.intermine.modelproduction
Class providing an InputStream interface to read a value from the database.
MetadataManager.LargeObjectOutputStream - Class in org.intermine.modelproduction
OutputStream class that writes to a large object in the database.
MetadataNode - Class in org.intermine.web.logic.query
Node used in displaying metadata
MetadataNode(String, List<String>, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile) - Constructor for class org.intermine.web.logic.query.MetadataNode
Constructor for a root node
MetadataNode(MetadataNode, String, String, List<String>, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile, Boolean) - Constructor for class org.intermine.web.logic.query.MetadataNode
Constructor for a non-root node
mFLOAT(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mFLOAT(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mGORNULL(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mGT(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mGT(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mIDENTIFIER(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mIDENTIFIER(boolean) - Method in class org.intermine.pathquery.LogicLexer
 
mIDENTIFIER(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
MigrationMapping - Class in org.intermine.web.struts.oauth2
A simple record that contains mapping information about the old id of a user.
MigrationMapping(String, String) - Constructor for class org.intermine.web.struts.oauth2.MigrationMapping
Construct a mapping for Google OpenID migration.
min - Variable in class org.intermine.objectstore.query.ResultsInfo
 
MIN - Static variable in class org.intermine.objectstore.query.QueryFunction
Mininum value of a number of rows
MIN - Static variable in class org.intermine.sql.query.Function
MIN(v) aggregate function - takes one operand.
MIN_CODE - Static variable in class org.intermine.pathquery.PathQuery
The lowest code value a constraint may be assigned.
MIN_LIMIT - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
The smallest legal result size you can request
minBagTableSize - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
Mine - Interface in org.intermine.api.mines
The type of objects that represent InterMine instances.
MineRequester - Interface in org.intermine.api.mines
The type of objects that can request data from mines.
MINIMAL - org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity
Just the results
MinimalJsonIterator - Class in org.intermine.webservice.server.output
 
MinimalJsonIterator(Iterator<List<ResultElement>>) - Constructor for class org.intermine.webservice.server.output.MinimalJsonIterator
Constructor
minRows - Variable in class org.intermine.task.PrecomputeTask
 
minRows - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
mINSIDE(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
minSize - Variable in class org.intermine.objectstore.query.ResultsBatches
 
MINUS - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
MINUS - Static variable in class org.intermine.sql.query.Function
MINUS function - takes two operands.
MINUS - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
mISNOTNULL(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mISNULL(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
MISSING_TABLES - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the missing tables string.
MissingParameterException - Exception in org.intermine.webservice.server.exceptions
 
MissingParameterException(String) - Constructor for exception org.intermine.webservice.server.exceptions.MissingParameterException
 
MissingParameterException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.MissingParameterException
 
mMINUS(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mMINUS(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mNOT_EQ(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mNOT_EQ(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
MockItemWriter - Class in org.intermine.dataconversion
Mimic behaviour of an ItemWriter but actually store Items in a Map rather than an ObjectStoreWriter
MockItemWriter(Map<String, Item>) - Constructor for class org.intermine.dataconversion.MockItemWriter
Constructor
MODE_NORMAL - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Normal operation - no logging
MODE_VERBOSE - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Normal operation, plus logging to stdout
MODE_VERBOSE_LIST - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Logs all generated queries to the stdout, without explaining
MODE_VERBOSE_SUMMARY - Static variable in class org.intermine.sql.precompute.QueryOptimiserContext
Summarises all generated queries to the stdout, without explaining
model - Variable in class org.intermine.api.bag.operations.BagOperation
 
model - Variable in class org.intermine.api.InterMineAPI
 
model - Variable in class org.intermine.api.results.WebResults
 
model - Variable in class org.intermine.codegen.JavaModelOutput
 
model - Variable in class org.intermine.dataconversion.ItemToObjectTranslator
 
model - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
model - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
model - Variable in class org.intermine.task.AnalyseDbTask
 
model - Variable in class org.intermine.task.ModelOutputTask
 
model - Variable in class org.intermine.util.XmlBinding
 
model - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
model - Variable in class org.intermine.webservice.server.core.JSONService
 
Model - Class in org.intermine.metadata
Represents a named business model, makes available metadata for each class within model.
Model(String, String, int, Collection<ClassDescriptor>) - Constructor for class org.intermine.metadata.Model
Construct a Model with a name and set of ClassDescriptors.
Model(String, String, Collection<ClassDescriptor>) - Constructor for class org.intermine.metadata.Model
Construct a model without a version.
MODEL - Static variable in class org.intermine.metadata.Util
Name of the key under which to store the serialized version of the model
MODEL - Static variable in class org.intermine.modelproduction.MetadataManager
Name of the key under which to store the serialized version of the model
Model.ModelAST - Class in org.intermine.metadata
A Map with slightly more type information.
ModelAST() - Constructor for class org.intermine.metadata.Model.ModelAST
 
ModelBrowserHelper - Class in org.intermine.web.logic.querybuilder
Static class holding methods for managing the model browser in the query builder.
ModelBrowserHelper.NodeBuilder - Class in org.intermine.web.logic.querybuilder
An object that will descend through the model and build a tree of metadata nodes.
modelDescriptors - Static variable in class org.intermine.dataloader.DataLoaderHelper
 
ModelFactory - Class in org.intermine.metadata
A class that loads a model given a name.
ModelFileMerger - Class in org.intermine.modelproduction
Methods for merging a model from a list of files.
modelKeys - Static variable in class org.intermine.metadata.PrimaryKeyUtil
 
ModelMerger - Class in org.intermine.modelproduction
Merge model additions into a source model to produce a new larger model.
ModelMergerException - Exception in org.intermine.modelproduction
An Exception that may be thrown by ModelMerger methods.
ModelMergerException() - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException
ModelMergerException(String) - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException with the specified detail message.
ModelMergerException(String, Throwable) - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException with the specified detail message and nested throwable.
ModelMergerException(Throwable) - Constructor for exception org.intermine.modelproduction.ModelMergerException
Constructs a ModelMergerException with the specified nested throwable.
ModelMergerTask - Class in org.intermine.task
Task to merge a single additions file into an intermine XML model.
ModelMergerTask() - Constructor for class org.intermine.task.ModelMergerTask
 
modelName - Variable in class org.intermine.task.StoreMetadataTask
 
ModelOutputTask - Class in org.intermine.task
Creates and runs a ModelOutput process to generate java or config files.
ModelOutputTask() - Constructor for class org.intermine.task.ModelOutputTask
 
ModelParser - Interface in org.intermine.metadata
Common interface for parsing source models into InterMine model format.
ModelParserException - Exception in org.intermine.metadata
An Exception that may be thrown by ModelMerger methods.
ModelParserException() - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException
ModelParserException(String) - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException with the specified detail message.
ModelParserException(String, Throwable) - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException with the specified detail message and nested throwable.
ModelParserException(Throwable) - Constructor for exception org.intermine.metadata.ModelParserException
Constructs a ModelParserException with the specified nested throwable.
ModelService - Class in org.intermine.webservice.server.model
Web service that returns a serialised representation of the data model.
ModelService(InterMineAPI) - Constructor for class org.intermine.webservice.server.model.ModelService
Constructor.
ModelServlet - Class in org.intermine.webservice.server.model
Runs ModelService web service.
ModelServlet() - Constructor for class org.intermine.webservice.server.model.ModelServlet
 
ModelUpdate - Class in org.intermine.api.profile
Update savedquery, savedtemplatequery and savedbag when the model has been changed
ModelUpdate(ObjectStore, ObjectStoreWriter, Model) - Constructor for class org.intermine.api.profile.ModelUpdate
Construct a ModelUpdate for updating items built in the userprofile with the oldModel given in input
ModelUpdateTask - Class in org.intermine.web.task
Task updating savedquery, savedtemplatequery and savedbag in the userprofile (identified by the userProfileAlias) when the model has been changed
ModelUpdateTask() - Constructor for class org.intermine.web.task.ModelUpdateTask
 
ModifyBagAction - Class in org.intermine.web.struts
Implementation of Action to modify bags
ModifyBagAction() - Constructor for class org.intermine.web.struts.ModifyBagAction
 
ModifyBagDetailsAction - Class in org.intermine.web.struts
 
ModifyBagDetailsAction() - Constructor for class org.intermine.web.struts.ModifyBagDetailsAction
 
ModifyBagDetailsForm - Class in org.intermine.web.struts
 
ModifyBagDetailsForm() - Constructor for class org.intermine.web.struts.ModifyBagDetailsForm
Constructor
ModifyBagForm - Class in org.intermine.web.struts
Form bean to used in combining bags
ModifyBagForm() - Constructor for class org.intermine.web.struts.ModifyBagForm
Constructor
ModifyDetails - Class in org.intermine.web.struts
Action to handle events related to displaying Report templates and displayers
ModifyDetails() - Constructor for class org.intermine.web.struts.ModifyDetails
 
modifyList(Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListTagAddingService
Modify the list by adding the tags.
modifyList(Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListTagRemovalService
 
ModifyQueryAction - Class in org.intermine.web.struts
Action that results from a button press on the user profile page.
ModifyQueryAction() - Constructor for class org.intermine.web.struts.ModifyQueryAction
 
ModifyQueryChangeAction - Class in org.intermine.web.struts
Implementation of Action that modifies a saved query or bag.
ModifyQueryChangeAction() - Constructor for class org.intermine.web.struts.ModifyQueryChangeAction
 
ModifyQueryForm - Class in org.intermine.web.struts
Form bean to used in combining queries
ModifyQueryForm() - Constructor for class org.intermine.web.struts.ModifyQueryForm
Constructor
ModifySuperUserAction - Class in org.intermine.web.struts
Implementation of Action to modify superuser role
ModifySuperUserAction() - Constructor for class org.intermine.web.struts.ModifySuperUserAction
 
ModifySuperUserForm - Class in org.intermine.web.struts
Form bean used in user admin page
ModifySuperUserForm() - Constructor for class org.intermine.web.struts.ModifySuperUserForm
Constructor
modifyTemplate(Set<String>, ApiTemplate) - Method in class org.intermine.webservice.server.template.TemplateTagAddingService
Modify the list by adding the tags.
modifyTemplate(Set<String>, ApiTemplate) - Method in class org.intermine.webservice.server.template.TemplateTagRemovalService
 
ModifyTemplateAction - Class in org.intermine.web.struts
Action that results from a button press on the user profile page.
ModifyTemplateAction() - Constructor for class org.intermine.web.struts.ModifyTemplateAction
 
ModifyTemplateForm - Class in org.intermine.web.struts
Form bean used on the saved template form.
ModifyTemplateForm() - Constructor for class org.intermine.web.struts.ModifyTemplateForm
Constructor
MODMINE_METADATA_CACHE - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the modMine MetaData cache
MODULE_NAME - Static variable in class org.intermine.webservice.server.WebServiceConstants
Name of module of web services.
MODULO - Static variable in class org.intermine.objectstore.query.QueryExpression
Return the modulo of two expressions, e.g.
MODULO - Static variable in class org.intermine.sql.query.Function
MODULO arithmetic function - takes two operands.
mOPEN_PAREN(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mOPEN_PAREN(boolean) - Method in class org.intermine.pathquery.LogicLexer
 
mOPEN_PAREN(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
moveColumnLeft(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Move a column left
moveColumnLeft(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't move columns any more
moveColumnRight(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Move a column right
moveColumnRight(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't move columns any more
moveLeft(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange
Shift a Node left in the view
moveRight(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange
Shift a Node right in the view
mOVERLAP(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
moveToRequest(String, HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
Move an attribute from the session to the request, removing it from the session.
mPERCENT(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mPERCENT(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mPLUS(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mPLUS(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mQUESTION_MARK(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mQUOTED_STRING(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mQUOTED_STRING(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mSEMI(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mSEMI(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mSURROUND(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
MULTI - org.intermine.api.searchengine.KeywordSearchFacetType
multiple values per document
MultipleInBagConstraint - Class in org.intermine.objectstore.query
Constraint type requiring any of the given QueryEvaluables to be in a given bag.
MultipleInBagConstraint(Collection<?>, List<? extends QueryEvaluable>) - Constructor for class org.intermine.objectstore.query.MultipleInBagConstraint
Constructor for this class.
multipleInBagConstraintToString(SqlGenerator.State, StringBuffer, MultipleInBagConstraint, Query, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a BagConstraint object into a String suitable for putting on an SQL query.
MULTIPLY - Static variable in class org.intermine.objectstore.query.QueryExpression
Multiplication of two numeric fields
MULTIPLY - Static variable in class org.intermine.sql.query.Function
MULTIPLY function - takes two or more operands.
MultiRow<E> - Class in org.intermine.api.results.flatouterjoins
A subclass of ArrayList returned by the ResultsFlatOuterJoinsImpl indicating a row that can be represented as multiple rows because of collections.
MultiRow() - Constructor for class org.intermine.api.results.flatouterjoins.MultiRow
 
MultiRow(Collection<? extends E>) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRow
 
MultiRowFirstValue<E> - Class in org.intermine.api.results.flatouterjoins
An object representing an entry in a MultiRow - the first instance of this value in a rowspan.
MultiRowFirstValue(E, int) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
Constructor.
MultiRowLaterValue<E> - Class in org.intermine.api.results.flatouterjoins
An object representing an entry in a MultiRow - entries other than the first value of the rowspan.
MultiRowLaterValue(MultiRowFirstValue<E>) - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
Constructor - should only really be called from MultiRowFirstValue.
MultiRowValue<E> - Class in org.intermine.api.results.flatouterjoins
An object representing an entry in a MultiRow.
MultiRowValue() - Constructor for class org.intermine.api.results.flatouterjoins.MultiRowValue
 
multitable() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
multiValueAttribute - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
mVERTBAR(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mVERTBAR(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
mWS(boolean) - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
mWS(boolean) - Method in class org.intermine.pathquery.LogicLexer
 
mWS(boolean) - Method in class org.intermine.sql.query.SqlLexer
 
MYMINE_PAGE - Static variable in class org.intermine.web.logic.Constants
Session attribute, name of tab selected on MyMine page.
MyMineController - Class in org.intermine.web.struts
Tiles controller for history tile (page).
MyMineController() - Constructor for class org.intermine.web.struts.MyMineController
 

N

n - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout
Number of milliseconds before timeout.
n_abstract_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_abstract_constraint_list(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_abstract_constraint_list_notand(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_abstract_constraint_list_notor(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_and_constraint_set(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_not_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
n_null_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
N_ONE_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A N:1 relationship.
n_or_constraint_set(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
name - Variable in class org.intermine.api.results.Column
 
name - Variable in class org.intermine.api.userprofile.SavedBag
 
name - Variable in class org.intermine.metadata.FieldDescriptor
 
name - Variable in class org.intermine.model.fulldata.Attribute
 
name - Variable in class org.intermine.model.fulldata.Reference
 
name - Variable in class org.intermine.model.fulldata.ReferenceList
 
name - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
name - Variable in class org.intermine.sql.query.Field
 
name - Variable in class org.intermine.sql.query.Table
 
name - Variable in class org.intermine.template.TemplateQuery
Template query name.
name - Variable in class org.intermine.util.ReferenceMap
 
name - Variable in class org.intermine.xml.full.ReferenceList
 
Name - org.intermine.api.profile.TagMapper.Field
The tag name
NAME_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The name of the new list
NAME_PARAMETER - Static variable in class org.intermine.webservice.server.template.result.TemplateResultService
Name of name parameter
Names - Class in org.intermine.webservice.server.jbrowse
 
Names(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.Names
 
NameSpacedProperties - Class in org.intermine.webservice.server.jbrowse.util
Class for simplifying access to sets of namespaces properties.
NameSpacedProperties(String, Properties) - Constructor for class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
Build a new name-spaced property set with a given parent set of properties, and the designated name-space.
namespaceToId - Variable in class org.intermine.dataconversion.ItemToObjectTranslator
 
NameUtil - Class in org.intermine.api.util
Utility methods for naming queries and lists.
NAND - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the NAND operation
NavigationBarTag - Class in org.intermine.web.tags.table
Class implementing rendering of html of navigation bar.
NavigationBarTag() - Constructor for class org.intermine.web.tags.table.NavigationBarTag
 
needsDistinct(Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns true if this query requires a DISTINCT keyword in the generated SQL.
negate() - Method in class org.intermine.api.query.range.ConstraintOptions
Return a new constraint set with each ConstraintOp negated.
negate() - Method in class org.intermine.metadata.ConstraintOp
Get the negated op
negate() - Method in class org.intermine.objectstore.query.Constraint
Negate this constraint.
negateAndSwap() - Method in class org.intermine.api.query.range.ConstraintOptions
Return a new constraint set with each ConstraintOp negated, and the left and right fields swapped.
NEGATIVE_SEGMENT - Static variable in class org.intermine.webservice.server.jbrowse.Segment
negative segment
neq(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be not equal to a value.
NEVER_EXPLAIN_TABLES - Static variable in class org.intermine.sql.precompute.BestQueryExplainer
 
NEW_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListRenameInput
The request parameter for the new name
NEW_TEMPLATE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the status new template
newBagName - Variable in class org.intermine.web.struts.ModifyBagForm
 
newBagName - Variable in class org.intermine.web.struts.SaveBagForm
 
newBagType - Variable in class org.intermine.web.struts.TriageBagForm
 
newConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Add a new constraint to the query.
NewDeletionTokenService - Class in org.intermine.webservice.server.user
A service that issues a deletion token to a user who intends to delete their profile.
NewDeletionTokenService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.NewDeletionTokenService
 
newId(String) - Method in class org.intermine.dataconversion.DataConverter
Generate an identifier for an item, assign ids sequentially with a different alias per class, e.g.
newpassword - Variable in class org.intermine.web.struts.PasswordResetForm
 
newpassword2 - Variable in class org.intermine.web.struts.PasswordResetForm
 
newPathQuery - Variable in class org.intermine.api.profile.PathQueryUpdate
 
newQuery(String, HttpSession) - Static method in class org.intermine.web.struts.QueryClassSelectAction
Add a new query, based on the specified class, to the session.
newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.ReferenceMap
Private method to create a new ReferenceWithKey object.
newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.SoftReferenceMap
Returns a new SoftReferenceWithKey object for the given objects.
newRef(Object, ReferenceQueue<Object>, K) - Method in class org.intermine.util.WeakReferenceMap
Returns a new WeakReferenceWithKey object for the given objects.
NewUserService - Class in org.intermine.webservice.server.user
Service for creating a new user.
NewUserService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.NewUserService
Constructor.
NewUserServlet - Class in org.intermine.webservice.server.user
Servlet for handing off requests to the a NewUserService.
NewUserServlet() - Constructor for class org.intermine.webservice.server.user.NewUserServlet
 
next() - Method in class org.intermine.api.results.ExportResultsIterator
next() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
next() - Method in class org.intermine.util.CombinedIterator
next() - Method in class org.intermine.util.ObjectPipe
next() - Method in class org.intermine.util.SynchronisedIterator
next() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
next() - Method in class org.intermine.webservice.server.output.FilteringResultIterator
 
next() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator
 
next() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
next() - Method in class org.intermine.webservice.server.output.JSONRowIterator
 
next() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator
 
nextPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the next page
nextToken() - Method in class org.intermine.objectstore.query.iql.IqlLexer
 
nextToken() - Method in class org.intermine.pathquery.LogicLexer
 
nextToken() - Method in class org.intermine.sql.query.SqlLexer
 
NO_ALIASES_ALL_FIELDS - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
I DON'T KNOW
NO_BAGS - Static variable in class org.intermine.api.profile.Profile
Empty typed map holding no bags - useful when creating profiles.
NO_NOTXML - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the noNotXml string.
NO_QUERIES - Static variable in class org.intermine.api.profile.Profile
Empty typed map holding no saved queries - useful when creating profiles.
NO_SPAM - Static variable in class org.intermine.web.logic.Constants
The preference set if the user does not like lots of emails
NO_TEMPLATES - Static variable in class org.intermine.api.profile.Profile
Empty typed map holding no templates - useful when creating profiles.
NoContent - Exception in org.intermine.api.bag.operations
 
NoContent() - Constructor for exception org.intermine.api.bag.operations.NoContent
Constructor
NoContentException - Exception in org.intermine.webservice.server.exceptions
The NoContentException is thrown by a service when the resource requested exists but has an empty representation.
NoContentException(String) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException
 
NoContentException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException
 
NoContentException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.NoContentException
 
Node - Class in org.intermine.pathquery
Superclass of left and right nodes
Node() - Constructor for class org.intermine.pathquery.LogicExpression.Node
 
Node(String) - Constructor for class org.intermine.pathquery.Node
Constructor for a root node
Node(Node, String, boolean) - Constructor for class org.intermine.pathquery.Node
Constructor for a non-root node.
NodeBuilder(boolean, PathQuery, Map<String, List<FieldDescriptor>>, BagManager, Profile, ObjectStoreSummary, WebConfig) - Constructor for class org.intermine.web.logic.querybuilder.ModelBrowserHelper.NodeBuilder
Construct a NodeBuilder
nodeToString(Query, Object, List<Object>, Set<QueryObjectPathExpression>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts an Object into a String.
NONCES - Static variable in class org.intermine.web.logic.Constants
The replay-attack prevention nonces
NONE - org.intermine.web.logic.widget.ErrorCorrection.Strategy
Do not perform error correction
NONE - org.intermine.webservice.server.ColumnHeaderStyle
 
NONE_OF - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is not one of a list of values
noneOfValues(String, Collection<String>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT ONE OF a collection of values.
NonFatalMetaDataException - Exception in org.intermine.metadata
An Exception that may be thrown if metadata is in an invalid state.
NonFatalMetaDataException() - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException
NonFatalMetaDataException(String) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException with the specified detail message.
NonFatalMetaDataException(String, Throwable) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException with the specified detail message and nested throwable.
NonFatalMetaDataException(Throwable) - Constructor for exception org.intermine.metadata.NonFatalMetaDataException
Constructs an MetaDataException with the specified nested throwable.
NonOverrideableProperties - Class in org.intermine.metadata
Subclass of java.util.Properties that rejects duplicate definitions of a given property.
NonOverrideableProperties() - Constructor for class org.intermine.metadata.NonOverrideableProperties
Empty constructor.
NonOverrideableProperties(Properties) - Constructor for class org.intermine.metadata.NonOverrideableProperties
Constructor with defaults.
NonUniqueName - Exception in org.intermine.api.bag.operations
Exception for non-unique name
NonUniqueName(String) - Constructor for exception org.intermine.api.bag.operations.NonUniqueName
 
NOR - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the NOR operation
NoServiceException - Exception in org.intermine.webservice.server.core
Exception to throw to signal that there is no service bound to a particular method on a particular endpoint.
NoServiceException() - Constructor for exception org.intermine.webservice.server.core.NoServiceException
 
NOT_ACCEPTABLE - Static variable in class org.intermine.webservice.server.output.Output
Request will only accept content in a format we cannot provide.
not_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
not_constraint() - Method in class org.intermine.sql.query.SqlParser
 
not_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
NOT_CONSTRAINT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
NOT_CONSTRAINT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
NOT_CURRENT - org.intermine.api.profile.BagState
 
NOT_EQ - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
NOT_EQ - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
NOT_EQUAL - Static variable in class org.intermine.sql.query.AbstractValue
Describes one AbstractValue as being definitely not equal to another AbstractValue.
NOT_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are not equal, ignoring case for strings
NOT_IN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is NOT IN the second
NOT_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
Not a relationship between objects
NotAcceptableException - Exception in org.intermine.webservice.server.exceptions
 
NotAcceptableException() - Constructor for exception org.intermine.webservice.server.exceptions.NotAcceptableException
Construct a NotAcceptableException
notAnalysed - Variable in class org.intermine.web.logic.widget.Widget
 
NotConstraint - Class in org.intermine.sql.query
A representation of a constraint that is represented here as the inverse of another Constraint.
NotConstraint(AbstractConstraint) - Constructor for class org.intermine.sql.query.NotConstraint
Constructor for a NotConstraint object.
NotCurrent - Exception in org.intermine.api.bag.operations
 
NotCurrent() - Constructor for exception org.intermine.api.bag.operations.NotCurrent
Constructor
notEqualTo(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare this value of this AbstractValue with another to see if it is not equal.
notEqualToLoop(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be not equal to a loopPath.
NotImplementedException - Exception in org.intermine.webservice.server.exceptions
 
NotImplementedException(Class<?>, String) - Constructor for exception org.intermine.webservice.server.exceptions.NotImplementedException
 
notIn(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT IN a named bag.
notInIds(String, Collection<Integer>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT IN a collection of ids.
notLike(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be NOT LIKE a value.
NOTLIKE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
NotPresentException - Exception in org.intermine.api.query
 
NotPresentException(String) - Constructor for exception org.intermine.api.query.NotPresentException
 
NotXmlParser - Class in org.intermine.objectstore.intermine
Parses a String suitable for storing in the OBJECT field of database tables into an Object.
NotXmlRenderer - Class in org.intermine.objectstore.intermine
Render on object into a String suitable for storing in the OBJECT field of database tables.
null_comparison() - Method in class org.intermine.sql.query.SqlParser
 
null_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
NULL_CONSTRAINT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
NULL_MODEL_ITEM_FACTORY - Static variable in class org.intermine.xml.full.ItemFactory
An ItemFactory constructed with no Model, so the Items it creates do no type checking.
NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
NULL_QUERY - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
NULL_TREE_LOOKAHEAD - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
NULL_TREE_LOOKAHEAD - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
NULL_TREE_LOOKAHEAD - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
NULL_VALUE - Static variable in class org.intermine.util.ReferenceMap
 
nullConstraint - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
NullFirstComparator - Class in org.intermine.util
A Comparator that uses the natural ordering of elements implementing Comparable, plus null is allowed and always before all other elements.
NullMailer - Class in org.intermine.web.context
An emailer that doesn't send emails, but does log what it has been asked to do.
NullMailer() - Constructor for class org.intermine.web.context.NullMailer
Get a new NullMailer
NullMailer(Properties) - Constructor for class org.intermine.web.context.NullMailer
Get a null mailer with certain properties.
NUMBER_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 

O

OAUTH2_PROVIDERS - Static variable in class org.intermine.web.logic.Constants
The key under which OAuth2 providers are stored
OAuthProvider - Interface in org.intermine.web.struts.oauth2
A description of an OAuth Provider that we can use as a source of identity information.
obj - Variable in class org.intermine.objectstore.query.ClassConstraint
 
obj - Variable in class org.intermine.objectstore.query.ContainsConstraint
 
obj - Variable in class org.intermine.objectstore.query.QueryFunction
 
OBJECT_VALUE - org.intermine.template.TemplateValue.ValueType
e.g.
ObjectDescription - Class in org.intermine.dataloader
Object class used by DataTracker for data tracking.
ObjectDescription() - Constructor for class org.intermine.dataloader.ObjectDescription
Constructs a new ObjectDescription.
ObjectDescription(ObjectDescription) - Constructor for class org.intermine.dataloader.ObjectDescription
Constructs a new ObjectDescription from an existing one.
ObjectDetails - Class in org.intermine.api.beans
An object that describes an object.
ObjectDetails() - Constructor for class org.intermine.api.beans.ObjectDetails
 
ObjectDetailsBeanInfo - Class in org.intermine.api.beans
An object that describes the ObjectDetails bean and supports DWR serialization.
ObjectDetailsBeanInfo() - Constructor for class org.intermine.api.beans.ObjectDetailsBeanInfo
 
ObjectFormatter - Class in org.intermine.webservice.server.jbrowse.util
Simpler version of JSONFormatter that doesn't add any extra information, except in case of error.
ObjectFormatter() - Constructor for class org.intermine.webservice.server.jbrowse.util.ObjectFormatter
 
objectIdentifier - Variable in class org.intermine.api.userprofile.Tag
 
ObjectPipe<E> - Class in org.intermine.util
This is a rather simple implementation of a queue designed for passing objects from one Thread to another to form a pipeline.
ObjectPipe() - Constructor for class org.intermine.util.ObjectPipe
Construct an ObjectPipe with a default maximum buffer size.
ObjectPipe(int) - Constructor for class org.intermine.util.ObjectPipe
Construct an ObjectPipe with a certain maximum buffer size.
objectPrimaryKeyNotNull(Model, InterMineObject, ClassDescriptor, PrimaryKey, Source, IntToIntMap) - Static method in class org.intermine.dataloader.DataLoaderHelper
Look a the values of the given primary key in the object and return true if and only if some part of the primary key is null.
ObjectRequest - Class in org.intermine.api.mines
A generic container for a request for information about an object.
ObjectRequest(String, String) - Constructor for class org.intermine.api.mines.ObjectRequest
Define a new object request.
Objects - Class in org.intermine.api.data
Helper class to encapsulate some common logic regarding the use of data objects.
OBJECTS - org.intermine.webservice.server.Format
JSON Object format constant
objectStore - Variable in class org.intermine.api.InterMineAPI
 
ObjectStore - Interface in org.intermine.objectstore
Gets the Results of a Query from an underlying store.
ObjectStoreAbstractImpl - Class in org.intermine.objectstore
Abstract implementation of the ObjectStore interface.
ObjectStoreAbstractImpl() - Constructor for class org.intermine.objectstore.ObjectStoreAbstractImpl
No-arg constructor for testing purposes
ObjectStoreAbstractImpl(Model) - Constructor for class org.intermine.objectstore.ObjectStoreAbstractImpl
Construct an ObjectStore with some metadata
objectStoreAlias - Variable in class org.intermine.task.PrecomputeTask
 
objectstorebag() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
ObjectStoreBag - Class in org.intermine.objectstore.query
Object representing a collection of objects which have been stored in the database.
ObjectStoreBag(int) - Constructor for class org.intermine.objectstore.query.ObjectStoreBag
Constructs a new ObjectStoreBag.
OBJECTSTOREBAG - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
ObjectStoreBagCombination - Class in org.intermine.objectstore.query
Object representing a combination of ObjectStoreBags.
ObjectStoreBagCombination(int) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagCombination
Constructs a new ObjectStoreBagCombination.
ObjectStoreBagsForObject - Class in org.intermine.objectstore.query
Object representing a query to fetch ObjectStoreBag IDs for ObjectStoreBags that contain a certain value.
ObjectStoreBagsForObject(Integer) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagsForObject
Constructs a new ObjectStoreBagsForObject with no limit on the ObjectStoreBags returned.
ObjectStoreBagsForObject(Integer, Collection<ObjectStoreBag>) - Constructor for class org.intermine.objectstore.query.ObjectStoreBagsForObject
Constructs a new ObjectStoreBagsForObject with a limited set of ObjectStoreBags that can be present in the results.
ObjectStoreDataLoader - Class in org.intermine.dataloader
Loads information from an ObjectStore into the InterMine database.
ObjectStoreDataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.ObjectStoreDataLoader
Construct an ObjectStoreDataLoader
ObjectStoreDataLoaderTask - Class in org.intermine.dataloader
Uses an IntegrationWriter to load data from another ObjectStore.
ObjectStoreDataLoaderTask() - Constructor for class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
ObjectStoreException - Exception in org.intermine.objectstore
An Exception that may be thrown by an ObjectStore indicating a fatal error.
ObjectStoreException() - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException
ObjectStoreException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException with the specified detail message.
ObjectStoreException(String, Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException with the specified detail message and nested throwable.
ObjectStoreException(Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreException
Constructs an ObjectStoreException with the specified nested throwable.
ObjectStoreFactory - Class in org.intermine.objectstore
Produce ObjectStores
ObjectStoreFastCollectionsForTranslatorImpl - Class in org.intermine.objectstore.fastcollections
Provides an implementation of an objectstore that explicitly materialises all the collections in the results set it provides, written for the translating objectstore.
ObjectStoreFastCollectionsForTranslatorImpl(ObjectStore) - Constructor for class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreFastCollectionsImpl - Class in org.intermine.objectstore.fastcollections
Provides an implementation of an objectstore that explicitly materialises all the collections in the results set it provides.
ObjectStoreFastCollectionsImpl(ObjectStore) - Constructor for class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreInterMineImpl - Class in org.intermine.objectstore.intermine
An SQL-backed implementation of the ObjectStore interface.
ObjectStoreInterMineImpl(Model) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Constructs an ObjectStoreInterMineImpl - for use by the ObjectStoreWriter only!
ObjectStoreInterMineImpl(Database, DatabaseSchema) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Constructs an ObjectStoreInterMineImpl, with a schema.
ObjectStoreInterMineImpl.BagTableToRemove - Class in org.intermine.objectstore.intermine
Class describing a temporary bag table, which can be removed.
ObjectStoreItemWriter - Class in org.intermine.dataconversion
Stores Items in an objectstore.
ObjectStoreItemWriter(ObjectStoreWriter) - Constructor for class org.intermine.dataconversion.ObjectStoreItemWriter
Constructs the ItemWriter with an ObjectStoreWriter.
ObjectStoreLimitReachedException - Exception in org.intermine.objectstore
An exception that may be thrown by the objectstore, when an access is made outside the allowable maximum query size.
ObjectStoreLimitReachedException() - Constructor for exception org.intermine.objectstore.ObjectStoreLimitReachedException
Constructs an ObjectStoreLimitReachedException.
ObjectStoreLimitReachedException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreLimitReachedException
Constructs an ObjectStoreLimitReachedException with the specified detail message.
ObjectStorePassthruImpl - Class in org.intermine.objectstore
A generic ObjectStore that passes through every request to an underlying ObjectStore.
ObjectStorePassthruImpl(ObjectStore) - Constructor for class org.intermine.objectstore.ObjectStorePassthruImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreQueryDurationException - Exception in org.intermine.objectstore
An Exception thrown if the estimated time to complete a query is greater than the maximum permitted.
ObjectStoreQueryDurationException() - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException.
ObjectStoreQueryDurationException(String) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException with the given detail message.
ObjectStoreQueryDurationException(String, Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException with the specified detail message and nested throwable.
ObjectStoreQueryDurationException(Throwable) - Constructor for exception org.intermine.objectstore.ObjectStoreQueryDurationException
Create a new ObjectStoreQueryDurationException with the specified nested throwable.
ObjectStoreSafeImpl - Class in org.intermine.objectstore.safe
Provides a safe implementation of an objectstore - that is, an implementation that works correctly if passed a Query object that has been modified since being used previously.
ObjectStoreSafeImpl(ObjectStore) - Constructor for class org.intermine.objectstore.safe.ObjectStoreSafeImpl
Creates an instance, from another ObjectStore instance.
ObjectStoreSummary - Class in org.intermine.objectstore
A summary of the data in an ObjectStore
ObjectStoreSummary(Properties) - Constructor for class org.intermine.objectstore.ObjectStoreSummary
Construct a summary from a properties object.
ObjectStoreSummary(ObjectStore, Properties) - Constructor for class org.intermine.objectstore.ObjectStoreSummary
Construct a summary from by running queries in the ObjectStore.
ObjectStoreTranslatingImpl - Class in org.intermine.objectstore.translating
ObjectStore that transparently translates incoming queries and outgoing objects
ObjectStoreTranslatingImpl(Model, ObjectStore, Translator) - Constructor for class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
Constructor
ObjectStoreWriter - Interface in org.intermine.objectstore
Store, update, and delete objects
ObjectStoreWriterFactory - Class in org.intermine.objectstore
Produce ObjectStoreWriters
ObjectStoreWriterInterMineImpl - Class in org.intermine.objectstore.intermine
An SQL-backed implementation of the ObjectStoreWriter interface, backed by ObjectStoreInterMineImpl.
ObjectStoreWriterInterMineImpl(ObjectStore) - Constructor for class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Constructor for this ObjectStoreWriter.
objectToString(Object) - Static method in class org.intermine.sql.DatabaseUtil
Generate an SQL compatible representation of an object.
objectToString(StringBuffer, Object) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts an Object to a String, in a form suitable for SQL.
ObjectTrailController - Class in org.intermine.web.struts
Controller for the object trail tile.
ObjectTrailController() - Constructor for class org.intermine.web.struts.ObjectTrailController
 
ObjectTrailController.TrailElement - Class in org.intermine.web.struts
Bean passed to JSP to represent an element in the trail.
ObjectValueContainer - Class in org.intermine.api.searchengine
container class to hold the name and value of an attribute for an object to be added as a field to the document
ObjectValueContainer(String, String, String) - Constructor for class org.intermine.api.searchengine.ObjectValueContainer
constructor
ObjectViewController - Class in org.intermine.web.struts
Controls display of data in results tables.
ObjectViewController() - Constructor for class org.intermine.web.struts.ObjectViewController
 
OFF - org.intermine.template.SwitchOffAbility
template constraint is not active
offset - Variable in class org.intermine.objectstore.query.ClobAccess
 
offset - Variable in class org.intermine.sql.query.Query
 
OLD - Static variable in class org.intermine.api.profile.ModelUpdate
suffix used to rename the previous items
OLD_NAME_PARAM - Static variable in class org.intermine.webservice.server.lists.ListRenameInput
The request parameter for the old name
oldModel - Variable in class org.intermine.api.profile.PathQueryUpdate
 
ON - org.intermine.template.SwitchOffAbility
the template constraint is active
onData(Map.Entry<String, Object>, boolean) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
onData(Map<String, Object>, boolean) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
ONE - Static variable in class org.intermine.web.logic.widget.ErrorCorrection
 
ONE_N_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A 1:N relationship.
ONE_OF - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument is one of a list a values
ONE_ONE_RELATION - Static variable in class org.intermine.metadata.FieldDescriptor
A 1:1 relationship
oneOfValues(String, Collection<String>) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be ONE OF a collection of values.
op - Variable in class org.intermine.objectstore.query.Constraint
 
op - Variable in class org.intermine.objectstore.query.QueryFunction
 
op - Variable in class org.intermine.pathquery.PathConstraint
 
OPEN_PAREN - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
OPEN_PAREN - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
OPEN_PAREN - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
OPENID_PROVIDERS - Static variable in class org.intermine.web.logic.Constants
The key for the open-id providers located in the servlet context.
OpenIDAuthenticator - Class in org.intermine.web.logic.login
Authenticate requests using OpenID
OpenIDAuthenticator() - Constructor for class org.intermine.web.logic.login.OpenIDAuthenticator
Default constructor.
openResource(String) - Method in class org.intermine.web.logic.ClassResourceOpener
 
openResource(String) - Method in interface org.intermine.web.logic.ResourceOpener
Open a resource by name, and return an InputStream to it.
openResource(String) - Method in class org.intermine.web.struts.ResourceFinder
 
operands - Variable in class org.intermine.sql.query.Function
 
operate() - Method in class org.intermine.api.bag.operations.BagOperation
Perform this bag operation.
operate() - Method in interface org.intermine.api.bag.operations.BagProducer
 
operation - Variable in class org.intermine.sql.query.Constraint
 
operation - Variable in class org.intermine.sql.query.Function
 
OPERATION - org.intermine.api.tracker.util.ListBuildMode
list operation
operationButton - Variable in class org.intermine.web.struts.SaveBagForm
 
operator - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
OPPOSITE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as being opposite to each other.
optimise - Variable in class org.intermine.objectstore.query.Results
 
optimise(String, Database) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query represented in the String, given the database.
optimise(String, Database, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query represented in the String, given the database.
optimise(String, Query, Object, Connection, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query represented in the String and Query, given the Connection and an object to lookup a PrecomputedTable
optimise(Query, Database) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query, given the database.
optimise(Query, Database, QueryOptimiserContext) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query, given the database.
OptimiserCache - Class in org.intermine.sql.precompute
A class that provides an implementation of a cache for String-based SQL query optimisation.
OptimiserCache() - Constructor for class org.intermine.sql.precompute.OptimiserCache
Constructor for this object.
OptimiserCacheLine - Class in org.intermine.sql.precompute
A class that provides an implementation of a cache line, encapsulating several pieces of data.
OptimiserCacheLine(String, int, String) - Constructor for class org.intermine.sql.precompute.OptimiserCacheLine
Constructor for this object.
OptimiserMappingChecker - Class in org.intermine.sql.precompute
Class for checking partial mappings for validity for the MappingUtil.
OptimiserMappingChecker(Set<AbstractConstraint>, Set<AbstractConstraint>) - Constructor for class org.intermine.sql.precompute.OptimiserMappingChecker
Constructor.
optimiseWith(String, Query, Database, Connection, QueryOptimiserContext, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Runs the optimiser through the query repesented in the String and Query, given the Connection and a set of PrecomputedTables.
OR - Static variable in class org.intermine.metadata.ConstraintOp
Combine constraints with the OR operation
OR - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints as following "constraint 1 OR constraint 2 IS TRUE".
or_constraint_set() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
or_constraint_set() - Method in class org.intermine.sql.query.SqlParser
 
or_constraint_set(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
OR_CONSTRAINT_SET - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
OR_CONSTRAINT_SET - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
OR_EXPR - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
order_clause() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
order_clause() - Method in class org.intermine.sql.query.SqlParser
 
order_clause(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
ORDER_CLAUSE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
ORDER_CLAUSE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
ORDER_DESC - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
ORDER_DESC - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
orderBags(Map<String, InterMineBag>) - Method in class org.intermine.api.bag.BagManager
Order a map of bags by im:order:n tag
orderBy - Variable in class org.intermine.sql.query.Query
 
ORDERBY_FIELD - Static variable in class org.intermine.sql.precompute.PrecomputedTable
The name of the field that is generated as the order by field
orderby_value() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
orderby_value() - Method in class org.intermine.sql.query.SqlParser
 
orderby_value(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
orderByField - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
OrderDescending - Class in org.intermine.objectstore.query
An element that can appear in the ORDER BY clause of a query, to reverse the order.
OrderDescending - Class in org.intermine.sql.query
A representation of an item that can be present in the ORDER BY section of an SQL query, but ordered descending..
OrderDescending(QueryOrderable) - Constructor for class org.intermine.objectstore.query.OrderDescending
Creates a new OrderDescending object from the given QueryOrderable.
OrderDescending(AbstractValue) - Constructor for class org.intermine.sql.query.OrderDescending
Constructor for OrderDescending.
OrderDirection - Enum in org.intermine.pathquery
An enumeration for the direction of sorting for results.
OrderElement - Class in org.intermine.pathquery
An element of the order by list of a PathQuery, containing a path and a direction.
OrderElement(String, OrderDirection) - Constructor for class org.intermine.pathquery.OrderElement
Constructor, taking a path and a direction.
orExpr() - Method in class org.intermine.pathquery.LogicParser
 
org.intermine - package org.intermine
 
org.intermine.api - package org.intermine.api
 
org.intermine.api.bag - package org.intermine.api.bag
 
org.intermine.api.bag.operations - package org.intermine.api.bag.operations
 
org.intermine.api.beans - package org.intermine.api.beans
 
org.intermine.api.config - package org.intermine.api.config
 
org.intermine.api.data - package org.intermine.api.data
 
org.intermine.api.idresolution - package org.intermine.api.idresolution
 
org.intermine.api.mines - package org.intermine.api.mines
 
org.intermine.api.profile - package org.intermine.api.profile
 
org.intermine.api.query - package org.intermine.api.query
 
org.intermine.api.query.codegen - package org.intermine.api.query.codegen
 
org.intermine.api.query.range - package org.intermine.api.query.range
 
org.intermine.api.results - package org.intermine.api.results
 
org.intermine.api.results.flatouterjoins - package org.intermine.api.results.flatouterjoins
 
org.intermine.api.search - package org.intermine.api.search
 
org.intermine.api.searchengine - package org.intermine.api.searchengine
 
org.intermine.api.searchengine.solr - package org.intermine.api.searchengine.solr
 
org.intermine.api.tag - package org.intermine.api.tag
 
org.intermine.api.template - package org.intermine.api.template
 
org.intermine.api.tracker - package org.intermine.api.tracker
 
org.intermine.api.tracker.factory - package org.intermine.api.tracker.factory
 
org.intermine.api.tracker.track - package org.intermine.api.tracker.track
 
org.intermine.api.tracker.util - package org.intermine.api.tracker.util
 
org.intermine.api.tracker.xml - package org.intermine.api.tracker.xml
 
org.intermine.api.types - package org.intermine.api.types
 
org.intermine.api.userprofile - package org.intermine.api.userprofile
 
org.intermine.api.util - package org.intermine.api.util
 
org.intermine.api.xml - package org.intermine.api.xml
 
org.intermine.codegen - package org.intermine.codegen
 
org.intermine.dataconversion - package org.intermine.dataconversion
 
org.intermine.dataloader - package org.intermine.dataloader
 
org.intermine.dwr - package org.intermine.dwr
 
org.intermine.metadata - package org.intermine.metadata
 
org.intermine.model - package org.intermine.model
 
org.intermine.model.fulldata - package org.intermine.model.fulldata
 
org.intermine.modelproduction - package org.intermine.modelproduction
 
org.intermine.objectstore - package org.intermine.objectstore
 
org.intermine.objectstore.fastcollections - package org.intermine.objectstore.fastcollections
 
org.intermine.objectstore.intermine - package org.intermine.objectstore.intermine
 
org.intermine.objectstore.proxy - package org.intermine.objectstore.proxy
 
org.intermine.objectstore.query - package org.intermine.objectstore.query
 
org.intermine.objectstore.query.iql - package org.intermine.objectstore.query.iql
 
org.intermine.objectstore.querygen - package org.intermine.objectstore.querygen
 
org.intermine.objectstore.safe - package org.intermine.objectstore.safe
 
org.intermine.objectstore.translating - package org.intermine.objectstore.translating
 
org.intermine.pathquery - package org.intermine.pathquery
 
org.intermine.postprocess - package org.intermine.postprocess
 
org.intermine.sql - package org.intermine.sql
 
org.intermine.sql.logging - package org.intermine.sql.logging
 
org.intermine.sql.precompute - package org.intermine.sql.precompute
 
org.intermine.sql.query - package org.intermine.sql.query
 
org.intermine.sql.writebatch - package org.intermine.sql.writebatch
 
org.intermine.task - package org.intermine.task
 
org.intermine.template - package org.intermine.template
 
org.intermine.template.xml - package org.intermine.template.xml
 
org.intermine.util - package org.intermine.util
 
org.intermine.web.autocompletion - package org.intermine.web.autocompletion
 
org.intermine.web.commandline - package org.intermine.web.commandline
 
org.intermine.web.context - package org.intermine.web.context
 
org.intermine.web.displayer - package org.intermine.web.displayer
 
org.intermine.web.fair - package org.intermine.web.fair
 
org.intermine.web.filters - package org.intermine.web.filters
 
org.intermine.web.logic - package org.intermine.web.logic
 
org.intermine.web.logic.aspects - package org.intermine.web.logic.aspects
 
org.intermine.web.logic.bag - package org.intermine.web.logic.bag
 
org.intermine.web.logic.config - package org.intermine.web.logic.config
 
org.intermine.web.logic.export - package org.intermine.web.logic.export
 
org.intermine.web.logic.export.http - package org.intermine.web.logic.export.http
 
org.intermine.web.logic.export.rowformatters - package org.intermine.web.logic.export.rowformatters
 
org.intermine.web.logic.export.string - package org.intermine.web.logic.export.string
 
org.intermine.web.logic.login - package org.intermine.web.logic.login
 
org.intermine.web.logic.pathqueryresult - package org.intermine.web.logic.pathqueryresult
 
org.intermine.web.logic.profile - package org.intermine.web.logic.profile
 
org.intermine.web.logic.query - package org.intermine.web.logic.query
 
org.intermine.web.logic.querybuilder - package org.intermine.web.logic.querybuilder
 
org.intermine.web.logic.results - package org.intermine.web.logic.results
 
org.intermine.web.logic.session - package org.intermine.web.logic.session
 
org.intermine.web.logic.template - package org.intermine.web.logic.template
 
org.intermine.web.logic.widget - package org.intermine.web.logic.widget
 
org.intermine.web.logic.widget.config - package org.intermine.web.logic.widget.config
 
org.intermine.web.registry.model - package org.intermine.web.registry.model
 
org.intermine.web.search - package org.intermine.web.search
 
org.intermine.web.security - package org.intermine.web.security
 
org.intermine.web.struts - package org.intermine.web.struts
 
org.intermine.web.struts.oauth2 - package org.intermine.web.struts.oauth2
 
org.intermine.web.tags.disclosure - package org.intermine.web.tags.disclosure
 
org.intermine.web.tags.table - package org.intermine.web.tags.table
 
org.intermine.web.tags.util - package org.intermine.web.tags.util
 
org.intermine.web.task - package org.intermine.web.task
 
org.intermine.web.uri - package org.intermine.web.uri
 
org.intermine.web.util - package org.intermine.web.util
 
org.intermine.webservice.server - package org.intermine.webservice.server
 
org.intermine.webservice.server.bg - package org.intermine.webservice.server.bg
 
org.intermine.webservice.server.branding - package org.intermine.webservice.server.branding
 
org.intermine.webservice.server.clob - package org.intermine.webservice.server.clob
 
org.intermine.webservice.server.core - package org.intermine.webservice.server.core
 
org.intermine.webservice.server.data - package org.intermine.webservice.server.data
 
org.intermine.webservice.server.exceptions - package org.intermine.webservice.server.exceptions
 
org.intermine.webservice.server.fair - package org.intermine.webservice.server.fair
 
org.intermine.webservice.server.filter - package org.intermine.webservice.server.filter
 
org.intermine.webservice.server.idresolution - package org.intermine.webservice.server.idresolution
 
org.intermine.webservice.server.jbrowse - package org.intermine.webservice.server.jbrowse
 
org.intermine.webservice.server.jbrowse.util - package org.intermine.webservice.server.jbrowse.util
 
org.intermine.webservice.server.lists - package org.intermine.webservice.server.lists
 
org.intermine.webservice.server.model - package org.intermine.webservice.server.model
 
org.intermine.webservice.server.oauth2 - package org.intermine.webservice.server.oauth2
 
org.intermine.webservice.server.output - package org.intermine.webservice.server.output
 
org.intermine.webservice.server.path - package org.intermine.webservice.server.path
 
org.intermine.webservice.server.query - package org.intermine.webservice.server.query
 
org.intermine.webservice.server.query.result - package org.intermine.webservice.server.query.result
 
org.intermine.webservice.server.search - package org.intermine.webservice.server.search
 
org.intermine.webservice.server.template - package org.intermine.webservice.server.template
 
org.intermine.webservice.server.template.result - package org.intermine.webservice.server.template.result
 
org.intermine.webservice.server.user - package org.intermine.webservice.server.user
 
org.intermine.webservice.server.webproperties - package org.intermine.webservice.server.webproperties
 
org.intermine.webservice.server.widget - package org.intermine.webservice.server.widget
 
org.intermine.xml - package org.intermine.xml
 
org.intermine.xml.full - package org.intermine.xml.full
 
origin - Variable in class org.intermine.api.search.OriginatingEvent
 
originalSql - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
OriginatingEvent - Class in org.intermine.api.search
A representation of a notification that something has happened that originated at a particular web searchable object.
OriginatingEvent(WebSearchable) - Constructor for class org.intermine.api.search.OriginatingEvent
Constructor.
originatingQuery - Variable in class org.intermine.api.results.ExportResultsIterator
 
os - Variable in class org.intermine.api.profile.ProfileManager
 
os - Variable in class org.intermine.api.query.QueryExecutor
 
os - Variable in class org.intermine.api.template.TemplateSummariser
 
os - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
os - Variable in class org.intermine.objectstore.ObjectStorePassthruImpl
 
os - Variable in class org.intermine.objectstore.query.ClobAccess
 
os - Variable in class org.intermine.objectstore.query.ResultsBatches
 
os - Variable in class org.intermine.objectstore.translating.Translator
 
os - Variable in class org.intermine.web.logic.widget.Widget
 
os - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
os - Variable in class org.intermine.web.task.CreateSearchIndexTask
 
os - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
os - Variable in class org.intermine.webservice.server.WebService
 
OS_FORMAT_VERSION - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store objectstore format version number.
OS_SUMMARY - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the objectstoresummary.properties file.
osAlias - Variable in class org.intermine.web.task.CreateSearchIndexTask
 
osb - Variable in class org.intermine.objectstore.query.BagConstraint
 
osbId - Variable in class org.intermine.api.userprofile.SavedBag
 
osname - Variable in class org.intermine.task.RetrieveMetadataTask
 
osName - Variable in class org.intermine.task.PostProcessorTask
 
osName - Variable in class org.intermine.task.StoreMetadataTask
 
oss - Variable in class org.intermine.api.InterMineAPI
 
osw - Variable in class org.intermine.api.template.TemplateSummariser
 
osw - Variable in class org.intermine.api.tracker.TrackerDelegate
 
osw - Variable in class org.intermine.api.tracker.xml.TrackHandler
 
osw - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
osw - Variable in class org.intermine.postprocess.PostProcessor
 
osWriter - Variable in class org.intermine.api.profile.TagManager
 
OTHER - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the input string
out - Variable in class org.intermine.webservice.server.WebService
 
OUTER - org.intermine.pathquery.OuterJoinStatus
 
OuterJoinStatus - Enum in org.intermine.pathquery
Enumeration for outer join status.
output - Variable in class org.intermine.webservice.server.WebService
The response to the outside world.
Output - Class in org.intermine.webservice.server.output
Abstract class representing an output of a web service.
Output() - Constructor for class org.intermine.webservice.server.output.Output
 
OUTPUT_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Name of format parameter that specifies format of returned results.
outputFile - Variable in class org.intermine.task.SummariseObjectStoreTask
 
outputModelFile - Variable in class org.intermine.task.ModelMergerTask
 
OUTSIDE - Static variable in class org.intermine.metadata.ConstraintOp
Require that some part of the first argument lie outside the second.
OVERLAP - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
OverlapConstraint - Class in org.intermine.objectstore.query
Represents a constraint comparing two range values on an object.
OverlapConstraint(OverlapRange, ConstraintOp, OverlapRange) - Constructor for class org.intermine.objectstore.query.OverlapConstraint
Construct a constraint.
overlapConstraintToString(SqlGenerator.State, StringBuffer, OverlapConstraint, Query, DatabaseSchema, int) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts an OverlapConstraint to a String suitable for putting in an SQL query.
OverlapRange - Class in org.intermine.objectstore.query
Represents a range value on an object.
OverlapRange(QueryEvaluable, QueryEvaluable, QueryObjectReference) - Constructor for class org.intermine.objectstore.query.OverlapRange
Constructor for this object.
OVERLAPS - Static variable in class org.intermine.metadata.ConstraintOp
Require that a range overlaps another range
Owner - org.intermine.api.profile.TagMapper.Field
The owner of the tag

P

packageName(String) - Static method in class org.intermine.metadata.TypeUtil
Returns the package name from a fully qualified class name
Page - Class in org.intermine.webservice.server.core
Parameter class for passing start and limit arguments to iterators.
Page(int) - Constructor for class org.intermine.webservice.server.core.Page
Construct a new page, going from a certain row to the end of the result set.
Page(int, Integer) - Constructor for class org.intermine.webservice.server.core.Page
Construct a new page.
PagedTable - Class in org.intermine.web.logic.results
Deprecated.
Use web-services instead.
PagedTable(WebTable) - Constructor for class org.intermine.web.logic.results.PagedTable
Deprecated.
Construct a PagedTable with a list of column names
PagedTable(WebTable, int) - Constructor for class org.intermine.web.logic.results.PagedTable
Deprecated.
Construct a PagedTable with a list of column names
pageName - Variable in class org.intermine.web.struts.ModifyBagForm
 
pageName - Variable in class org.intermine.web.struts.ModifyTemplateForm
 
PageOutOfRangeException - Exception in org.intermine.web.logic.results
PageOutOfRangeException class
PageOutOfRangeException(String) - Constructor for exception org.intermine.web.logic.results.PageOutOfRangeException
Create a new PageOutOfRangeException.
PageOutOfRangeException(String, Throwable) - Constructor for exception org.intermine.web.logic.results.PageOutOfRangeException
Create a new PageOutOfRangeException.
pageSize - Variable in class org.intermine.web.struts.ChangeTableSizeForm
 
PageTableQueryMonitor - Class in org.intermine.web.logic.query
An implementation of QueryMonitor that maintains a timeout and remembers which PagedTable it is monitoring
PageTableQueryMonitor(int, PagedTable) - Constructor for class org.intermine.web.logic.query.PageTableQueryMonitor
Construct a new instance of QueryMonitorTimeout.
Pair<A,​B> - Class in org.intermine.webservice.server.core
A tuple of order two.
Pair(A, B) - Constructor for class org.intermine.webservice.server.core.Pair
Construct a pair of two things
parallel - Variable in class org.intermine.sql.Database
The number of worker threads to use for background SQL statements
ParallelBatchingFetcher - Class in org.intermine.dataloader
Class providing EquivalentObjectFetcher functionality that fetches batches of equivalent objects in parallel to improve performance.
ParallelBatchingFetcher(BaseEquivalentObjectFetcher, DataTracker, Source) - Constructor for class org.intermine.dataloader.ParallelBatchingFetcher
Constructor
ParallelPrecomputer - Class in org.intermine.objectstore.intermine
An object that can perform a set of precomputes in parallel.
ParallelPrecomputer(ObjectStoreInterMineImpl, int) - Constructor for class org.intermine.objectstore.intermine.ParallelPrecomputer
Constructor.
ParallelPrecomputer.Job - Class in org.intermine.objectstore.intermine
Class representing a precomputing job to be performed.
parameterIsRequired(String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
Declare that a particular parameter is required.
params - Variable in class org.intermine.web.struts.ForwardParameters
Map from parameter name to parameter value.
paren_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
paren_constraint() - Method in class org.intermine.sql.query.SqlParser
 
paren_value() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
paren_value() - Method in class org.intermine.sql.query.SqlParser
 
parent - Variable in class org.intermine.objectstore.query.OverlapRange
 
parse(InputStream) - Static method in class org.intermine.xml.full.FullParser
Parse a InterMine Full XML file
parse(String, Class<?>) - Static method in class org.intermine.pathquery.ConstraintValueParser
Parses a value.
parse(String, ObjectStoreInterMineImpl) - Static method in class org.intermine.objectstore.intermine.NotXmlParser
Parse the given NotXml String into an Object.
parse(ServletContext, Model) - Static method in class org.intermine.web.logic.config.WebConfig
Parse a WebConfig XML file
parse(Model, String) - Static method in class org.intermine.pathquery.JSONQueryHandler
Parse PathQuery from JSON
parse(IqlQuery) - Static method in class org.intermine.objectstore.query.iql.IqlQueryParser
Construct a new query by parsing a String.
parse(ResultsRow<?>) - Method in interface org.intermine.webservice.server.core.ResultRowParser
Parse result row to list of strings.
parse(TemplateQuery, Model, String) - Static method in class org.intermine.pathquery.JSONQueryHandler
Parse PathQuery from JSON.
parse(InputSource, DefaultHandler) - Static method in class org.intermine.metadata.SAXParser
Parse the an xml file
parse(InputSource, DefaultHandler) - Static method in class org.intermine.util.SAXParser
Parse the an xml file
parse(InputSource, DefaultHandler, boolean) - Static method in class org.intermine.metadata.SAXParser
Parse the an xml file
parse(InputSource, DefaultHandler, boolean) - Static method in class org.intermine.util.SAXParser
Parse the an xml file
parseConstraints(HttpServletRequest) - Static method in class org.intermine.web.logic.template.Templates
Given a HTTP request, parse out the template values.
parseCsvDelimitedReader(Reader) - Static method in class org.intermine.util.FormattedTextParser
Return an Iterator over a comma/tab delimited file.
parseDelimitedReader(Reader, char) - Static method in class org.intermine.util.FormattedTextParser
Return an Iterator over a delimited file.
parseFormatFromPathInfo(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
Parse a format from the path-info of the request.
parseRange(String) - Method in class org.intermine.api.query.range.AbstractHelper
Construct a Range object from a string defining one of the ranges this constraint operates on.
parseRequest(HttpServletRequest, WebServiceInput) - Method in class org.intermine.webservice.server.WebServiceRequestParser
Parses common parameters for all web services.
parseResults(InterMineAPI, WebConfig, Collection<KeywordSearchResultContainer>) - Static method in class org.intermine.web.search.SearchUtils
Parse the results into a human friendly form
parseTabDelimitedReader(Reader) - Static method in class org.intermine.util.FormattedTextParser
Return an Iterator over a tab delimited file.
parseValue(String, Class<?>, ActionMessages) - Static method in class org.intermine.web.struts.QueryBuilderConstraintForm
Parse an attribute value
ParseValueException - Exception in org.intermine.pathquery
Exception thrown during parsing constraint value.
ParseValueException(String) - Constructor for exception org.intermine.pathquery.ParseValueException
Constructor
ParseValueException(String, Throwable) - Constructor for exception org.intermine.pathquery.ParseValueException
Constructor.
PartnerLink - Class in org.intermine.api.beans
A bean that contains the information to define a matching set of objects.
PartnerLink() - Constructor for class org.intermine.api.beans.PartnerLink
 
PartnerLinkBeanInfo - Class in org.intermine.api.beans
An object that describes the PartnerLink bean and supports DWR serialization.
PartnerLinkBeanInfo() - Constructor for class org.intermine.api.beans.PartnerLinkBeanInfo
 
password - Variable in class org.intermine.api.profile.Profile
 
password - Variable in class org.intermine.api.userprofile.UserProfile
 
password - Variable in class org.intermine.web.struts.CreateAccountForm
 
password - Variable in class org.intermine.web.struts.LoginForm
 
password - Variable in class org.intermine.web.struts.RequestPasswordForm
 
password2 - Variable in class org.intermine.web.struts.CreateAccountForm
 
PasswordHasher - Class in org.intermine.util
Utility methods for managing hashed passwords
PasswordResetAction - Class in org.intermine.web.struts
Action to change a user's password with the authority of a token previously emailed to them.
PasswordResetAction() - Constructor for class org.intermine.web.struts.PasswordResetAction
 
PasswordResetController - Class in org.intermine.web.struts
Controller for the password reset page.
PasswordResetController() - Constructor for class org.intermine.web.struts.PasswordResetController
 
PasswordResetForm - Class in org.intermine.web.struts
The form for resetting a password.
PasswordResetForm() - Constructor for class org.intermine.web.struts.PasswordResetForm
 
path - Variable in class org.intermine.pathquery.PathConstraint
 
path - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
Path - Class in org.intermine.pathquery
Object to represent a path through an InterMine model.
Path(Model, String) - Constructor for class org.intermine.pathquery.Path
Create a new Path object.
Path(Model, String, Map<String, String>) - Constructor for class org.intermine.pathquery.Path
Create a Path object using class constraints from a Map.
PATH - org.intermine.api.searchengine.KeywordSearchFacetType
path (takes array of field names, converts them to A/B/C format expected by bobo)
PATH - org.intermine.webservice.server.ColumnHeaderStyle
 
PATH_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
PathConstraint - Class in org.intermine.pathquery
Representation of a constraint in the PathQuery.
PathConstraint(String, ConstraintOp) - Constructor for class org.intermine.pathquery.PathConstraint
Constructs a new PathConstraint.
PathConstraintAttribute - Class in org.intermine.pathquery
Representation of a normal attribute constraint in the PathQuery
PathConstraintAttribute(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintAttribute
Constructs a new PathConstraintAttribute.
PathConstraintBag - Class in org.intermine.pathquery
Representation of a constraint to a bag in the PathQuery
PathConstraintBag(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintBag
Constructs a new PathConstraintBag.
PathConstraintIds - Class in org.intermine.pathquery
Representation of a constraint to a collection of object ids in a query.
PathConstraintIds(String, ConstraintOp, Collection<Integer>) - Constructor for class org.intermine.pathquery.PathConstraintIds
Constructs a new PathConstraintIds.
PathConstraintLookup - Class in org.intermine.pathquery
Representation of a lookup constraint in the PathQuery
PathConstraintLookup(String, String, String) - Constructor for class org.intermine.pathquery.PathConstraintLookup
Constructs a new PathConstraintLookup.
PathConstraintLoop - Class in org.intermine.pathquery
Representation of a loop constraint in the PathQuery
PathConstraintLoop(String, ConstraintOp, String) - Constructor for class org.intermine.pathquery.PathConstraintLoop
Constructs a new PathConstraintLoop from one path to another.
PathConstraintMultitype - Class in org.intermine.pathquery
A constraint that restricts a path to inhabiting one of a list of types.
PathConstraintMultitype(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintMultitype
Construct a multi-type constraint.
PathConstraintMultiValue - Class in org.intermine.pathquery
Representation of a constraint to a collection of values in a query.
PathConstraintMultiValue(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintMultiValue
Constructs a new PathConstraintMultiValue.
PathConstraintNull - Class in org.intermine.pathquery
Representation of a null attribute constraint in the PathQuery
PathConstraintNull(String, ConstraintOp) - Constructor for class org.intermine.pathquery.PathConstraintNull
Constructs a new PathConstraintNull.
PathConstraintRange - Class in org.intermine.pathquery
A constraint that restrict a path to a particular relationship with a set of ranges.
PathConstraintRange(String, ConstraintOp, Collection<String>) - Constructor for class org.intermine.pathquery.PathConstraintRange
Constructs a new PathConstraintRange.
PathConstraintSubclass - Class in org.intermine.pathquery
Representation of a subclass constraint in the PathQuery.
PathConstraintSubclass(String, String) - Constructor for class org.intermine.pathquery.PathConstraintSubclass
Constructs a new PathConstraintSubclass.
PathException - Exception in org.intermine.pathquery
An Exception thrown if there is a problem in the Path class.
PathException(String, String) - Constructor for exception org.intermine.pathquery.PathException
Create a new PathException with the given message.
PathExpressionField - Class in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a part of the SELECT list of a QueryObjectPathExpression in single-row mode.
PathExpressionField(QueryObjectPathExpression, int) - Constructor for class org.intermine.objectstore.query.PathExpressionField
Constructor.
PathLengthComparator - Class in org.intermine.pathquery
 
PathLengthComparator() - Constructor for class org.intermine.pathquery.PathLengthComparator
protected constructor
pathQuery - Variable in class org.intermine.api.profile.PathQueryUpdate
 
PathQuery - Class in org.intermine.pathquery
Class to represent a path-based query.
PathQuery(Model) - Constructor for class org.intermine.pathquery.PathQuery
Constructor.
PathQuery(PathQuery) - Constructor for class org.intermine.pathquery.PathQuery
Constructor.
PathQueryAPI - Class in org.intermine.api.query
Provides methods to obtain PathQueryExecutors and WebResultsExecutors
PathQueryBinding - Class in org.intermine.pathquery
Convert PathQueries to and from XML or JSON
PathQueryBinding() - Constructor for class org.intermine.pathquery.PathQueryBinding
 
PathQueryBuilder - Class in org.intermine.webservice.server.query.result
PathQueryBuilder builds PathQuery object from xml and validates it.
PathQueryBuilder(InterMineAPI, String, String, Producer<Map<String, InterMineBag>>) - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilder
PathQueryBuilder constructor.
PathQueryBuilderForJSONObj - Class in org.intermine.webservice.server.query.result
 
PathQueryBuilderForJSONObj() - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Constructor.
PathQueryBuilderForJSONObj(String, String, Producer<Map<String, InterMineBag>>) - Constructor for class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Constructor
PathQueryExecutor - Class in org.intermine.api.query
Executes path query and returns results in form suitable for export or web services.
PathQueryExecutor(ObjectStore, Profile, BagQueryRunner, BagManager) - Constructor for class org.intermine.api.query.PathQueryExecutor
Constructor with necessary objects.
pathQueryFormat - Variable in class org.intermine.api.profile.ProfileManager
Number determining format of queries in the database
PathQueryHandler - Class in org.intermine.pathquery
Extension of DefaultHandler to handle parsing PathQuery objects
PathQueryHandler(Map<String, PathQuery>, int) - Constructor for class org.intermine.pathquery.PathQueryHandler
Constructor
PathQueryHandler(Map<String, PathQuery>, int, Model) - Constructor for class org.intermine.pathquery.PathQueryHandler
Constructor.
pathQueryIsPublic(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.web.struts.WebserviceCodeGenAction
Utility function to determine whether the PathQuery is publicly accessible.
pathQueryIsPublic(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.webservice.server.query.CodeService
Utility function to determine whether the PathQuery is publicly accessible.
PathQueryResultHelper - Class in org.intermine.web.logic.pathqueryresult
Helper for everything related to PathQueryResults
pathQueryToOSQ(PathQuery) - Static method in class org.intermine.webservice.server.jbrowse.Queries
For making queries that will not require LOOKUP constraints.
pathQueryToOSQ(PathQuery, BagQueryRunner) - Static method in class org.intermine.webservice.server.jbrowse.Queries
For making queries that will or might require LOOKUP constraints.
PathQueryUpdate - Class in org.intermine.api.profile
Class for updating a pathquery with a new model
PathQueryUpdate() - Constructor for class org.intermine.api.profile.PathQueryUpdate
Default constructor
PathQueryUpdate(PathQuery, Model) - Constructor for class org.intermine.api.profile.PathQueryUpdate
Construct with pathquery and former model
pathToIndex - Variable in class org.intermine.api.results.WebResults
 
PathUtil - Class in org.intermine.api.util
Utility methods for Paths
pathWithNoConstraints(String) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
 
pending - Static variable in class org.intermine.objectstore.query.PrefetchManager
Pending set of requests - always accessed inside a synchronise on sync.
PENDING - org.intermine.api.idresolution.Job.JobStatus
job is pending
PendingClob - Class in org.intermine.objectstore.query
Subclass of ClobAccess that contains data to be written to the database instead of access to data already in the database.
PendingClob(String) - Constructor for class org.intermine.objectstore.query.PendingClob
Construct a PendingClob from a String.
PER_PAGE - Static variable in class org.intermine.api.searchengine.KeywordSearchPropertiesManager
maximum number of items to be displayed on a page
PERCENT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
PERCENT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
PerformanceTester - Class in org.intermine.web.commandline
Class to run a performance test on a production database by loading a set of template queries from a userprofile database and running them in varying numbers of threads.
performUnsafeOperation(String, SQLOperation<T>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Convenience wrapper to manage the boilerplate when performing unsafe operations.
perm - Variable in class org.intermine.task.GrantTask
 
PermanentToken - Class in org.intermine.api.userprofile
 
PermanentToken() - Constructor for class org.intermine.api.userprofile.PermanentToken
 
permanentTokens - Variable in class org.intermine.api.userprofile.UserProfile
 
PermanentURIHelper - Class in org.intermine.web.logic
Utility class used to build the permanent URI and permanent URL Permanent URLs are used in the Share button and to set the attribute 'url' in Schema.org Permanent URIs are used to set the attribute 'identifier' in Schema.org and in RDF Examples of permanent URIs 1-If the mine is registered in identifiers.org and you've set in the mine properties file identifier.uri.base=identifiers.org/biotestmine, the permanent URI will be identifiers.org/biotestmine/protein:P31946 2-If you use a redirection system and you've set in the mine properties file identifier.uri.base=purl.biotestmine.org/biotestmine, the permanent URI will be purl.biotestmine.org/biotestmine/protein:P31946 3-If identifier.uri.base is not set, the uri generated will be based on {webapp.baseurl}/{webapp.path}/protein:P31946
PermanentURIHelper(HttpServletRequest) - Constructor for class org.intermine.web.logic.PermanentURIHelper
Constructor
PermanentURLFilter - Class in org.intermine.web.filters
Filter applied to all the requests to the InterMine server in order to catch the requests with permanent URL and redirect to the report page.
PermanentURLFilter() - Constructor for class org.intermine.web.filters.PermanentURLFilter
 
PermanentURLService - Class in org.intermine.webservice.server.fair
Generate a permanent URL given a type and internal InterMine ID Permanent URLs are used in the Share button and to set the attribute 'url' in Schema.org The url returned will be empty in the following cases: type is not defined in the model, type is defined in the model but we are not able to generate a permanent URI id is wrong
PermanentURLService(InterMineAPI) - Constructor for class org.intermine.webservice.server.fair.PermanentURLService
The constructor
PermaTokenDeletionService - Class in org.intermine.webservice.server.user
Does what it says on the tin.
PermaTokenDeletionService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.PermaTokenDeletionService
Constructor.
PermaTokenInfoService - Class in org.intermine.webservice.server.user
 
PermaTokenInfoService(InterMineAPI, String) - Constructor for class org.intermine.webservice.server.user.PermaTokenInfoService
 
PermaTokens - Class in org.intermine.webservice.server.user
 
PermaTokensServlet - Class in org.intermine.webservice.server.user
 
PermaTokensServlet() - Constructor for class org.intermine.webservice.server.user.PermaTokensServlet
 
pilferObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Gets a object from the cache if it is present.
pilferObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Gets a object from the cache if it is present.
pilferObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Gets a object from the cache if it is present.
pilferObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Gets a object from the cache if it is present.
pkQueryFruitless(Class<? extends FastPathObject>, String, Object) - Method in class org.intermine.dataloader.EquivalentObjectHints
Returns true if there were no instances of the given class with the given field set to the given value.
PkQueryIdUpgrader - Class in org.intermine.api.bag
Bag object id upgrader that uses the primary keys to find the objects in the new ObjectStore.
PkQueryIdUpgrader(String, ObjectStore) - Constructor for class org.intermine.api.bag.PkQueryIdUpgrader
Construct with the name of a source - will use defined keys to upgrade bags.
PkQueryIdUpgrader(ObjectStore) - Constructor for class org.intermine.api.bag.PkQueryIdUpgrader
No argument constructor - will use all available keyDefs to upgrade bags.
PLAIN_TEXT - Static variable in class org.intermine.webservice.server.lists.ListUploadService
 
PlainFormatter - Class in org.intermine.webservice.server.output
Simplest possible formatting.
PlainFormatter() - Constructor for class org.intermine.webservice.server.output.PlainFormatter
 
PlainText - org.intermine.api.mines.ContentType
The plain text content type
platform - Variable in class org.intermine.sql.Database
 
pluralise(String) - Static method in class org.intermine.metadata.StringUtil
Returns a pluralised version of the given String
PLUS - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
PLUS - Static variable in class org.intermine.sql.query.Function
PLUS function - takes two or more operands.
PLUS - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
POLL_REFRESH_SECONDS - Static variable in class org.intermine.web.logic.Constants
Refresh period specified on query poll page.
PollQueryAction - Class in org.intermine.web.struts
Repeatedly poll the status of a running query and forward client to appropriate page each time.
PollQueryAction() - Constructor for class org.intermine.web.struts.PollQueryAction
 
poplationCount - Variable in class org.intermine.web.logic.widget.Widget
 
popTag() - Method in class org.intermine.webservice.server.output.XMLFormatter
Say that we are finished with the current tag.
populateIds(Connection, InterMineObject) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Populates the object o with IDs.
populateList(List<String>, String) - Method in class org.intermine.webservice.server.lists.ListInput
read the parameters into a list.
populateListMap(Map<String, InterMineBag>, String) - Method in class org.intermine.webservice.server.lists.ListInput
Fill a map with intermine bags from the names in a parameter.
populateNormedList(List<String>, String) - Method in class org.intermine.webservice.server.lists.ListInput
Read parameters into a list, normalising the values.
populateObject(Item, Map<String, FastPathObject>, boolean, boolean, FastPathObject) - Static method in class org.intermine.xml.full.FullParser
Fill in fields of an outline business object which is in the map under item.identifier Note that this modifies the relevant object in the map It also returns the object for convenience
populateRequest(HttpServletRequest, HttpServletResponse) - Static method in class org.intermine.web.struts.QueryBuilderController
Populate the request with the necessary attributes to render the query builder page.
populateSearchItems() - Method in class org.intermine.api.search.GlobalRepository
 
populateSearchItems() - Method in class org.intermine.api.search.SearchRepository
Collect the search items we are interested in initially.
populateSearchItems() - Method in class org.intermine.api.search.UserRepository
 
populateTemplateOneConstraint(TemplateQuery, ConstraintOp, String) - Static method in class org.intermine.api.template.TemplatePopulator
Populate a TemplateQuery that has a single editable constraint with the given value.
populateTemplateWithBag(TemplateQuery, InterMineBag) - Static method in class org.intermine.api.template.TemplatePopulator
Constrain a template query with a single editable constraint to be in the given bag.
populateTemplateWithObject(TemplateQuery, InterMineObject) - Static method in class org.intermine.api.template.TemplatePopulator
Constrain a template query with a single editable constraint to be the given object.
populationBagName - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
populationIds - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
PopulationInfo - Class in org.intermine.web.logic.widget
Container for size and extra attribute (e.g.
PopulationInfo(int, float) - Constructor for class org.intermine.web.logic.widget.PopulationInfo
Constructor
PORTAL_MSG - Static variable in class org.intermine.web.logic.Constants
Session attribute that temporarily holds messages from the Portal
PortalHelper - Class in org.intermine.web.logic
Util methods for the portal
PortalQueryAction - Class in org.intermine.web.struts
The portal query action handles links into flymine from external sites.
PortalQueryAction() - Constructor for class org.intermine.web.struts.PortalQueryAction
 
possibleValues - Variable in class org.intermine.api.template.TemplateSummariser
 
PossibleValuesService - Class in org.intermine.webservice.server.path
A service for retrieving the possible values for a path in the data model.
PossibleValuesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.path.PossibleValuesService
A service for providing column summary information.
PossibleValuesServlet - Class in org.intermine.webservice.server.path
A servlet for routing requests to the possible values service.
PossibleValuesServlet() - Constructor for class org.intermine.webservice.server.path.PossibleValuesServlet
Constructor.
POST - org.intermine.webservice.server.core.WebServiceServlet.Method
POST
postDeleteBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
PostgresByteArrayOutputStream - Class in org.intermine.sql.writebatch
A subclass of SensibleByteArrayOutputStream that has extra methods useful for reducing the memory footprint of the Postgres database write operations.
PostgresByteArrayOutputStream() - Constructor for class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
see ByteArrayOutputStream
PostgresByteArrayOutputStream(int) - Constructor for class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
see ByteArrayOutputStream
PostgresDataOutputStream - Class in org.intermine.sql.writebatch
A subclass of DataOutputStream that has extra methods useful for reducing the memory footprint of the Postgres database write operations.
PostgresDataOutputStream(OutputStream) - Constructor for class org.intermine.sql.writebatch.PostgresDataOutputStream
 
PostgresExplainResult - Class in org.intermine.sql.query
Subclass of ExplainResult specific to PostgreSQL.
PostgresExplainResult() - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of PostgresExplainResult without any data.
PostgresExplainResult(String, Connection) - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of PostgresExplainResult for a given Query String and database Connection.
PostgresExplainResult(PreparedStatement) - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of ExplainResult given a PreparedStatement object.
PostgresExplainResult(Query, Connection) - Constructor for class org.intermine.sql.query.PostgresExplainResult
Constructs an instance of PostgresExplainResult for a given Query and database Connection.
postInit() - Method in class org.intermine.webservice.server.core.JSONService
 
postInit() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
 
postInit() - Method in class org.intermine.webservice.server.path.PossibleValuesService
 
postInit() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
 
postInit() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
postInit() - Method in class org.intermine.webservice.server.query.result.QueryResultService
 
postInit() - Method in class org.intermine.webservice.server.WebService
Subclasses can hook in here to do common behaviour that needs to happen after initialisation.
postProcess() - Method in class org.intermine.postprocess.PostProcessor
All subclasses should override this method so they can be called in a generic fashion.
PostProcessor - Class in org.intermine.postprocess
Generic defn of a post process step...
PostProcessor(ObjectStoreWriter) - Constructor for class org.intermine.postprocess.PostProcessor
Typical constructor with a handle to the object store we are working on.
PostProcessorTask - Class in org.intermine.task
Generic defn of a post process step...
PostProcessorTask() - Constructor for class org.intermine.task.PostProcessorTask
 
POWER - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
POWER - Static variable in class org.intermine.sql.query.Function
POWER function - takes two operands.
POWER - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
precompute(boolean, ObjectStore, int) - Method in class org.intermine.task.PrecomputeTask
Create precomputed tables for the given ObjectStore.
precompute(Collection<ParallelPrecomputer.Job>) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Perform a load of precompute operations in parallel.
precompute(Query, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, Collection<? extends QueryNode>, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, Collection<? extends QueryNode>, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables for the given query.
precompute(Query, Collection<QueryNode>, String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Call ObjectStoreInterMineImpl.precompute() with the given Query.
preCompute(String) - Method in class org.intermine.dwr.AjaxServices
Precomputes the given template query
PRECOMPUTE_CATEGORY_TEMPLATE - Static variable in class org.intermine.web.task.PrecomputeTemplatesTask
The precompute category to use for templates.
PrecomputedTable - Class in org.intermine.sql.precompute
Represents a Precomputed table in a database.
PrecomputedTable(Query, String, String, String, Connection) - Constructor for class org.intermine.sql.precompute.PrecomputedTable
Construct a new PrecomputedTable
PrecomputedTableManager - Class in org.intermine.sql.precompute
Manages all the Precomputed tables in a given database.
PrecomputedTableManager(Connection) - Constructor for class org.intermine.sql.precompute.PrecomputedTableManager
Create a PrecomputedTableManager for a given Connection.
PrecomputedTableManager(Database) - Constructor for class org.intermine.sql.precompute.PrecomputedTableManager
Create a PrecomputedTableManager for the given underlying database.
precomputedTables - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
precomputePropertiesPath - Variable in class org.intermine.task.PrecomputeTask
 
precomputeQuery(String, Query, Collection<? extends QueryNode>, boolean, String, int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Call ObjectStoreInterMineImpl.precompute() with the given Query.
PrecomputeTask - Class in org.intermine.task
A Task that reads a list of queries from a properties file (eg.
PrecomputeTask() - Constructor for class org.intermine.task.PrecomputeTask
 
precomputeTemplate(TemplateQuery) - Method in class org.intermine.api.query.WebResultsExecutor
Precomputes a template query if it is not already precomputed, returning whether precomputing was necessary.
precomputeTemplates() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Create precomputed tables for all template queries in the given ObjectStore.
PrecomputeTemplatesTask - Class in org.intermine.web.task
A Task that reads a list of queries from a properties file (eg.
PrecomputeTemplatesTask() - Constructor for class org.intermine.web.task.PrecomputeTemplatesTask
 
precomputeWithConnection(Connection, Query, Collection<? extends QueryNode>, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Creates precomputed tables with the given query and connection.
preDeleteBatch - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
Predicate<T> - Interface in org.intermine.webservice.server.core
The type of functions that test things.
PreferencesHandler - Class in org.intermine.api.profile
 
PreferencesHandler(Map<String, String>) - Constructor for class org.intermine.api.profile.PreferencesHandler
 
PreferencesManager - Class in org.intermine.api.profile
Class encapsulating the logic for reading user preferences in and out of the DB.
PreferencesManager(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.PreferencesManager
Constructor
prefers(String) - Method in class org.intermine.api.profile.Profile
Determine whether a user perfers a certain thing or not.
prefetch - Variable in class org.intermine.objectstore.query.Results
 
prefetch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Prefetch into memory the batch indicated with the given batch number.
prefetchIds(Set<Integer>) - Method in class org.intermine.dataloader.DataTracker
Prefetches data for a specified set of object ids.
PrefetchManager - Class in org.intermine.objectstore.query
A manager for the prefetch mechanism for the Results object.
prefetchObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Prefetches an object into the objectstore getObjectById cache.
prefetchObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
Prefetches an object into the objectstore getObjectById cache.
prefetchObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
Prefetches an object into the objectstore getObjectById cache.
prefetchObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
Prefetches an object into the objectstore getObjectById cache.
prettyList(Collection<String>) - Static method in class org.intermine.metadata.StringUtil
Take a collection of Strings and return a combined string as a comma separated list with 'and' between the final pair.
prettyList(Collection<String>, boolean) - Static method in class org.intermine.metadata.StringUtil
Take a collection of Strings and return a combined string as a comma separated list with 'and' between the final pair.
PREV_TEMPLATE_NAME - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the previous template name
previousPage() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Go to the previous page
PrimaryKey - Class in org.intermine.metadata
Class representing a primary key as a list of field names
PrimaryKey(String, String, ClassDescriptor) - Constructor for class org.intermine.metadata.PrimaryKey
Constructor
primaryKeyCache - Static variable in class org.intermine.metadata.PrimaryKeyUtil
 
PrimaryKeyUtil - Class in org.intermine.metadata
Utility methods for PrimaryKey objects.
println() - Method in class org.intermine.web.logic.export.CustomPrintWriter
printStyleAndClass(JspWriter) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Prints 'style' and 'class' attributes of element.
priorityConfig - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
PriorityConfig - Class in org.intermine.dataloader
Class holding data source priority configuration for a Model.
PriorityConfig(Model) - Constructor for class org.intermine.dataloader.PriorityConfig
Constructor.
PRIVATEKEY_ALIAS - Static variable in class org.intermine.web.task.IssueTokenTask
The alias of the private key
PRIVATEKEY_PASSWORD - Static variable in class org.intermine.web.task.IssueTokenTask
The password of the private key.
process() - Method in class org.intermine.codegen.JavaModelOutput
Perform the mapping.
process() - Method in class org.intermine.dataconversion.DBConverter
Query from database and write items to the writer.
process() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
Process the schema and put the output in the file.
process() - Method in class org.intermine.task.DirectDataLoaderTask
Called by execute() to process the data.
process() - Method in class org.intermine.task.FileDirectDataLoaderTask
 
process() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
process() - Method in class org.intermine.web.logic.widget.GraphWidget
Process the data and create the widget
process() - Method in class org.intermine.web.logic.widget.HTMLWidget
 
process() - Method in class org.intermine.web.logic.widget.TableWidget
Process the data and create the widget
process() - Method in class org.intermine.web.logic.widget.Widget
Process the data and create the widget
process(File) - Method in class org.intermine.dataconversion.DirectoryConverter
Perform the conversion files in the directory
process(Reader) - Method in class org.intermine.dataconversion.FileConverter
Perform the currentFile conversion
process(Reader) - Method in class org.intermine.dataconversion.FullXmlConverter
Unmarshal the Items from the input XML file, and write them to the writer.
process(Reader) - Method in class org.intermine.metadata.InterMineModelParser
Read source model information in InterMine XML format and construct a InterMine Model object.
process(Reader) - Method in interface org.intermine.metadata.ModelParser
Read source model information and construct a InterMine Model object.
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.FlatWidgetProcessor
 
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.JSONWidgetProcessor
 
process(String, WidgetConfig) - Method in interface org.intermine.webservice.server.widget.WidgetProcessor
Process a widget.
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
Process a list called x with a widget y
process(String, WidgetConfig) - Method in class org.intermine.webservice.server.widget.XMLWidgetProcessor
 
process(ObjectStore, Source, Source) - Method in class org.intermine.dataloader.ObjectStoreDataLoader
Performs the loading operation, reading data from the given ObjectStore, which must use the same model as the destination IntegrationWriter.
process(ObjectStore, Source, Source, Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.ObjectStoreDataLoader
Loads only a specified class reading data from the given ObjectStore, which must use the same model as the destination IntegrationWriter.
processConstraint(PathQuery, String, Map<String, String>, Collection<String>) - Method in class org.intermine.pathquery.PathQueryHandler
Process a constraint from the xml attributes.
processFile(File) - Method in class org.intermine.task.FileDirectDataLoaderTask
Called by process() once for each File we need to process.
processFile(File) - Method in class org.intermine.task.TSVFileReaderTask
Query all objects of the class given by the className specified in the configurationFile.
processForwardConfig(HttpServletRequest, HttpServletResponse, ForwardConfig) - Method in class org.intermine.web.struts.InterMineRequestProcessor
Overridden to copy errors and messages to session before performing a redirecting forward.
processGroupClause(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a GROUP clause.
processIdentifiers(String, ListCreationInput, Set<String>, Set<String>, InterMineBag) - Method in class org.intermine.webservice.server.lists.ListUploadService
Process the identifiers.
processItem(DataConverter, Item) - Method in interface org.intermine.dataconversion.DataConverterStoreHook
This method is called before storing an Item.
processLimitClause(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a Limit clause.
processNewAbstractConstraint(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes an AbstractConstraint.
processNewAbstractValue(AST) - Method in class org.intermine.sql.query.Query
Processes a single AST node that describes an AbstractValue.
processNewField(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a Field.
processNewSafeFunction(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a safe function.
processNewSelect(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a SelectValue.
processNewTypecast(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a typecast.
processNewUnsafeFunction(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes an unsafe function.
processOrderClause(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a ORDER clause.
processPreprocess(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.InterMineRequestProcessor
This is called during the processing of every controller.
processQuery(PathQuery) - Static method in class org.intermine.webservice.server.query.result.FrictionlessDataPackage
Transform a query from a standard one into one that conforms to the requirements of JSON objects.
processQuery(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
Transform a query from a standard one into one that conforms to the requirements of JSON objects.
processResults(List<AcceptanceTestResult>, PrintWriter) - Method in class org.intermine.task.AcceptanceTestTask
Write a formatted HTML summary of the given AcceptanceTestResult objects to the PrintWriter.
processSelectList(AST) - Method in class org.intermine.sql.query.Query
Processes an AST node that describes a SELECT list.
processXml(InputStream, Source, Source) - Method in class org.intermine.dataloader.XmlDataLoader
Static method to unmarshall business objects from a given xml file and call store on each.
produce() - Method in class org.intermine.webservice.server.core.ListManager
 
produce() - Method in interface org.intermine.webservice.server.core.Producer
 
produceName() - Method in class org.intermine.webservice.server.lists.ListInput
 
produceName() - Method in class org.intermine.webservice.server.lists.ListRenameInput
 
Producer<T> - Interface in org.intermine.webservice.server.core
The type of functions that take no input and produce a value.
profile - Variable in class org.intermine.api.query.QueryExecutor
The profile to use to find bags from.
profile - Variable in class org.intermine.api.search.SearchRepository
 
profile - Variable in class org.intermine.web.uri.InterMineLUIConverter
 
profile - Variable in class org.intermine.webservice.server.lists.ListInput
 
profile - Variable in class org.intermine.webservice.server.query.QueryUploadService
 
Profile - Class in org.intermine.api.profile
Class to represent a user of the webapp The profile is responsible for informing its search repository of all web-searchable objects created or deleted on its watch.
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, InterMineBag>, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a Profile
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, ApiTemplate>, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a profile without an API key
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, Map<String, InterMineBag>, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a Profile
Profile(ProfileManager, String, Integer, String, Map<String, SavedQuery>, BagSet, Map<String, ApiTemplate>, String, boolean, boolean) - Constructor for class org.intermine.api.profile.Profile
Construct a Profile
PROFILE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the user's Profile
PROFILE_FORMAT_VERSION - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store profile format version.
ProfileAlreadyExistsException - Exception in org.intermine.api.profile
Exception thrown when attempting to create a profile element with a name that already exists.
ProfileAlreadyExistsException(String) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException
Constructs an ProfileNameAlreadyExistsExceptionException with the specified detail message.
ProfileAlreadyExistsException(String, Throwable) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException
Constructs an ProfileAlreadyExistsExceptionException with the specified detail message and nested throwable.
ProfileAlreadyExistsException(Throwable) - Constructor for exception org.intermine.api.profile.ProfileAlreadyExistsException
Constructs an ProfileAlreadyExistsExceptionException with the specified nested throwable.
ProfileBinding - Class in org.intermine.api.xml
Code for reading and writing Profile objects as XML.
profileCache - Variable in class org.intermine.api.profile.ProfileManager
 
profileId - Variable in class org.intermine.api.profile.StorableBag
 
profileManager - Variable in class org.intermine.api.bag.SharedBagManager
 
profileManager - Variable in class org.intermine.api.InterMineAPI
 
ProfileManager - Class in org.intermine.api.profile
Class to manage and persist user profile data such as saved bags
ProfileManager(ObjectStore, ObjectStoreWriter) - Constructor for class org.intermine.api.profile.ProfileManager
Construct a ProfileManager for the webapp
ProfileManager.ApiPermission - Class in org.intermine.api.profile
A representation of the level of permissions granted to a user.
ProfileManager.ApiPermission.Level - Enum in org.intermine.api.profile
The possible permission levels.
ProfileManager.AuthenticationException - Exception in org.intermine.api.profile
Exception thrown when the authentication fails.
ProfileManagerBinding - Class in org.intermine.api.xml
Code for reading and writing ProfileManager objects as XML
ProfileMergeIssues - Class in org.intermine.web.logic.profile
The problems that arose when merging two profiles.
ProfileMergeIssues() - Constructor for class org.intermine.web.logic.profile.ProfileMergeIssues
 
ProfileReadTask - Class in org.intermine.web.task
Task to read an XML file of a webapp userprofiles into a userprofile ObjectStore.
ProfileReadTask() - Constructor for class org.intermine.web.task.ProfileReadTask
 
ProfileWriteTask - Class in org.intermine.web.task
Task to write an XML file of a webapp userprofile object store.
ProfileWriteTask() - Constructor for class org.intermine.web.task.ProfileWriteTask
 
PROPERTIES_ORIGINS - Static variable in class org.intermine.web.logic.Constants
Attribute used to store origin information about properties in the context of this web application.
PropertiesUtil - Class in org.intermine.util
Convenience class for working with global properties
PropertyChangeEvent - Class in org.intermine.api.search
A representation of a notification that a property of a web searchable has changed.
PropertyChangeEvent(WebSearchable) - Constructor for class org.intermine.api.search.PropertyChangeEvent
Constructor.
propertyNames() - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
PROVIDER - Static variable in class org.intermine.web.logic.Constants
The name of the current open-id provider
proxGetItem() - Method in class org.intermine.model.fulldata.Attribute
 
proxGetItem() - Method in class org.intermine.model.fulldata.Reference
 
proxGetItem() - Method in class org.intermine.model.fulldata.ReferenceList
 
proxGetTemplate() - Method in class org.intermine.api.userprofile.TemplateSummary
 
proxGetUserProfile() - Method in class org.intermine.api.userprofile.PermanentToken
 
proxGetUserProfile() - Method in class org.intermine.api.userprofile.SavedBag
 
proxGetUserProfile() - Method in class org.intermine.api.userprofile.SavedQuery
 
proxGetUserProfile() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
proxGetUserProfile() - Method in class org.intermine.api.userprofile.Tag
 
ProxyCollection<E> - Class in org.intermine.objectstore.proxy
Class which holds a reference to a collection in the database
ProxyCollection(ObjectStore, InterMineObject, String, Class<? extends E>) - Constructor for class org.intermine.objectstore.proxy.ProxyCollection
Construct a ProxyCollection object.
proxyItem(ProxyReference) - Method in class org.intermine.model.fulldata.Attribute
 
proxyItem(ProxyReference) - Method in class org.intermine.model.fulldata.Reference
 
proxyItem(ProxyReference) - Method in class org.intermine.model.fulldata.ReferenceList
 
ProxyReference - Class in org.intermine.objectstore.proxy
Class which holds a reference to an object in the database
ProxyReference(ObjectStore, Integer, Class<? extends InterMineObject>) - Constructor for class org.intermine.objectstore.proxy.ProxyReference
Construct a ProxyReference object.
proxyTemplate(ProxyReference) - Method in class org.intermine.api.userprofile.TemplateSummary
 
proxyUserProfile(ProxyReference) - Method in class org.intermine.api.userprofile.PermanentToken
 
proxyUserProfile(ProxyReference) - Method in class org.intermine.api.userprofile.SavedBag
 
proxyUserProfile(ProxyReference) - Method in class org.intermine.api.userprofile.SavedQuery
 
proxyUserProfile(ProxyReference) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
proxyUserProfile(ProxyReference) - Method in class org.intermine.api.userprofile.Tag
 
PseudoSet<E> - Class in org.intermine.util
A Set that does not actually contain objects, but provides useful results for the contains method.
PseudoSet() - Constructor for class org.intermine.util.PseudoSet
 
PswResetService - Class in org.intermine.webservice.server.user
Change a user's password with the authority of a token previously emailed to them.
PswResetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.PswResetService
Constructor
PswResetServlet - Class in org.intermine.webservice.server.user
Runs the PswReset service
PswResetServlet() - Constructor for class org.intermine.webservice.server.user.PswResetServlet
 
PUBLIC_TAG_LIST - Static variable in class org.intermine.web.struts.InitialiserPlugin
The list of tags that mark something as public
PUBLICIDENTITY - Static variable in class org.intermine.web.task.IssueTokenTask
The identity of the issuing entity (i.e.
PublicKeySource - Interface in org.intermine.web.security
An object that can provide public keys by name, or all known keys, or a subset of keys.
pureObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
This is a list of the objects that did not merge with anything from a previous data source
pushTag(String) - Method in class org.intermine.webservice.server.output.XMLFormatter
Set the current tag we are working within.
put(int, int) - Method in class org.intermine.util.IntToIntMap
Creates a mapping in the object.
put(E) - Method in class org.intermine.util.ObjectPipe
Adds an Object onto the end of the queue.
put(E, E) - Method in class org.intermine.util.IdentityMap
put(Integer, Integer) - Method in class org.intermine.util.IntToIntMap
Puts a mapping in the object.
put(Object, Object) - Method in class org.intermine.metadata.NonOverrideableProperties
Override put, but do not allow existing values to be changed.
put(Object, Object) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
put(String, String) - Method in class org.intermine.api.profile.UserPreferences
 
put(String, Source) - Method in class org.intermine.dataloader.ObjectDescription
Adds a fieldname-source mapping for this ObjectDescription that is not present in the backing database.
put(K, V) - Method in class org.intermine.api.util.DevNullMap
 
put(K, V) - Method in class org.intermine.util.AlwaysMap
put(K, V) - Method in class org.intermine.util.ReferenceMap
put(InterMineObject, ReportObject) - Method in class org.intermine.web.logic.results.ReportObjectFactory
Disable this method.
PUT - org.intermine.webservice.server.core.WebServiceServlet.Method
PUT
putAll(Collection<? extends E>) - Method in class org.intermine.util.ObjectPipe
Adds a whole Collection of Objects onto the end of the queue, in the order that the Collection's Iterator presents them.
putAll(Map<? extends E, ? extends E>) - Method in class org.intermine.util.IdentityMap
putAll(Map<? extends Object, ? extends Object>) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
putAll(Map<? extends String, ? extends String>) - Method in class org.intermine.api.profile.UserPreferences
 
putAll(Map<? extends K, ? extends V>) - Method in class org.intermine.util.AlwaysMap
putAll(Map<? extends K, ? extends V>) - Method in class org.intermine.util.ReferenceMap
putClean(String, Source) - Method in class org.intermine.dataloader.ObjectDescription
Adds a fieldname-source mapping for this ObjectDescription while keeping it clean.
putQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore
 
putQuery(String) - Method in interface org.intermine.api.query.QueryStore
 

Q

q - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
qc - Variable in class org.intermine.objectstore.query.QueryForeignKey
 
qc - Variable in class org.intermine.objectstore.query.QueryReference
 
qc1 - Variable in class org.intermine.objectstore.query.ClassConstraint
 
qc2 - Variable in class org.intermine.objectstore.query.ClassConstraint
 
qcb - Variable in class org.intermine.objectstore.query.QueryCollectionReference
 
qcObj - Variable in class org.intermine.objectstore.query.QueryCollectionReference
 
qe - Variable in class org.intermine.objectstore.query.SubqueryConstraint
 
qe1 - Variable in class org.intermine.objectstore.query.SimpleConstraint
 
qe2 - Variable in class org.intermine.objectstore.query.SimpleConstraint
 
qn - Variable in class org.intermine.objectstore.query.BagConstraint
 
queries - Variable in class org.intermine.sql.precompute.BestQueryStorer
 
Queries - Class in org.intermine.webservice.server.jbrowse
 
QUERIES_PARAMETER - Static variable in class org.intermine.webservice.server.query.QueryUploadService
The key for the queries parameter
queriesInUnion - Variable in class org.intermine.sql.query.Query
 
query - Variable in class org.intermine.api.userprofile.SavedQuery
 
query - Variable in class org.intermine.objectstore.query.ResultsBatches
 
query - Variable in class org.intermine.pathquery.PathQueryHandler
 
query - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
query - Variable in class org.intermine.sql.precompute.BestQueryFallback
 
query - Variable in class org.intermine.sql.query.SubQuery
 
query - Variable in class org.intermine.task.RunIqlQueryTask
 
Query - Class in org.intermine.objectstore.query
This class provides an implementation-independent abstract representation of a query
Query - Class in org.intermine.sql.query
Represents an SQL query in parsed form.
Query() - Constructor for class org.intermine.objectstore.query.Query
Empty constructor.
Query() - Constructor for class org.intermine.sql.query.Query
Construct a new Query.
Query(String) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(String, boolean) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(String, boolean, Long) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(String, Long) - Constructor for class org.intermine.sql.query.Query
Construct a new parsed Query from a String.
Query(Map<String, AbstractTable>) - Constructor for class org.intermine.sql.query.Query
Construct a new Query.
Query(Map<String, AbstractTable>, List<Query>) - Constructor for class org.intermine.sql.query.Query
Construct a new Query.
QUERY - org.intermine.api.tracker.util.ListBuildMode
query
QUERY - org.intermine.web.struts.oauth2.MessageFormat
This provider expects parameters in the query string
QUERY - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the current query
query_class_bag() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
query_class_bag_multi() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
QUERY_FOR_COUNTING - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery only for counting.
QUERY_FOR_GOFASTER - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
query for go faster
QUERY_FOR_PRECOMP - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
query for precomputing
QUERY_NORMAL - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
normal query
QUERY_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
Name of parameter with query
QUERY_SUBQUERY_CONSTRAINT - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery in CONSTRAINT
QUERY_SUBQUERY_EXISTS - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery exists
QUERY_SUBQUERY_FROM - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
subquery in FROM
QUERY_TIMEOUT_SECONDS - Static variable in class org.intermine.web.logic.Constants
Period of time to wait for client to poll a running query before cancelling the query.
QUERY_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks queries
QUERY_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks queries
Queryable - Interface in org.intermine.objectstore.query
An interface for an object that has a SELECT list and a WHERE clause, like a Query.
QueryAndClass(Query, Class<?>) - Constructor for class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
Constructor.
QueryBuilderChange - Class in org.intermine.web.struts
Action to handle links on main query builder tile.
QueryBuilderChange() - Constructor for class org.intermine.web.struts.QueryBuilderChange
 
QueryBuilderConstraintAction - Class in org.intermine.web.struts
Action to handle button presses on the main tile
QueryBuilderConstraintAction() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintAction
 
QueryBuilderConstraintController - Class in org.intermine.web.struts
Controller for the main constraint editing tile
QueryBuilderConstraintController() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintController
 
QueryBuilderConstraintForm - Class in org.intermine.web.struts
The form used for editing QueryBuilder constraints
QueryBuilderConstraintForm() - Constructor for class org.intermine.web.struts.QueryBuilderConstraintForm
 
QueryBuilderController - Class in org.intermine.web.struts
Controller for the main query builder tile.
QueryBuilderController() - Constructor for class org.intermine.web.struts.QueryBuilderController
 
QueryBuilderSummaryController - Class in org.intermine.web.struts
Controller for the QueryBuilder summary tile.
QueryBuilderSummaryController() - Constructor for class org.intermine.web.struts.QueryBuilderSummaryController
 
QueryBuilderSummaryHelper - Class in org.intermine.web.logic.querybuilder
Methods to generate summary information for a PathQuery for use in display of QueryBuilder summary section.
QueryBuilderViewAction - Class in org.intermine.web.struts
Action to run constructed query.
QueryBuilderViewAction() - Constructor for class org.intermine.web.struts.QueryBuilderViewAction
 
QueryBuilderViewChange - Class in org.intermine.web.struts
Action to handle links on view tile
QueryBuilderViewChange() - Constructor for class org.intermine.web.struts.QueryBuilderViewChange
 
queryCancelled() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called when the query is cancelled.
queryCancelled() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Called when the query is cancelled.
queryCancelledWithError() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called when the query stopped with an error.
queryCancelledWithError() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Called when the query stopped with an error.
QueryCast - Class in org.intermine.objectstore.query
Represents a type cast in a Query.
QueryCast(QueryEvaluable, Class<?>) - Constructor for class org.intermine.objectstore.query.QueryCast
Construct a QueryCast.
queryClass - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
QueryClass - Class in org.intermine.objectstore.query
Represents the database extent of a Java class NOTE - No equals() method is defined for this class and none should be.
QueryClass(Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryClass
Constructs a QueryClass representing the specified array of classes
QueryClass(Class<? extends FastPathObject>) - Constructor for class org.intermine.objectstore.query.QueryClass
Constructs a QueryClass representing the specified Java class
QueryClass(Set<Class<?>>) - Constructor for class org.intermine.objectstore.query.QueryClass
Constructs a QueryClass representing the specified set of classes
QueryClassBag - Class in org.intermine.objectstore.query
An element that can appear in the FROM clause of a query
QueryClassBag(Class<? extends InterMineObject>, Collection<?>) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClassBag representing the specified Java class and bag of objects.
QueryClassBag(Class<? extends InterMineObject>, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClassBag representing the specified Java class and ObjectStoreBag.
QueryClassBag(Set<Class<?>>, Collection<?>) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClass representing the specified set of classes and bag of objects.
QueryClassBag(Set<Class<?>>, ObjectStoreBag) - Constructor for class org.intermine.objectstore.query.QueryClassBag
Constructs a QueryClass representing the specified set of classes and ObjectStoreBag.
queryClassInQuery - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
QueryClassSelectAction - Class in org.intermine.web.struts
Implementation of Action that processes QueryClass selection form.
QueryClassSelectAction() - Constructor for class org.intermine.web.struts.QueryClassSelectAction
 
QueryClassSelectForm - Class in org.intermine.web.struts
Form bean for selection of a new query class.
QueryClassSelectForm() - Constructor for class org.intermine.web.struts.QueryClassSelectForm
 
queryClassToString(StringBuffer, QueryClass, Query, DatabaseSchema, int, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a QueryClass to a String.
QueryCloner - Class in org.intermine.objectstore.query
This is a static class that provides a method to clone a Query object.
QueryCollectionPathExpression - Class in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a collection or reference referenced in an object in the results.
QueryCollectionPathExpression(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionPathExpression
Constructs a QueryCollectionPathExpression representing a reference from the given QueryClass to the given field name.
QueryCollectionPathExpression(QueryClass, String, Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryCollectionPathExpression
Constructs a QueryCollectionPathExpression representing a reference from the given QueryClass to the given field name, constrained to be a particular subclass.
queryCollectionPathExpressionToString(Query, List<Object>, QueryCollectionPathExpression) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryObjectPathExpression into a String.
QueryCollectionReference - Class in org.intermine.objectstore.query
Represents a field of a QueryClass that is a collection
QueryCollectionReference(InterMineObject, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference
Constructs a QueryCollectionReference representing the specified field of an object
QueryCollectionReference(QueryClassBag, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference
Constructs a QueryCollectionReference representing the specified field of a QueryClassBag
QueryCollectionReference(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryCollectionReference
Constructs a QueryCollectionReference representing the specified field of a QueryClass
queryCompleted() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called when the query has completed.
queryCompleted() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Called when the query has completed.
QueryCountQueryMonitor - Class in org.intermine.web.logic.session
A QueryMonitor that maintains a timeout and is used when counting the number of rows a query returns.
QueryCountQueryMonitor(int, Query) - Constructor for class org.intermine.web.logic.session.QueryCountQueryMonitor
Construct a new instance of QueryCountQueryMonitor.
QueryCreator - Class in org.intermine.objectstore.query
Class that helps build queries or parts of queries for common situations.
queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.BatchingFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
queryEquivalentObjects(InterMineObject, Source) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
queryEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.HintingFetcher
Returns a Set of objects that are equivalent to the given object, according to the primary keys defined by the given Source.
QueryEvaluable - Interface in org.intermine.objectstore.query
An element that can be evaluated for comparison (one that represents an atomic type)
queryEvaluableToString(StringBuffer, QueryEvaluable, Query, SqlGenerator.State) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a QueryEvaluable into a String suitable for an SQL query String.
QueryExecutor - Class in org.intermine.api.query
Common superclass of query executors that holds cache of pathToQueryNode maps per query.
QueryExecutor() - Constructor for class org.intermine.api.query.QueryExecutor
 
QueryExpression - Class in org.intermine.objectstore.query
Represents an arithmetic or substring expression, analogous to those in SQL
QueryExpression(int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression
Constructs a String QueryExpression to perform upper and lowercase conversions.
QueryExpression(QueryEvaluable, int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression
Constructs an arithmetic QueryExpression from two evaluable items
QueryExpression(QueryEvaluable, QueryEvaluable, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryExpression
Constructs a substring QueryExpression from a QueryEvaluable and start and length QueryEvaluables
queryExpressionToString(Query, QueryExpression, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryExpression into a String.
QueryField - Class in org.intermine.objectstore.query
Represents a QueryClass field that is neither a collection or reference to another business object.
QueryField(FromElement, String, String, Class<?>) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField object - intended for cloning operations.
QueryField(QueryClassBag) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs the id QueryField for the given QueryClassBag.
QueryField(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField representing the specified field of a QueryClass
QueryField(Query, QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField representing the specified field of the specified QueryClass, as seen outside the specified subquery.
QueryField(Query, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryField
Constructs a QueryField representing the specified entry from the SELECT list of the specified subquery.
QueryForeignKey - Class in org.intermine.objectstore.query
Represents the ID of a field of a QueryClass that is a business object
QueryForeignKey(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryForeignKey
Constructs a QueryForeignKey representing the specified field of a QueryClass
QueryForm - Class in org.intermine.web.struts
Action form that holds query XML.
QueryForm() - Constructor for class org.intermine.web.struts.QueryForm
 
queryForTypesInCollection(InterMineObject, String, ObjectStore) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
Search for the classes in a collection for a given InterMineObject, for example find all of the sub-classes of Employee in the Department.employees collection of a given Department.
QueryFunction - Class in org.intermine.objectstore.query
A QueryFunction represents an aggregate
QueryFunction() - Constructor for class org.intermine.objectstore.query.QueryFunction
Creates a COUNT aggregate function.
QueryFunction(QueryEvaluable, int) - Constructor for class org.intermine.objectstore.query.QueryFunction
 
QueryFunction(QueryEvaluable, int, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.QueryFunction
Constructor for functions that take two parameters.
QueryGenUtil - Class in org.intermine.objectstore.querygen
Utility methods for paths.
QueryGenUtil.QueryAndClass - Class in org.intermine.objectstore.querygen
Class to allow returning of two arguments from a method.
QueryHelper - Class in org.intermine.objectstore.query
Static methods to assist with query generation from front end.
queryHistory - Variable in class org.intermine.api.profile.Profile
 
QueryListAppendService - Class in org.intermine.webservice.server.query
Append items to a list from the results of a query.
QueryListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryListAppendService
Constructor.
QueryListAppendServlet - Class in org.intermine.webservice.server.query
Runs the query-to-list service to run queries and save them as lists.
QueryListAppendServlet() - Constructor for class org.intermine.webservice.server.query.QueryListAppendServlet
 
QueryLogger - Class in org.intermine.sql.logging
Provides a logging facility for a Query
QueryMonitor - Interface in org.intermine.web.logic.query
Interface passed to SessionMethods runQuery method which is polled every so-often while the query runs in order to decide whether or not to cancel the query.
QueryMonitorTimeout - Class in org.intermine.web.logic.query
QueryMonitor that cancels a query after a given timeout period.
QueryMonitorTimeout(int) - Constructor for class org.intermine.web.logic.query.QueryMonitorTimeout
Construct a new instance of QueryMonitorTimeout.
queryName - Variable in class org.intermine.web.struts.SaveQueryForm
 
QueryNode - Interface in org.intermine.objectstore.query
An element that can appear in the SELECT, ORDER BY or GROUP BY clause of a query.
QueryObjectPathExpression - Class in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results - namely a object referenced by some other object in the results.
QueryObjectPathExpression(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryObjectPathExpression
Constructs a QueryObjectPathExpression representing an object reference from the given QueryClass to the given fieldname.
QueryObjectPathExpression(QueryClass, String, Class<?>...) - Constructor for class org.intermine.objectstore.query.QueryObjectPathExpression
Constructs a QueryObjectPathExpression representing an object reference from the given QueryClass to the given fieldname, constrained to be a particular subclass.
queryObjectPathExpressionToString(Query, List<Object>, QueryObjectPathExpression) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryObjectPathExpression into a String.
QueryObjectReference - Class in org.intermine.objectstore.query
Represents a field of a QueryClass that is a business object
QueryObjectReference(QueryClass, String) - Constructor for class org.intermine.objectstore.query.QueryObjectReference
Constructs a QueryObjectReference representing the specified field of a QueryClass
QueryOptimiser - Class in org.intermine.sql.precompute
A static class providing the code to optimise a query, given a database (presumably with a table describing the available precomputed tables).
QueryOptimiser.AbstractTableComparator - Class in org.intermine.sql.precompute
Compares two AbstractTables using their equalsIgnoreAlias() method.
QueryOptimiserContext - Class in org.intermine.sql.precompute
A class describing settings for the optimiser.
QueryOptimiserContext() - Constructor for class org.intermine.sql.precompute.QueryOptimiserContext
 
QueryOptimiserException - Exception in org.intermine.sql.precompute
An Exception that may be thrown by a QueryOptimiser method.
QueryOptimiserException() - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException
QueryOptimiserException(String) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException with the specified detail message.
QueryOptimiserException(String, Throwable) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException with the specified detail message and nested throwable.
QueryOptimiserException(Throwable) - Constructor for exception org.intermine.sql.precompute.QueryOptimiserException
Constructs an QueryOptimiserException with the specified nested throwable.
QueryOrderable - Interface in org.intermine.objectstore.query
An element that can appear in the ORDER BY clause of a query.
QueryParseTimeoutException - Exception in org.intermine.sql.query
Exception thrown when parsing a query from SQL string to org.intermine.sql.Query object.
QueryParseTimeoutException() - Constructor for exception org.intermine.sql.query.QueryParseTimeoutException
 
QueryPathExpression - Interface in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query, representing extra data to be collected for the Results, usually in a separate database operation.
QueryPathExpressionWithSelect - Interface in org.intermine.objectstore.query
A Path Expression that has a Select list.
QueryReference - Class in org.intermine.objectstore.query
Represents a field of a QueryClass that is a non-primitive type.
QueryReference() - Constructor for class org.intermine.objectstore.query.QueryReference
 
queryReferenceToString(Query, QueryReference, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
Converts a QueryReference into a String.
QueryRemovalService - Class in org.intermine.webservice.server.query
A service that removes a saved query from profile's collection of saved queries.
QueryRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryRemovalService
 
QueryRequestParser - Class in org.intermine.webservice.server.query
Processes query request parameters.
QueryRequestParser(QueryStore, HttpServletRequest) - Constructor for class org.intermine.webservice.server.query.QueryRequestParser
RequestProcessor constructor.
QueryResultInput - Class in org.intermine.webservice.server.query.result
QueryServiceInput is parameter object representing parameters for QueryResultService web service.
QueryResultInput() - Constructor for class org.intermine.webservice.server.query.result.QueryResultInput
 
QueryResultLinkGenerator - Class in org.intermine.webservice.server.query.result
Class that implements generating links for QueryResultService web service.
QueryResultLinkGenerator() - Constructor for class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
 
QueryResultRequestParser - Class in org.intermine.webservice.server.query.result
Processes service request.
QueryResultRequestParser(QueryStore, HttpServletRequest) - Constructor for class org.intermine.webservice.server.query.result.QueryResultRequestParser
RequestProcessor constructor.
QueryResultService - Class in org.intermine.webservice.server.query.result
Executes query and returns results.
QueryResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.result.QueryResultService
Constructor
QueryResultServlet - Class in org.intermine.webservice.server.query.result
Servlet that runs QueryResultService.
QueryResultServlet() - Constructor for class org.intermine.webservice.server.query.result.QueryResultServlet
 
QueryRetrieverService - Class in org.intermine.webservice.server.query
A service that retrieves a stored query by qid.
QueryRetrieverService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryRetrieverService
 
QuerySelectable - Interface in org.intermine.objectstore.query
An element that can appear in the SELECT clause of a query.
queryStore - Variable in class org.intermine.api.InterMineAPI
 
QueryStore - Interface in org.intermine.api.query
 
QueryStoreException - Exception in org.intermine.api.query
 
QueryStoreException(String) - Constructor for exception org.intermine.api.query.QueryStoreException
 
QueryStoreException(String, Exception) - Constructor for exception org.intermine.api.query.QueryStoreException
 
QueryStoreService - Class in org.intermine.webservice.server.query
A service that stores a query and associates it with an id.
QueryStoreService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryStoreService
 
queryString - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
queryString - Variable in class org.intermine.sql.precompute.BestQueryFallback
 
QueryToListService - Class in org.intermine.webservice.server.query
A service for transforming a query, represented as a PathQuery serialised to XML, to a list.
QueryToListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryToListService
Constructor.
QueryToListServlet - Class in org.intermine.webservice.server.query
Runs the query-to-list service to run queries and save them as lists.
QueryToListServlet() - Constructor for class org.intermine.webservice.server.query.QueryToListServlet
 
queryToPathToQueryNode - Static variable in class org.intermine.api.query.QueryExecutor
A cache of pathToQueryNode maps that is shared between subclasses of QueryExecutor.
QueryTrack - Class in org.intermine.api.tracker.track
 
QueryTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.QueryTrack
 
QUERYTRACK - Static variable in class org.intermine.api.tracker.xml.QueryTrackBinding
label for XML
QueryTrackBinding - Class in org.intermine.api.tracker.xml
 
QueryTracker - Class in org.intermine.api.tracker
 
QueryTracker(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.QueryTracker
Build a query tracker
QUERYTRACKS - Static variable in class org.intermine.api.tracker.xml.QueryTrackBinding
label for XML
QueryUpdateService - Class in org.intermine.webservice.server.query
Same in all respects as the upload service, but this class overwrites queries with the provided names.
QueryUpdateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryUpdateService
 
QueryUploadService - Class in org.intermine.webservice.server.query
A service to enable queries to be uploaded programmatically.
QueryUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.QueryUploadService
Constructor.
QueryUploadServlet - Class in org.intermine.webservice.server.query
Runs the query Upload Service to handle user query uploads.
QueryUploadServlet() - Constructor for class org.intermine.webservice.server.query.QueryUploadServlet
 
QueryValue - Class in org.intermine.objectstore.query
Represents a constant in a Query
QueryValue(Object) - Constructor for class org.intermine.objectstore.query.QueryValue
Construct a QueryValue
QUESTION_MARK - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
queue - Variable in class org.intermine.util.ReferenceMap
 
queueMessage(MailAction) - Static method in class org.intermine.web.context.InterMineContext
Queue up a message to an emailer.
QuickSearch - Class in org.intermine.webservice.server.search
A service that runs key-word searches.
QuickSearch(InterMineAPI, ServletContext) - Constructor for class org.intermine.webservice.server.search.QuickSearch
 
QuickSearchJSONProcessor - Class in org.intermine.webservice.server.search
A class that renders quick search results as JSON.
QuickSearchJSONProcessor() - Constructor for class org.intermine.webservice.server.search.QuickSearchJSONProcessor
 
QuickSearchResultProcessor - Interface in org.intermine.webservice.server.search
The type of objects that can handle keyword search results.
QuickSearchServlet - Class in org.intermine.webservice.server.search
 
QuickSearchServlet() - Constructor for class org.intermine.webservice.server.search.QuickSearchServlet
 
QuickSearchTextProcessor - Class in org.intermine.webservice.server.search
A result processor that outputs results as plain text.
QuickSearchTextProcessor(String) - Constructor for class org.intermine.webservice.server.search.QuickSearchTextProcessor
 
QuickSearchXMLProcessor - Class in org.intermine.webservice.server.search
A result processor that outputs results as XML.
QuickSearchXMLProcessor() - Constructor for class org.intermine.webservice.server.search.QuickSearchXMLProcessor
 
QUOTED_STRING - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
QUOTED_STRING - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 

R

rand - Static variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
random - Static variable in class org.intermine.web.task.LoadDefaultTemplatesTask
 
range(int, int) - Method in class org.intermine.objectstore.query.Results
Returns a range of rows of results.
range(int, int) - Method in class org.intermine.objectstore.query.SingletonResults
Returns a range of rows of results.
Range - Interface in org.intermine.api.query.range
 
RANGE_DEFINITIONS - Static variable in class org.intermine.modelproduction.MetadataManager
Description of range type columns defined in the database.
rangeConstraint - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
RangeHelper - Interface in org.intermine.api.query
 
rangeHelpers - Static variable in class org.intermine.api.query.MainHelper.RangeConfig
 
rangeOp - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
ranges - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
RateLimitException - Exception in org.intermine.webservice.server.exceptions
Exception representation for denying service based on rate limits.
RateLimitException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.RateLimitException
Constructor
RateLimitHistory - Class in org.intermine.webservice.server.core
A class for making sure that certain resources don't get hammered.
RateLimitHistory(int, int) - Constructor for class org.intermine.webservice.server.core.RateLimitHistory
Constructor
read() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
 
read(byte[], int, int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
 
readBagQueryConfig(Model, InputStream) - Static method in class org.intermine.api.bag.BagQueryHelper
Read the bag query configuration from the given stream.
readKeys(Model, Properties) - Static method in class org.intermine.api.config.ClassKeyHelper
Read class keys from a properties into a map from classname to set of available keys.
readLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Returns an InputStream object with which to read a large binary value from the database.
readOneTestConfig(LineNumberReader) - Static method in class org.intermine.task.AcceptanceTestTask
Read and return one AcceptanceTest object from the given Reader.
ReadPreferencesService - Class in org.intermine.webservice.server.user
A service for reading the current state of a user's preferences.
ReadPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.ReadPreferencesService
 
readWebProperties(Properties) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
ReadWriteJSONService - Class in org.intermine.webservice.server.core
Convenience for services that need to combine JSON service behaviour with strict RW authorisation.
ReadWriteJSONService(InterMineAPI) - Constructor for class org.intermine.webservice.server.core.ReadWriteJSONService
Construct a read/write service.
real - org.intermine.sql.DatabaseUtil.Type
real
realiseObjects(Collection<Item>, Model, boolean) - Static method in class org.intermine.xml.full.FullParser
Create business objects from a collection of Items.
realiseObjects(Collection<Item>, Model, boolean, boolean) - Static method in class org.intermine.xml.full.FullParser
Create business objects from a collection of Items.
ReallyFlatIterator - Class in org.intermine.api.results.flatouterjoins
An Iterator that flattens the contents of another Iterator.
ReallyFlatIterator(Iterator) - Constructor for class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
Constructs a ReallyFlatIterator from another Iterator.
receiveEvent(ChangeEvent) - Method in class org.intermine.api.search.SearchRepository
 
receiveEvent(ChangeEvent) - Method in interface org.intermine.api.search.WebSearchWatcher
Receive notification of a change to a WebSearchable somewhere in the universe.
recentSequences - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
reconstruct(String) - Method in class org.intermine.sql.precompute.LimitOffsetQuery
Reconstruct a SQL string, given this alternative SQL query-part.
reconstructAbstractConstraint(AbstractConstraint, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Field, int, Field, boolean, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Reconstructs an AbstractConstraint object, using reconstructAbstractValue.
reconstructAbstractConstraints(Set<AbstractConstraint>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Set<AbstractConstraint>, Set<AbstractConstraint>, Field, int, Field, boolean, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Populates the WHERE list of a new Query object, given the old Query's WHERE (or HAVING) list to use as a reference.
reconstructAbstractValue(AbstractValue, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Reconstructs an AbstractValue, to form the part of an SQL Query that has been replaced with a PrecomputedTable.
reconstructAbstractValues(Collection<AbstractValue>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Collection<AbstractValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Reconstructs a Collection of AbstractValue objects, calling reconstructAbstractValue on each one before adding it to another Collection.
reconstructSelectValues(List<SelectValue>, Table, Map<AbstractValue, SelectValue>, Set<AbstractTable>, boolean, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Populates the SELECT list of a new Query object, given an old Query's SELECT list to use as a reference, a valueMap (to pass to reconstructAbstractValue), and a Table to represent the PrecomputedTable.
recordError(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Record an error.
recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as an error for this Action
recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as an error for this Action and log the error
recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as an error for this Action and log the error
recordError(ActionMessage, HttpServletRequest, Exception, Logger) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as an error for this Action and log the error
recordMessage(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Record a message that will be stored in the session until it is displayed to the user.
recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineAction
Add the given ActionMessage as a message for this Action
recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineDispatchAction
Add the given ActionMessage as a message for this Action
recordMessage(ActionMessage, HttpServletRequest) - Method in class org.intermine.web.struts.InterMineLookupDispatchAction
Add the given ActionMessage as a message for this Action
recordRequest(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
Record that a request was made.
recursiveOptimise(Set<PrecomputedTable>, Query, BestQuery, Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Recursively optimises the query, given the set of precomputed tables, and updates the BestQuery object with each Query found.
recursiveOptimiseCheckSubquery(Set<PrecomputedTable>, Query, BestQuery) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Recursively optimises the query, given the set of precomputed tables, and updates the BestQuery object with each Query found.
ref - Variable in class org.intermine.objectstore.query.ContainsConstraint
 
reference(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
Reference - Class in org.intermine.model.fulldata
 
Reference - Class in org.intermine.xml.full
Representation of an Reference in an object
Reference() - Constructor for class org.intermine.model.fulldata.Reference
 
Reference() - Constructor for class org.intermine.xml.full.Reference
Constructor
Reference(String, String) - Constructor for class org.intermine.xml.full.Reference
Construnctor
REFERENCE - org.intermine.webservice.server.jbrowse.Commands.Action
reference
REFERENCE - Static variable in class org.intermine.api.tag.TagTypes
Reference.
REFERENCE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The lists to subtract from
referencedClassDesc - Variable in class org.intermine.metadata.ReferenceDescriptor
 
ReferenceDescriptor - Class in org.intermine.metadata
Describes a field that references a single other class (i.e.
ReferenceDescriptor(String, String, String) - Constructor for class org.intermine.metadata.ReferenceDescriptor
Construct a ReferenceDescriptor.
referencedType - Variable in class org.intermine.metadata.ReferenceDescriptor
 
ReferenceList - Class in org.intermine.model.fulldata
 
ReferenceList - Class in org.intermine.xml.full
Representation of a field in an object.
ReferenceList() - Constructor for class org.intermine.model.fulldata.ReferenceList
 
ReferenceList() - Constructor for class org.intermine.xml.full.ReferenceList
Constructor
ReferenceList(String) - Constructor for class org.intermine.xml.full.ReferenceList
Constructor
ReferenceList(String, List<String>) - Constructor for class org.intermine.xml.full.ReferenceList
Constructor
ReferenceMap<K,​V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
ReferenceMap() - Constructor for class org.intermine.util.ReferenceMap
 
ReferenceMap.ReferenceWithKey<K> - Interface in org.intermine.util
Interface for entries in the map.
references - Variable in class org.intermine.model.fulldata.Item
 
refId - Variable in class org.intermine.model.fulldata.Reference
 
refIds - Variable in class org.intermine.model.fulldata.ReferenceList
 
refIds - Variable in class org.intermine.xml.full.ReferenceList
 
register(String, String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
Register exporter.
registerObject(Object) - Static method in class org.intermine.util.ShutdownHook
Registers an object with the shutdown hook.
registerOffset(Query, int, DatabaseSchema, Database, Object, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Registers an offset for a given query.
registerRequestId(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method registers a Thread with a request ID.
registerStatement(Statement) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
This method registers a Statement with the current Thread's request ID, or throws an exception if that request is black-listed, or does nothing if no request ID is present for this Thread.
RegistryResponse - Class in org.intermine.web.registry.model
Pojo class to map the response from the intermine registry
RegistryResponse() - Constructor for class org.intermine.web.registry.model.RegistryResponse
 
rejectInvitation(SharingInvite) - Static method in class org.intermine.api.bag.SharedBagManager
Reject this invitation.
RELATED_DATA_CONSTRAINT_1 - Static variable in class org.intermine.api.config.Constants
Constraint for related data template
RELATED_DATA_CONSTRAINT_2 - Static variable in class org.intermine.api.config.Constants
Constraint for related data template
RELATED_DATA_TEMPLATE - Static variable in class org.intermine.api.config.Constants
queries for data related to current object
relationType() - Method in class org.intermine.metadata.AttributeDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.CollectionDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.FieldDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
relationType() - Method in class org.intermine.metadata.ReferenceDescriptor
Return an integer describing the type of relationship this field represents, where relationship types are 1:1, 1:N, N:1, M:N and "not a relationship".
RelativeComplement - Class in org.intermine.api.bag.operations
 
RelativeComplement(Model, Profile, Collection<InterMineBag>, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.RelativeComplement
 
releaseConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows one to put a connection back.
releaseConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Allows one to put a connection back.
ReleaseEtagFilter - Class in org.intermine.web.filters
Return responses tagged with the release version.
ReleaseEtagFilter() - Constructor for class org.intermine.web.filters.ReleaseEtagFilter
 
releaseGoFaster() - Method in class org.intermine.api.results.ExportResultsIterator
Switches off the goFaster mode in the objectstore for this query.
releaseGoFaster() - Method in class org.intermine.api.results.WebResults
Calls ObjectStore.releaseGoFaster() if this object wraps a Results object from an ObjectStoreInterMineImpl.
releaseGoFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Releases the resources used by goFaster().
releaseResources() - Method in class org.intermine.api.tracker.xml.TrackHandler
 
releaseResources(ResultSet, Statement) - Method in class org.intermine.api.tracker.AbstractTracker
Close the result set and statement objects specified in input
remapAliases(Map<AbstractTable, AbstractTable>, Set<AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Alters all the aliases of the tables being mapped to, to equal the alias of the table mapping to them.
remapAliasesToAvoidPrecomputePrefix(Query) - Static method in class org.intermine.sql.precompute.QueryOptimiser
Remaps the aliases of any table that starts with the ALIAS_PREFIX, to avoid clashes with future precomputed tables.
RemoteMine - Class in org.intermine.api.mines
An object that represents an InterMine application hosted somewhere else.
RemoteMine(String, MineRequester, int) - Constructor for class org.intermine.api.mines.RemoteMine
Create a representation of a remotely accessible mine.
remove() - Method in class org.intermine.api.results.ExportResultsIterator
This method is not supported.
remove() - Method in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
This operation is not supported.
remove() - Method in class org.intermine.util.CombinedIterator
This operation is not supported.
remove() - Method in class org.intermine.util.ObjectPipe
remove() - Method in class org.intermine.util.SynchronisedIterator
remove() - Method in class org.intermine.webservice.server.core.TableRowIterator
 
remove() - Method in class org.intermine.webservice.server.output.FilteringResultIterator
 
remove() - Method in class org.intermine.webservice.server.output.JSONDataTableRowIterator
 
remove() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Remove is not supported.
remove() - Method in class org.intermine.webservice.server.output.JSONRowIterator
 
remove() - Method in class org.intermine.webservice.server.output.MinimalJsonIterator
 
remove(Object) - Method in class org.intermine.api.profile.UserPreferences
 
remove(Object) - Method in class org.intermine.util.AlwaysMap
remove(Object) - Method in class org.intermine.util.IdentityMap
remove(Object) - Method in class org.intermine.util.PseudoSet
remove(Object) - Method in class org.intermine.util.ReferenceMap
removeAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Removes a collection of elements from an ObjectStoreBag, delegate to internal ObjectStoreWriter.
removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Removes a collection of elements from an ObjectStoreBag.
removeAllFromBag(ObjectStoreBag, Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Removes a collection of elements from an ObjectStoreBag.
removeAllFromBagWithConnection(Connection, ObjectStoreBag, Collection<Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Removes elements from the given bag.
removeAllInvitesBy(Integer) - Method in class org.intermine.api.bag.SharedBagManager
Removes all invitations to share resources that were issued by the user with the given id.
removeAllIrrelevant() - Method in class org.intermine.pathquery.PathQuery
Removes everything from this query that is irrelevant, and therefore making the query invalid.
removeAllSharesInvolving(Integer) - Method in class org.intermine.api.bag.SharedBagManager
Removes all shares from or to the user with the given id.
removeAllTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil
Removes every single table from the database given.
removeAllUnder(String) - Method in class org.intermine.pathquery.PathQuery
Removes everything under a given path from the query, such that if the query was valid before, it will be valid after this method.
removeAllVariablesExcept(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression
Remove any variables that aren't in the given set.
removeAttribute(String) - Method in class org.intermine.xml.full.Item
Remove a attribute of the specified name if it exists.
removeCollection(String) - Method in class org.intermine.xml.full.Item
Remove a collection of the specified name if it exists.
removeConstraint(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Remove a constraint identified by its code from the query.
removeConstraint(Constraint) - Method in class org.intermine.objectstore.query.ConstraintSet
Remove specified constraint
removeConstraint(PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Removes a constraint from this query.
removeConstraint(PathConstraint) - Method in class org.intermine.template.TemplateQuery
Removes a constraint from this query.
REMOVED - org.intermine.api.search.TaggingEvent.TagChange
 
removeDirectAttributesFromView(TemplateQuery) - Static method in class org.intermine.api.template.TemplateHelper
Removed from the view all the direct attributes that aren't editable constraints
removeEldestEntry(Map.Entry) - Method in class org.intermine.api.util.LimitedMap
 
removeFieldDescriptor(Set<? extends FieldDescriptor>, String) - Static method in class org.intermine.modelproduction.ModelMerger
Remove a FieldDescriptor from a Set of FieldDescriptors by name.
removeFromBag(ObjectStoreBag, Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Removes an element from an ObjectStoreBag, delegate to internal ObjectStoreWriter.
removeFromBag(ObjectStoreBag, Integer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Removes an element from an ObjectStoreBag.
removeFromBag(ObjectStoreBag, Integer) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Removes an element from an ObjectStoreBag.
removeFromConstraintLogic(LogicExpression, String) - Static method in class org.intermine.api.query.MainHelper
Remove a constraint code from a logic expression, e.g.
removeFromView(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderViewChange
Remove a Node from the results view
removeIdFromBag(Integer) - Method in class org.intermine.api.profile.InterMineBag
Remove the given id from the bag, this updates the bag contents in the database
removeIdsFromBag(Collection<Integer>, boolean) - Method in class org.intermine.api.profile.InterMineBag
Remove the given ids from the bag, this updates the bag contents in the database
removeJob(String) - Method in class org.intermine.api.idresolution.IDResolver
 
removeNode(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Remove everything in a query under a given path.
removeObserver(WebSearchWatcher) - Method in class org.intermine.api.profile.StorableBag
 
removeObserver(WebSearchWatcher) - Method in interface org.intermine.api.search.WebSearchable
Remove this observer from the list of interested parties.
removeObserver(WebSearchWatcher) - Method in class org.intermine.api.template.ApiTemplate
 
removeOrderBy(String) - Method in class org.intermine.pathquery.PathQuery
Removes an element from the order by list of this query.
removePermanentToken(PermanentToken) - Method in class org.intermine.api.profile.ProfileManager
 
removeQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
Removes the current query from the session.
removeRedundancy(Map<String, ClassDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
When changes are made to the inheritance hierarchy (especially the addition of superinterfaces), fields may be defined on superinterfaces making previous definitions further down the inheritance hierarchy redundant.
removeReference(String) - Method in class org.intermine.xml.full.Item
Remove a reference of the specified name if it exists.
removeSelectedFromBag(InterMineBag, HttpSession) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
remove the selected elements from the bag.
removeSequence(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil
Remove the sequence from the database given.
removeSubclass(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Remove a subclass constraint from the query.
removeSubclassAndFixUp(String) - Method in class org.intermine.pathquery.PathQuery
Removes a subclass from the query, and removes any parts of the query that relied on it.
removeTempBagTable(Connection, ObjectStoreInterMineImpl.BagTableToRemove) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Removes a temporary bag table, given a BagTableToRemove object.
removeToken(DeletionToken) - Method in class org.intermine.webservice.server.user.DeletionTokens
Remove this token.
removeTokensForProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Remove auth tokens for a specified users.
removeVariable(String) - Method in class org.intermine.pathquery.LogicExpression
Remove a variable from the expression.
removeView(String) - Method in class org.intermine.pathquery.PathQuery
Removes a single element from the view list.
removeView(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil
Remove the view from the database given.
rename(String) - Method in class org.intermine.api.profile.InvalidBag
Returns a new Invalid Bag identical to this one, but with the given name.
rename(String, String, String) - Method in class org.intermine.dwr.AjaxServices
Rename a element such as history, name, bag
RENAME - Static variable in class org.intermine.api.profile.ModelUpdate
label in modelUpdate.properties file to identify renamed classes or fields
renameBag(String, String) - Method in class org.intermine.api.profile.Profile
Rename an existing bag, throw exceptions when bag doesn't exist of if new name already exists.
renameHistory(String, String) - Method in class org.intermine.api.profile.Profile
Rename an item in the history.
render(Object) - Static method in class org.intermine.objectstore.intermine.NotXmlRenderer
Render the given object as NotXml.
render(Collection<FastPathObject>, Model) - Static method in class org.intermine.xml.full.FullRenderer
Render a collection of objects as XML in InterMine Full format.
render(Collection<Item>) - Static method in class org.intermine.xml.full.FullRenderer
Render a collection of items in InterMine Full XML format.
render(XMLStreamWriter, Item) - Static method in class org.intermine.xml.full.FullRenderer
Render the given Item as XML using an XMLStreamWriter
render(FastPathObject, Model) - Static method in class org.intermine.xml.full.FullRenderer
Render an Object as Xml in Full Data format.
render(Item) - Static method in class org.intermine.xml.full.FullRenderer
Render the given Item as XML
RendererComparator - Class in org.intermine.xml.full
An implementation of Comparator to order pairs of Class objects.
RendererComparator() - Constructor for class org.intermine.xml.full.RendererComparator
 
renderImpl(XMLStreamWriter, Item) - Static method in class org.intermine.xml.full.FullRenderer
Render the given Item as XML using an XMLStreamWriter
reorder(String, String) - Method in class org.intermine.dwr.AjaxServices
AJAX request - reorder view.
reorderConstraints(String, String) - Method in class org.intermine.dwr.AjaxServices
AJAX request - reorder the constraints.
REPLACE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
Whether to overwrite existing lists of the same name
replaceClob(Clob, String) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Replaces the contents of the given Clob with the given String.
replaceClob(Clob, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Replaces the contents of the given Clob with the given String.
replaceClob(Clob, String) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Replaces the contents of the given Clob with the given String.
replaceClobWithConnection(Connection, Clob, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Replaces the contents of the given Clob with the given String.
replaceConstraint(PathConstraint, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Replaces a constraint in the query with a different, carrying over the constraint code, and preserving the constraint logic.
replaceConstraint(PathConstraint, PathConstraint) - Method in class org.intermine.template.TemplateQuery
Replaces a constraint in the query with a different, carrying over the constraint code, and preserving the constraint logic.
replaceSpecialChars(String) - Static method in class org.intermine.api.util.NameUtil
Takes a string and replaces special characters with the text value, e.g.
REPORT_OBJECT_CACHE - Static variable in class org.intermine.web.logic.Constants
The session attribute that holds the ReportObjectCache object for the session.
REPORT_TEMPLATE - Static variable in class org.intermine.api.config.Constants
checks for object in other mine
ReportAspectController - Class in org.intermine.web.struts
Controller for the reportAspect tile.
ReportAspectController() - Constructor for class org.intermine.web.struts.ReportAspectController
 
ReportController - Class in org.intermine.web.struts
New objectDetails.
ReportController() - Constructor for class org.intermine.web.struts.ReportController
 
ReportDisplayer - Class in org.intermine.web.displayer
Parent class for report displayers that appear on report pages.
ReportDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.web.displayer.ReportDisplayer
Construct with config information read from webconfig-model.xml and the API.
ReportDisplayerConfig - Class in org.intermine.web.logic.config
Bean to hold configuration for report displayers.
ReportDisplayerConfig() - Constructor for class org.intermine.web.logic.config.ReportDisplayerConfig
 
ReportDisplayerController - Class in org.intermine.web.struts
Execute a ReportDisplayer placed on the context.
ReportDisplayerController() - Constructor for class org.intermine.web.struts.ReportDisplayerController
 
reportDone(PrefetchManager.Request) - Static method in class org.intermine.objectstore.query.PrefetchManager
Allows a system to report that it has finished servicing a particular request.
ReportInList - Class in org.intermine.web.logic.results
Wrapper, mainly to provide size
ReportInList(Collection<InterMineBag>) - Constructor for class org.intermine.web.logic.results.ReportInList
Setup
ReportInListController - Class in org.intermine.web.struts
 
ReportInListController() - Constructor for class org.intermine.web.struts.ReportInListController
 
ReportObject - Class in org.intermine.web.logic.results
Object to be displayed on report.do
ReportObject(InterMineObject, WebConfig, InterMineAPI, Properties) - Constructor for class org.intermine.web.logic.results.ReportObject
Setup internal ReportObject
ReportObject.TitleValue - Class in org.intermine.web.logic.results
Holder for formatted and unformatted versions of a title part.
ReportObjectFactory - Class in org.intermine.web.logic.results
A factory for ReportObjects.
ReportObjectFactory(InterMineAPI, WebConfig, Properties) - Constructor for class org.intermine.web.logic.results.ReportObjectFactory
Create a new ReportObjectCache for the given session.
ReportObjectField - Class in org.intermine.web.logic.results
Object field, used in header the summary of ReportObject
ReportObjectField(String, String, Object, String, boolean, boolean) - Constructor for class org.intermine.web.logic.results.ReportObjectField
Constructor
ReportObjectField(String, String, Object, String, boolean, boolean, String) - Constructor for class org.intermine.web.logic.results.ReportObjectField
Constructor
ReportTemplateController - Class in org.intermine.web.struts
Controller for an inline table created by running a template on a report page.
ReportTemplateController() - Constructor for class org.intermine.web.struts.ReportTemplateController
 
request - Variable in class org.intermine.webservice.server.lists.ListInput
 
request - Variable in class org.intermine.webservice.server.query.QueryRequestParser
 
request - Variable in class org.intermine.webservice.server.WebService
The servlet request.
requestIsOfSuitableType() - Method in class org.intermine.webservice.server.lists.ListUploadService
Determine if we should service this request.
RequestPasswordAction - Class in org.intermine.web.struts
Action to handle button presses RequestPasswordForm
RequestPasswordAction() - Constructor for class org.intermine.web.struts.RequestPasswordAction
 
RequestPasswordForm - Class in org.intermine.web.struts
Form used to request a password
RequestPasswordForm() - Constructor for class org.intermine.web.struts.RequestPasswordForm
 
RequestPswResetService - Class in org.intermine.webservice.server.user
This service sends a password change email to the user email address
RequestPswResetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.RequestPswResetService
Constructor
RequestPswResetServlet - Class in org.intermine.webservice.server.user
Runs the RequestPswReset service
RequestPswResetServlet() - Constructor for class org.intermine.webservice.server.user.RequestPswResetServlet
 
RequestSubClassFilter - Class in org.intermine.webservice.server.filter
Filter to wrap all web service requests in a custom delegating wrapper that prevents sessions being created.
RequestSubClassFilter() - Constructor for class org.intermine.webservice.server.filter.RequestSubClassFilter
 
requestURL(String, ContentType) - Method in class org.intermine.api.mines.HttpRequester
 
requestURL(String, ContentType) - Method in interface org.intermine.api.mines.MineRequester
Request information as encoded in a string.
RequestUtil - Class in org.intermine.web.logic
Util methods for HttpServletRequest.
RESERVED_KEYS - Static variable in class org.intermine.webservice.server.output.JSONFormatter
keys which you aren't allowed to set.
reset() - Static method in class org.intermine.api.query.MainHelper.RangeConfig
reset
reset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Resets the IntegrationWriter, clearing the id map and the hints
reset() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Resets the IntegrationWriter, clearing the id map and the hints
reset() - Method in class org.intermine.web.struts.ImportQueriesForm
Reset the form.
reset() - Method in class org.intermine.web.struts.ImportTagsForm
Reset the form.
reset() - Method in class org.intermine.web.struts.ImportXMLForm
Reset the form.
reset() - Method in class org.intermine.web.struts.TemplateForm
Reset the form
reset() - Method in class org.intermine.web.struts.TemplatesImportForm
Reset the form.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.BuildBagForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangePasswordForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangeTableSizeForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
Reset form bean.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.CreateAccountForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.EditPropertiesForm
 
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.FindInListForm
Reset form bean.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportTagsForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportXMLForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.InvitationForm
 
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.LoginForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyBagForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyQueryForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifySuperUserForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyTemplateForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.PasswordResetForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryForm
 
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.RequestPasswordForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveBagForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveQueryForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TableExportForm
Reset the form to the initial state
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateForm
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateSettingsForm
Reset the form bean taking initial state from current TemplateBuildState session attribute.
reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.WidgetForm
ResolutionJob - Class in org.intermine.api.idresolution
 
ResolutionJob(UUID, BagQueryRunner, JobInput) - Constructor for class org.intermine.api.idresolution.ResolutionJob
 
resolveCollectionPath(Path, Object) - Static method in class org.intermine.api.util.PathUtil
Return the object at the end of a given path, starting from the given object.
resolveInvitation(SharingInvite, Profile, boolean) - Method in class org.intermine.api.bag.SharedBagManager
Either reject or accept an invitation to share a list.
resolvePath(Path, Object) - Static method in class org.intermine.api.util.PathUtil
Return the object at the end of a given path, starting from the given object.
resolveValue(FastPathObject, String) - Static method in class org.intermine.webservice.server.jbrowse.Queries
 
ResourceFinder - Class in org.intermine.web.struts
A class for finding resources in the WEB-INF directory at run-time based on patterns.
ResourceFinder(ServletContext) - Constructor for class org.intermine.web.struts.ResourceFinder
Constructor.
ResourceNotFoundException - Exception in org.intermine.webservice.server.exceptions
The ResourceNotFoundException is thrown by a service provider when an attempt is made to perform an operation upon a resource that cannot be found.
ResourceNotFoundException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException
 
ResourceNotFoundException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ResourceNotFoundException
 
ResourceOpener - Interface in org.intermine.web.logic
The type of objects that can open resources by names.
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.core.WebServiceServlet
Respond to a request.
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
 
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet
 
respond(WebServiceServlet.Method, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.user.PermaTokensServlet
 
response - Variable in class org.intermine.webservice.server.WebService
The servlet response.
ResponseType - Enum in org.intermine.web.struts.oauth2
 
ResponseUtil - Class in org.intermine.web.logic.export
Response util that sets content type and header for various formats and has util methods for setting headers controlling cache.
RestfulServlet - Class in org.intermine.webservice.server.core
 
RestfulServlet() - Constructor for class org.intermine.webservice.server.core.RestfulServlet
 
ResultCell - Interface in org.intermine.api.results
An interface for result cells
ResultElement - Class in org.intermine.api.results
Cell of results table containing information for the parent Object
ResultElement(Object) - Constructor for class org.intermine.api.results.ResultElement
Create a ResultElement that displays a single raw value.
ResultElement(FastPathObject, Path, boolean) - Constructor for class org.intermine.api.results.ResultElement
Constructs a new ResultCell object
ResultElementConverter - Class in org.intermine.web.logic.export
 
ResultElementConverter() - Constructor for class org.intermine.web.logic.export.ResultElementConverter
 
ResultProcessor - Class in org.intermine.webservice.server.core
Processor of Results object for easy accessing and parsing of results to list of strings.
ResultProcessor() - Constructor for class org.intermine.webservice.server.core.ResultProcessor
Constructor.
ResultRowParser - Interface in org.intermine.webservice.server.core
Interface of parser that parses row of results to list of strings.
results - Variable in class org.intermine.api.results.ExportResultsIterator
 
results - Variable in class org.intermine.objectstore.query.ClobAccess
 
results - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
results(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadTemplateAction
Load a template from template name passed as parameter.
Results - Class in org.intermine.objectstore.query
Results representation as a List of ResultRows.
Results() - Constructor for class org.intermine.objectstore.query.Results
No argument constructor for testing purposes
Results(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.Results
Constructor for a Results object.
Results(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.Results
Constructor for a Results object, given a ResultsBatches object.
RESULTS_TABLE_SIZE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store the size of table with results.
ResultsAction - Class in org.intermine.web.struts
ResultsAction is called before results table is rendered.
ResultsAction() - Constructor for class org.intermine.web.struts.ResultsAction
 
resultsAsList - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
resultsBatches - Variable in class org.intermine.objectstore.query.Results
 
ResultsBatches - Class in org.intermine.objectstore.query
Class holding the data batches for the Results object.
ResultsBatches(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.ResultsBatches
Construct a new ResultsBatches object.
resultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
ResultsConverter - Class in org.intermine.objectstore.intermine
Provides a method to convert from SQL ResultSet data to InterMine object-based data.
ResultsFlatOuterJoinsImpl - Class in org.intermine.api.results.flatouterjoins
Provides an implementation of List that encapsulates another List (like a Results object), and translates row into flat MultiRow format in a way suitable for displaying in the webapp.
ResultsFlatOuterJoinsImpl(List<ResultsRow>, Query) - Constructor for class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
Constructor for this object.
ResultsInfo - Class in org.intermine.objectstore.query
Represents a result from the estimate() method of an ObjectStore.
ResultsInfo() - Constructor for class org.intermine.objectstore.query.ResultsInfo
No-arg constructor to allow serialization
ResultsInfo(long, long, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo
Constructs an instance of ResultsInfo with all new parameters, without min and max.
ResultsInfo(long, long, int, int, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo
Constructs an instance of ResultsInfo with all new parameters.
ResultsInfo(ResultsInfo, int, int) - Constructor for class org.intermine.objectstore.query.ResultsInfo
Constructs an instance of ResultsInfo from another ResultsInfo and a new min and max.
ResultsRow<E> - Class in org.intermine.objectstore.query
 
ResultsRow() - Constructor for class org.intermine.objectstore.query.ResultsRow
 
ResultsRow(Collection<? extends E>) - Constructor for class org.intermine.objectstore.query.ResultsRow
 
retainAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
retrieve(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Retrieve the value for a given key from the metadata table of the database
retrieveBag(String) - Method in class org.intermine.webservice.server.widget.WidgetService
Get the bag in question.
retrieveBLOBInputStream(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Retrieve the BLOB value for a given key from the metadata table of the database
retrieveExplainString(Statement) - Method in class org.intermine.sql.query.PostgresExplainResult
Retrieve EXPLAIN String from post-7.3 databases
RetrieveMetadataTask - Class in org.intermine.task
Retrieve the model metadata from a database
RetrieveMetadataTask() - Constructor for class org.intermine.task.RetrieveMetadataTask
 
retrieveToken(UUID) - Method in class org.intermine.webservice.server.user.DeletionTokens
Retrieve a token by its identifier.
returnNewTableRow() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Create a table row object
returnNewTableRow() - Method in class org.intermine.web.logic.results.InlineResultsTable
Create a table row object, overriden on BagUploadConfirm where we go custom
returnToString - Variable in class org.intermine.web.struts.LoginForm
 
reverseCapitalisation(String) - Static method in class org.intermine.metadata.StringUtil
Reverses the capitalisation of the first character of the given String.
reverseRefDesc - Variable in class org.intermine.metadata.ReferenceDescriptor
 
reverseRefName - Variable in class org.intermine.metadata.ReferenceDescriptor
 
right - Variable in class org.intermine.objectstore.query.OverlapConstraint
 
right - Variable in class org.intermine.sql.query.Constraint
 
right - Variable in class org.intermine.sql.query.InListConstraint
 
right - Variable in class org.intermine.sql.query.SubQueryConstraint
 
Right(B) - Constructor for class org.intermine.webservice.server.core.Either.Right
Construct a right.
RIGHT_BRACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
RIGHT_FALSE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the right is always false.
RIGHT_TRUE - Static variable in class org.intermine.sql.query.AbstractConstraint
Describes two constraints, where the right is always true.
RO - org.intermine.api.profile.ProfileManager.ApiPermission.Level
 
ROUND - Static variable in class org.intermine.objectstore.query.QueryFunction
Round to a given number of decimal places.
Row - Class in org.intermine.sql.writebatch
Stores two ints.
Row(int, int) - Constructor for class org.intermine.sql.writebatch.Row
Constructor.
ROW_SEPARATOR - Static variable in class org.intermine.metadata.TextTable
An object representing a horizontal line separating two rows - treated as a row.
RowFormatter - Interface in org.intermine.web.logic.export
Interface denoting that object is able format list of objects to string.
RowFormatterImpl - Class in org.intermine.web.logic.export
Implements RowFormatter interface.
RowFormatterImpl(String, boolean) - Constructor for class org.intermine.web.logic.export.RowFormatterImpl
Constructor.
rowObjects - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
rows - Variable in class org.intermine.objectstore.query.ResultsInfo
 
rows - Variable in class org.intermine.sql.query.ExplainResult
 
ROWS - org.intermine.webservice.server.Format
JSON Row format constant
run() - Method in interface org.intermine.api.idresolution.Job
run job
run() - Method in class org.intermine.api.idresolution.ResolutionJob
 
run() - Method in class org.intermine.api.idresolution.UpgradeJob
 
run() - Method in class org.intermine.api.searchengine.solr.SolrObjectHandler
fetch objects from database, create documents and add them to the queue
run() - Method in class org.intermine.api.tracker.TrackerLogger
run() - Method in class org.intermine.util.ShutdownHook
 
run() - Method in class org.intermine.web.context.MailDaemon
 
run() - Method in class org.intermine.web.logic.profile.UpgradeBagList
 
run() - Method in class org.intermine.webservice.server.idresolution.JobJanitor
 
run(PreparedStatement) - Method in class org.intermine.objectstore.intermine.SQLOperation
The code that the operation represents.
run(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
Excecute a query.
run(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
runAllTests(Database, LineNumberReader) - Method in class org.intermine.task.AcceptanceTestTask
Run all the tests and return a List of AcceptanceTestResult objects.
runBagUpgrade(UpgradeBagList, InterMineAPI, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
Kick off a bag upgrade for current user.
RunIqlQueryTask - Class in org.intermine.task
Ant task to read an IQL query from a -Pquery="QUERY" parameter and execute it in the database.
RunIqlQueryTask() - Constructor for class org.intermine.task.RunIqlQueryTask
 
runLuceneSearch(String, SearchTarget, SearchRepository) - Static method in class org.intermine.api.search.SearchResults
Search a Lucene index and return a search result.
RUNNING - org.intermine.api.idresolution.Job.JobStatus
job is currently running
RUNNING_QUERIES - Static variable in class org.intermine.web.logic.Constants
Session attribute.
runPathQuery(PathQuery, int, int) - Method in class org.intermine.webservice.server.query.result.QueryResultService
Runs path query and returns to output obtained results.
runPathQuery(PathQuery, int, int) - Method in class org.intermine.webservice.server.query.result.TableRowService
 
runQuery(HttpSession, MessageResources, String, SessionMethods.Action, SessionMethods.CompletionCallBack) - Static method in class org.intermine.web.logic.session.SessionMethods
Executes an action and call a callback when it completes successfully.
RunQueryAction - Class in org.intermine.web.struts
Run a query as passed in directly as XML.
RunQueryAction() - Constructor for class org.intermine.web.struts.RunQueryAction
 
runTemplate(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Show in table for inline template queries.
RW - org.intermine.api.profile.ProfileManager.ApiPermission.Level
 

S

safe_abstract_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
safe_abstract_constraint() - Method in class org.intermine.sql.query.SqlParser
 
safe_abstract_value() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
safe_abstract_value() - Method in class org.intermine.sql.query.SqlParser
 
safe_function() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
safe_function() - Method in class org.intermine.sql.query.SqlParser
 
safe_function(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
SAFE_FUNCTION - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SAFE_FUNCTION - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
SAFENESS_ANTISAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
Safeness value indicating a situation safe for ContainsConstraint DOES NOT CONTAIN
SAFENESS_SAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
Safeness value indicating a situation safe for ContainsConstraint CONTAINS
SAFENESS_UNSAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
Safeness value indicating a situation unsafe for ContainsConstraint
save() - Method in class org.intermine.api.bag.SharingInvite
 
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
Save a query from the history.
saveBag(String, InterMineBag) - Method in class org.intermine.api.profile.Profile
Stores a new bag in the profile.
saveBag(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction
Save the selected objects to a bag on the session
saveBag(InterMineBag) - Method in class org.intermine.api.profile.Profile
Stores a new bag in the profile.
SaveBagAction - Class in org.intermine.web.struts
Saves selected items in a new bag or combines with existing bag.
SaveBagAction() - Constructor for class org.intermine.web.struts.SaveBagAction
 
saveBagDescription(String, String) - Method in class org.intermine.dwr.AjaxServices
For a given bag, set its description
SaveBagForm - Class in org.intermine.web.struts
Form bean for the results table and bag creation form.
SaveBagForm() - Constructor for class org.intermine.web.struts.SaveBagForm
Constructor
saveClassKeys(String, File) - Static method in class org.intermine.modelproduction.MetadataManager
Save the class keys, in serialized form, to the specified directory
SAVED_BAG_STATUS - Static variable in class org.intermine.web.logic.Constants
key for the map saved in the session containing the status of saved bags
SavedBag - Class in org.intermine.api.userprofile
 
SavedBag() - Constructor for class org.intermine.api.userprofile.SavedBag
 
savedBagId - Variable in class org.intermine.api.profile.StorableBag
 
savedBags - Variable in class org.intermine.api.profile.Profile
 
savedBags - Variable in class org.intermine.api.userprofile.UserProfile
 
savedCounts - Variable in class org.intermine.dataloader.HintingFetcher
 
savedInvalidBags - Variable in class org.intermine.api.profile.Profile
 
savedQueries - Variable in class org.intermine.api.profile.Profile
 
SavedQuery - Class in org.intermine.api.profile
Container for a saved query.
SavedQuery - Class in org.intermine.api.userprofile
 
SavedQuery() - Constructor for class org.intermine.api.userprofile.SavedQuery
 
SavedQuery(String, Date, PathQuery) - Constructor for class org.intermine.api.profile.SavedQuery
Construct a new instance of SavedQuery.
SavedQueryBinding - Class in org.intermine.api.xml
Convert SavedQuerys to and from XML
SavedQueryHandler - Class in org.intermine.api.xml
Extension of PathQueryHandler to handle parsing SavedQuerys
SavedQueryHandler(Map<String, SavedQuery>, Map, int) - Constructor for class org.intermine.api.xml.SavedQueryHandler
Constructor
SavedQueryRetrievalService - Class in org.intermine.webservice.server.query
 
SavedQueryRetrievalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.SavedQueryRetrievalService
 
savedQuerys - Variable in class org.intermine.api.userprofile.UserProfile
 
savedTemplateQuery - Variable in class org.intermine.api.template.ApiTemplate
SavedTemplateQuery object in the UserProfile database, so we can update summaries.
SavedTemplateQuery - Class in org.intermine.api.userprofile
 
SavedTemplateQuery() - Constructor for class org.intermine.api.userprofile.SavedTemplateQuery
 
savedTemplateQuerys - Variable in class org.intermine.api.userprofile.UserProfile
 
savedTemplates - Variable in class org.intermine.api.profile.Profile
 
savedTimes - Variable in class org.intermine.dataloader.HintingFetcher
 
SaveFromIdsToBagAction - Class in org.intermine.web.struts
Saves selected items with InterMine ids and a Type in a new bag or combines with existing bag.
SaveFromIdsToBagAction() - Constructor for class org.intermine.web.struts.SaveFromIdsToBagAction
 
saveHistory(SavedQuery) - Method in class org.intermine.api.profile.Profile
Save a query to the query history.
saveKeyDefinitions(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager
Save the key definitions, in serialized form, to the specified directory
saveModel(Model, File) - Static method in class org.intermine.modelproduction.MetadataManager
Save a model, in serialized form, to the specified directory
saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Set InterMine Object id for the table row
saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
Used on BagUploadConfirm
savePopulation - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
saveProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
Synchronise a user's Profile with the backing store
saveProperties(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager
Save the objectstore summary, in serialized form, to the specified directory
saveQueries(Map<? extends String, ? extends PathQuery>) - Method in class org.intermine.api.profile.Profile
Save the map of queries as given to the user's profile, avoiding all possible name collisions.
saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUpdateService
 
saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUploadService
Save the given queries.
saveQuery(String, SavedQuery) - Method in class org.intermine.api.profile.Profile
Save or update a query.
saveQuery(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Save a clone of a query to the user's Profile.
saveQuery(HttpSession, String, PathQuery, Date) - Static method in class org.intermine.web.logic.session.SessionMethods
Save a clone of a query to the user's Profile.
SaveQueryAction - Class in org.intermine.web.struts
Implementation of Action that saves a Query from a session.
SaveQueryAction() - Constructor for class org.intermine.web.struts.SaveQueryAction
 
SaveQueryForm - Class in org.intermine.web.struts
Form bean to represent the inputs to the query saving action
SaveQueryForm() - Constructor for class org.intermine.web.struts.SaveQueryForm
 
saveQueryToHistory(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Save a clone of a query to the user's Profile history.
saveTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile
Save a template
saveToggleState(String, boolean) - Static method in class org.intermine.dwr.AjaxServices
Saves information, that some element was toggled - displayed or hidden.
saveWithBagValues(Integer, Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag
Save the bag into the userprofile database, along with information about what kinds of values this bag contains.
savingDisabled - Variable in class org.intermine.api.profile.Profile
 
SAXParser - Class in org.intermine.metadata
Basic SAX Parser
SAXParser - Class in org.intermine.util
Basic SAX Parser
sb - Variable in class org.intermine.sql.logging.DatabaseWriter
 
SC_BAD_REQUEST - Static variable in class org.intermine.webservice.server.output.Output
Bad request http status code.
SC_FORBIDDEN - Static variable in class org.intermine.webservice.server.output.Output
Forbidden http status code.
SC_INTERNAL_SERVER_ERROR - Static variable in class org.intermine.webservice.server.output.Output
Internal server http status code.
SC_NO_CONTENT - Static variable in class org.intermine.webservice.server.output.Output
No content http status code.
SC_NOT_FOUND - Static variable in class org.intermine.webservice.server.output.Output
Resource not found http status code.
SC_OK - Static variable in class org.intermine.webservice.server.output.Output
OK http status code.
SC_UNAUTHORIZED - Static variable in class org.intermine.webservice.server.output.Output
Request is legal, but requires authentication, which was either not provided, or failed.
schema - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
 
schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask
 
schema - Variable in class org.intermine.sql.Database
 
SchemaListService - Class in org.intermine.webservice.server
Serve up the list of schemata that we have.
SchemaListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SchemaListService
Constructor
SchemaServlet - Class in org.intermine.webservice.server
Returns a requested schema.
SchemaServlet() - Constructor for class org.intermine.webservice.server.SchemaServlet
 
Scope - Class in org.intermine.api.search
Scope constants.
SCOPES - Static variable in class org.intermine.api.search.Scope
The possible scopes.
score(int) - Method in class org.intermine.sql.precompute.OptimiserCacheLine
Scores this cache line according to how far away the required limit is from the limit used to create the line.
search(String, Collection<String>, String, boolean, boolean, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
Given an input list of string identifiers search for corresponding objects.
SEARCH_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the search index.
SEARCH_INDEX_DIRECTORY - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key to use to store the search Directory.
SEARCH_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks searches
SEARCH_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks searches
SearchFilterEngine - Class in org.intermine.api.search
Class filtering web searchables according to the associated tags.
SearchFilterEngine() - Constructor for class org.intermine.api.search.SearchFilterEngine
 
searchForBag(String, List<String>, String, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
Given an input list of string identifiers search for corresponding objects.
searchForBag(String, List<String>, String, boolean, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
Given an input list of string identifiers search for corresponding objects.
searchItems - Variable in class org.intermine.api.search.SearchRepository
 
SearchRepository - Class in org.intermine.api.search
The base class for search repositories.
SearchRepository(Profile) - Constructor for class org.intermine.api.search.SearchRepository
Constructor.
SearchResult - Class in org.intermine.api.search
A single item in a set or returned results formed by searching the web-searchable indices with Lucene.
SearchResults - Class in org.intermine.api.search
Representations of Lucene search results over the web-searchable data of the user-profile and the mechanisms for generating a set of such results.
SearchTarget - Class in org.intermine.api.search
An object for encapsulating the scope and type of object requested from a Lucene search of the user profile web searchable items.
SearchTarget(String, String) - Constructor for class org.intermine.api.search.SearchTarget
Constructor.
SEARCHTRACK - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding
label for XML
SearchTrackBinding - Class in org.intermine.api.tracker.xml
 
SEARCHTRACKS - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding
label for XML
SearchUtils - Class in org.intermine.web.search
The bits of the search infrastructure that belong in the web-package because they have view dependent logic.
seenBrokenOneToMany - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
Segment - Class in org.intermine.webservice.server.jbrowse
Represents an interbase segment.
select - Variable in class org.intermine.sql.query.Query
 
select(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
select_command() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
select_command() - Method in class org.intermine.sql.query.SqlParser
 
select_list() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
select_list() - Method in class org.intermine.sql.query.SqlParser
 
select_list(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
SELECT_LIST - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SELECT_LIST - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
select_value() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
select_value() - Method in class org.intermine.sql.query.SqlParser
 
select_value(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
SELECT_VALUE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SELECT_VALUE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
selectable - Variable in class org.intermine.api.results.Column
 
selectAll(int, String) - Static method in class org.intermine.dwr.AjaxServices
Select all the elements in a PagedTable
selected - Variable in class org.intermine.web.struts.ModifyTemplateForm
 
selectedBags - Variable in class org.intermine.web.struts.ModifyBagForm
 
selectedElements - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
 
selectedIdsIterator() - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Return an Iterator over the selected Ids
selectedObjects - Variable in class org.intermine.web.struts.SaveBagForm
 
selectedQueries - Variable in class org.intermine.web.struts.ModifyQueryForm
 
selectEncoding(ServletRequest) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
Select an appropriate character encoding to be used, based on the characteristics of the current request and/or filter initialization parameters.
selectId(Integer, int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Add an object id and its field value that has been selected in the table.
selectId(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
Add an ID to the PagedTable selection
SelectValue - Class in org.intermine.sql.query
Represents an AbstractValue with an alias, suitable for use in the SELECT portion of an SQL query.
SelectValue(AbstractValue, String) - Constructor for class org.intermine.sql.query.SelectValue
Construct a new SelectValue.
SemanticMarkupFormatter - Class in org.intermine.web.fair
Class providing schema/bioschemas markups
SEMI - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SEMI - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
sendFareWell(String, String) - Method in class org.intermine.util.Emailer
Bid a user farewell from the system.
SensibleByteArrayOutputStream - Class in org.intermine.util
A subclass of ByteArrayOutputStream that behaves a little more sensibly when handling large writes followed by small writes.
SensibleByteArrayOutputStream() - Constructor for class org.intermine.util.SensibleByteArrayOutputStream
 
SensibleByteArrayOutputStream(int) - Constructor for class org.intermine.util.SensibleByteArrayOutputStream
 
SEPARATOR - Static variable in class org.intermine.api.tag.TagNames
Tag separator.
sequence - Variable in class org.intermine.objectstore.query.ResultsBatches
 
SEQUENCE_IGNORE - Static variable in interface org.intermine.objectstore.ObjectStore
Object representing no fail-fast concurrency checks required.
SEQUENCE_MULTIPLE - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
sequenceBase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
sequenceKeys - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
sequenceNumber - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
 
sequenceOffset - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
SequenceService - Class in org.intermine.webservice.server.clob
A service to provide access to substrings of ClobAccess data.
SequenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.clob.SequenceService
 
sequential - Variable in class org.intermine.objectstore.query.Results
 
SERIAL_NUMBER - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the serial number identifying the production db
serialize(Properties) - Static method in class org.intermine.util.PropertiesUtil
Serialize properties to a string suitable for a subsequent load()
serializedSortOrderToMap(String) - Static method in class org.intermine.metadata.StringUtil
Make a Map from the serialized String returned by jQuery.sortable("serialize").
serveToken(DeletionToken) - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
Serve a token to the outside world.
service(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.WebService
Starting method of web service.
SERVICE_FAILED_MSG - Static variable in class org.intermine.webservice.server.WebServiceConstants
Error message returned in case of unexpected service failure.
serviced - Static variable in class org.intermine.objectstore.query.PrefetchManager
Set of requests currently being serviced.
ServiceException - Exception in org.intermine.webservice.server.exceptions
ServiceException is a base class for all service exceptions.
ServiceException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(String, Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceException(Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
 
ServiceForbiddenException - Exception in org.intermine.webservice.server.exceptions
The ServiceForbiddenException is thrown by a service when an attempt is made to service that is disabled.
ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
 
ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
 
ServiceListingHandler - Class in org.intermine.webservice.server
 
ServiceListingHandler() - Constructor for class org.intermine.webservice.server.ServiceListingHandler
 
ServicesListingsServlet - Class in org.intermine.webservice.server
Provide a list of all the services available at this mine.
ServicesListingsServlet() - Constructor for class org.intermine.webservice.server.ServicesListingsServlet
 
serviceThreads - Static variable in class org.intermine.objectstore.query.PrefetchManager
 
SessionActivationListener - Class in org.intermine.web.logic.session
Added to each session to monitor activation events.
SessionActivationListener() - Constructor for class org.intermine.web.logic.session.SessionActivationListener
 
sessionCreated(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener
sessionDestroyed(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener
sessionDidActivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener
Called after a session is unserialised.
sessionIdentifier - Variable in class org.intermine.api.tracker.track.TrackAbstract
 
SessionlessRequest - Class in org.intermine.webservice.server.core
 
SessionlessRequest(HttpServletRequest) - Constructor for class org.intermine.webservice.server.core.SessionlessRequest
Construct a request by wrapping the given request.
SessionListener - Class in org.intermine.web.logic.session
Perform InterMine-specific actions when a Session is constructed or destroyed
SessionListener() - Constructor for class org.intermine.web.logic.session.SessionListener
 
SessionMethods - Class in org.intermine.web.logic.session
Business logic that interacts with session data.
SessionService - Class in org.intermine.webservice.server
Open a new 24-hour session.
SessionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SessionService
 
sessionWillPassivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener
Called just before serialising to disk.
set(int, boolean) - Method in class org.intermine.util.IntPresentSet
Adds the given int to the set.
setAccepted(Boolean) - Method in class org.intermine.api.bag.SharingInvite
 
setAction(String) - Method in class org.intermine.web.struts.WidgetForm
 
setActionType(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
 
setAdditionalProperty(String, Object) - Method in class org.intermine.web.registry.model.Instance
 
setAdditionalProperty(String, Object) - Method in class org.intermine.web.registry.model.RegistryResponse
 
setAdditionsFile(String) - Method in class org.intermine.task.ModelMergerTask
The file name containing model additions.
setAdditionsFiles(List<String>) - Method in class org.intermine.task.ModelMergerTask
The file names containing model additions.
setAlias(String) - Method in class org.intermine.sql.query.AbstractTable
Sets the alias for this AbstractTable object.
setAlias(String) - Method in class org.intermine.task.CreateIndexesTask
Set the ObjectStore alias.
setAlias(String) - Method in class org.intermine.task.DropPrecomputedTablesTask
Set the ObjectStore alias
setAlias(String) - Method in class org.intermine.task.RunIqlQueryTask
Set the ObjectStore alias.
setAlias(String) - Method in class org.intermine.task.SummariseObjectStoreTask
Set the ObjectStore alias
setAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the ObjectStore alias
setAllFieldDescriptors() - Method in class org.intermine.metadata.ClassDescriptor
Sets up the object a little.
setAllSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Select a whole column.
setAllSources(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the list of data sources present in the project.xml, for the purposes of verifying the priorities properties file.
setAPI(InterMineAPI) - Method in class org.intermine.api.template.ApiTemplate
Only used on export so we can get the tags related to this template.
setApiKey(String) - Method in class org.intermine.api.profile.Profile
Set the API token for this user, and save it in the backing DB.
setApiKey(String) - Method in class org.intermine.api.userprofile.UserProfile
 
setApiVersion(String) - Method in class org.intermine.web.registry.model.Instance
 
setAppendConfig(Boolean) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Set whether to append config from parent
setAspectDisplayers(Map<String, List<Displayer>>) - Method in class org.intermine.web.logic.config.Type
 
setAspects(String) - Method in class org.intermine.web.logic.config.Displayer
Set the aspects of this displayer
setAspects(ServletContext, Map<String, Aspect>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the Map of aspects.
setAttribute(String, Object) - Static method in class org.intermine.web.context.InterMineContext
Set an attribute of the context.
setAttribute(String, String) - Method in class org.intermine.xml.full.Item
Add an attribute to this item.
setAttributeIfNotNull(String, String) - Method in class org.intermine.xml.full.Item
Add an attribute to this item only if value is not empty or NULL
setAttributeIndexes(boolean) - Method in class org.intermine.task.CreateIndexesTask
Set the attributeIndexes flag.
setAttributeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of attributeOp
setAttributeOps(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set an attribute op
setAttributeOps(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Set the attribute ops
setAttributeOptions(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of attributeOptions
setAttributes(Set<Attribute>) - Method in class org.intermine.model.fulldata.Item
 
setAttributeToEmptyString(String) - Method in class org.intermine.xml.full.Item
Add an attribute to this item and set it to the empty string.
setAttributeValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of attributeValue
setAttributeValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm
Set an attribute value
setAttributeValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Set the attribute values
setAutoCompleter(ServletContext, AutoCompleter) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the AutoCompleter into the ServletContext.
setBag(String, Object) - Method in class org.intermine.web.struts.TemplateForm
Set the bag name.
setBag(InterMineBag) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setBagName(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
name of bag that this widget is using.
setBagName(String) - Method in class org.intermine.web.struts.FindInListForm
 
setBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Set the value of bagName
setBagName(String) - Method in class org.intermine.web.struts.WidgetForm
name of bag that this widget is using.
setBagOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of bagOp
setBagOp(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set bag operation.
setBagSelected(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set if the bag is selected, used by the method isBagSelected that returns true, even if the constraint is an attribute constraint
setBagTableNames(Map<Object, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
setBagType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setBagType(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the bag type
setBagType(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setBagType(String) - Method in class org.intermine.web.struts.WidgetForm
 
setBagValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of bagValue
setBaseLink(String) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setBasicInstanceInfo(ServletContext, Instance) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the instance to use.
setBatchSize(int) - Method in class org.intermine.api.query.PathQueryExecutor
Sets batch size.
setBatchSize(int) - Method in interface org.intermine.objectstore.proxy.LazyCollection
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchSize(int) - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchSize(int) - Method in class org.intermine.objectstore.query.Results
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches
Sets the number of rows requested from the ObjectStore whenever an execute call is made
setBatchWriter(BatchWriter) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Allows the changing of the BatchWriter that this ObjectStoreWriter uses.
setBatchWriter(BatchWriter) - Method in class org.intermine.sql.writebatch.Batch
Changes the BatchWriter for a new one.
setBuildDir(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setCaseSensitive(boolean) - Method in class org.intermine.web.struts.BuildBagForm
 
setCategories(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the aspect categories into the servlet context.
setCategoryPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
SetCharacterEncodingFilter - Class in org.intermine.web.filters
Example filter that sets the character encoding to be used in parsing the incoming request, either unconditionally or only if the client did not specify a character encoding.
SetCharacterEncodingFilter() - Constructor for class org.intermine.web.filters.SetCharacterEncodingFilter
 
setClassConfig(Type) - Method in class org.intermine.web.logic.config.FieldConfig
 
setClassDescriptor(String) - Method in class org.intermine.xml.full.Item
Set the classDescriptor attribute to be the ClassDescriptor for the given className in the Model set by setModel().
setClassDescriptor(ClassDescriptor) - Method in class org.intermine.metadata.FieldDescriptor
Set the parent ClassDescriptor - should be called when this is added to a ClassDescriptor.
setClasses(Map<String, Map<String, Object>>) - Method in class org.intermine.metadata.Model.ModelAST
 
setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.bag.operations.BagOperation
 
setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setClassLoader(ClassLoader) - Method in class org.intermine.web.task.CreateSearchIndexTask
Set the class loader
setClassName(String) - Method in class org.intermine.model.fulldata.Item
 
setClassName(String) - Method in class org.intermine.task.AnalyseDbTask
Set an optional class name, must also set model name
setClassName(String) - Method in class org.intermine.task.StaticMethodTask
Set class name on which to call static method.
setClassName(String) - Method in class org.intermine.web.logic.config.TableExportConfig
Set the className of this TableExportConfig
setClassName(String) - Method in class org.intermine.web.logic.config.Type
Set the unqualified class name for this Type (from fully-qualified)
setClassName(String) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
 
setClassName(String) - Method in class org.intermine.web.struts.QueryClassSelectForm
Set the class name
setClassName(String) - Method in class org.intermine.web.uri.InterMineLUI
Set the className
setClassName(String) - Method in class org.intermine.xml.full.Item
Set the class of this item.
setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
Set a class name on table row
setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
Set a class name on table row, used for type safety as overriden on BagUploadConfirm
setClsName(String) - Method in class org.intermine.task.DBConverterTask
Set the source specific subclass of FileConverter to run
setClsName(String) - Method in class org.intermine.task.DirectoryConverterTask
Set the source specific subclass of DirectoryConverter to run
setClsName(String) - Method in class org.intermine.task.FileConverterTask
Set the source specific subclass of FileConverter to run
setClsName(String) - Method in class org.intermine.task.PostProcessorTask
Set the name of the PostProcessor sub-class to load to do the postprocessing.
setCode(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setCode(String) - Method in class org.intermine.web.logic.template.ConstraintInput
 
setCollection(String, List<String>) - Method in class org.intermine.xml.full.Item
Set a collection.
setCollections(Set<ReferenceList>) - Method in class org.intermine.model.fulldata.Item
 
setColumnId(String) - Method in class org.intermine.api.results.Column
 
setColumnNames(List<String>) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Set the column names
setColumnNames(List<String>) - Method in class org.intermine.web.tags.table.TableTag
 
setColumnTitle(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setComment(String) - Method in class org.intermine.template.TemplateQuery
Set the private comment for this template.
setComment(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
Set the comment
setComplete(long) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the estimated amount of time taken to produce the entire set of results.
setComputeTotalCount(boolean) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Sets true if compute total count of all available results.
setConfigFile(File) - Method in class org.intermine.task.AcceptanceTestTask
Set the File to read configuration from
setConfigFileName(String) - Method in class org.intermine.task.SummariseObjectStoreTask
Set the name of the Properties file containing the names of the classes and fields to summarise.
setConfigurationFile(File) - Method in class org.intermine.task.TSVFileReaderTask
Set the configuration file to use.
setConnectField(String) - Method in class org.intermine.api.bag.BagQueryConfig
Set the connecting field for adding an extra constraint to bag queries.
setConstrainField(String) - Method in class org.intermine.api.bag.BagQueryConfig
Set the field to constrain when making an extra constraint.
setConstraint(Constraint) - Method in class org.intermine.objectstore.query.Query
Constrain this Query using either a single constraint or a set of constraints
setConstraint(Constraint) - Method in interface org.intermine.objectstore.query.Queryable
Sets the additional constraint.
setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Sets the additional constraint.
setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
Sets the additional constraint.
setConstraint(TemplateQuery, TemplateValue) - Static method in class org.intermine.api.template.TemplatePopulator
Set the value for a constraint in the template query with the given TemplateValue.
setConstraintDescription(PathConstraint, String) - Method in class org.intermine.template.TemplateQuery
Sets the description for a constraint.
setConstraintLogic(String) - Static method in class org.intermine.dwr.AjaxServices
Set the constraint logic on a query to be the given expression.
setConstraintLogic(String) - Method in class org.intermine.pathquery.PathQuery
Sets the current constraint logic.
setConstraintOp(ConstraintOp) - Method in class org.intermine.web.logic.template.ConstraintInput
Sets constraint operation.
setConstraints(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setConstraints(Map<String, List<ConstraintInput>>) - Method in class org.intermine.web.logic.template.TemplateResultInput
Sets constraints.
setConstraintsForView(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setContent(String) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
Set the content of the widget.
setCorrection(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setCorrectionCoefficient(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setCount(int) - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
Set the query count/size.
setCreatedAt(String) - Method in class org.intermine.web.registry.model.Instance
 
setCSVContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets comma separated values content type.
setCSVHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for comma separated values output.
setCurrentFile(File) - Method in class org.intermine.dataconversion.FileConverter
Set the current File that is being processed.
setCurrentMapFromCurrentArray() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Sets the current map to work with by getting the last one from the current array.
setCurrentMapFromCurrentArray(ResultElement) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Finds the object we should be dealing with by getting it from the current array.
setCurrentPage(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setCustomContentType(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets content type to the parameter specified
setCustomTypeHeader(HttpServletResponse, String, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for a custom content type.
setDatabase(String) - Method in class org.intermine.task.AcceptanceTestTask
Set the database alias
setDatabase(String) - Method in class org.intermine.task.GrantTask
Set the database alias
setDataDir(String) - Method in class org.intermine.task.DirectoryConverterTask
Set the dataDir.
setDate(Date) - Method in class org.intermine.api.profile.InterMineBag
Sets date when bag was created.
setDateCreated(Date) - Method in class org.intermine.api.userprofile.PermanentToken
 
setDateCreated(Date) - Method in class org.intermine.api.userprofile.SavedBag
 
setDb(Database) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
setDbAlias(String) - Method in class org.intermine.task.DBConverterTask
Set the Database to read from
setDefaultValue(String, String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
Set a parameter default.
setDeleteTracks(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm
Set the deleteTracks flag.
setDescr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setDescription(String) - Method in class org.intermine.api.profile.InterMineBag
 
setDescription(String) - Method in class org.intermine.api.template.ApiTemplate
 
setDescription(String) - Method in class org.intermine.api.userprofile.SavedBag
 
setDescription(String) - Method in class org.intermine.pathquery.PathQuery
Sets the description for this PathQuery.
setDescription(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setDescription(String) - Method in class org.intermine.web.registry.model.Instance
 
setDescription(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
Set the description
setDescription(String, String) - Method in class org.intermine.pathquery.PathQuery
Sets the description for a given path.
setDescriptor(FieldDescriptor) - Method in class org.intermine.web.logic.results.InlineList
Set FieldDescriptor so we can work with placements
setDestDir(File) - Method in class org.intermine.task.GenerateUpdateTriggersTask
Sets the destination directory for the SQL files.
setDestDir(File) - Method in class org.intermine.task.ModelOutputTask
Sets the directory that output should be written to.
setDestDir(File) - Method in class org.intermine.task.RetrieveMetadataTask
Sets the destination directory
setDestFile(File) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
Sets the file to which the data should be written.
setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the disableResultsCache configuration option.
setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the disableResultsCache configuration option.
setDisplayer(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the displayer
setDisplayFields(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setDistinct(boolean) - Method in class org.intermine.objectstore.query.Query
Set the value of the distinct property, which determines whether duplicates are permitted in the results returned by this Query
setDistinct(boolean) - Method in class org.intermine.sql.query.Query
Sets the distinct status of this query.
setDoGzip(boolean) - Method in class org.intermine.web.struts.TableExportForm
Set whether the output should be GZIPped.
setDomain(String) - Method in class org.intermine.api.beans.PartnerLink
 
setDomainLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Set the value of domainLabel
setDoNotTruncate(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
If set to true, don't truncate long fields or put in a [View all...] link in the object details page.
seteditable(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setEditable(boolean) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the editable flag (when building a template).
setEditable(PathConstraint, boolean) - Method in class org.intermine.template.TemplateQuery
Sets a constraint to be editable or not.
setEditableConstraints(List<PathConstraint>) - Method in class org.intermine.template.TemplateQuery
Sets the list of editable constraints to exactly that provided, in the given order.
setEditableInTemplate(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setEdited(boolean) - Method in class org.intermine.template.TemplateQuery
Set the query as being edited.
setEditingConstraintCode(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the code of an existing constraint that is being edited.
setEmail(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setEnrich(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setEnrichIdentifier(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setEof(HintingFetcher) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Sets the equivalent object fetcher.
setErr(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask
Set the error handler
setError(String, int) - Method in class org.intermine.webservice.server.output.Output
Sets the error message
setErrorCorrection(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setErrorCorrection(String) - Method in class org.intermine.web.struts.WidgetForm
 
setErrorOnInitialiser(ServletContext, Map<String, String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the blocking error codes into the servlet context.
setEscapeXml(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
If set to true, don't escape the field value on object details page.
setEstimatedRows(long) - Method in class org.intermine.sql.query.ExplainResult
Use this to provide the object with a "better" estimate of the number of rows in the results of this Query.
setExcludeList(String) - Method in class org.intermine.task.ConverterTask
Sets the list of classes to NOT try and convert
setExecutionTime(String) - Method in class org.intermine.web.registry.model.RegistryResponse
 
setExistingBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Sets the value of existingBagName
setExistingBagName(String) - Method in class org.intermine.web.struts.SaveBagForm
Sets the value of existingBagName
setExpiry(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setExplain(boolean) - Method in class org.intermine.sql.query.Query
Sets the explain status of this query.
setExportField(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setExporttype(String) - Method in class org.intermine.web.struts.WidgetForm
 
setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
setExternalLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setExternalLinkLabel(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
setExtraAttribute(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setExtraConstraintClassName(String) - Method in class org.intermine.api.bag.BagQueryConfig
Set the class name of extra constraint to use in BagQuery objects using this config object.
setExtraFieldValue(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the extra field value
setExtraFieldValue(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the extra field value.
setExtraFieldValue(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
 
setExtraThreads(int) - Method in class org.intermine.task.CreateIndexesTask
Set the number of extra worker threads.
setExtraValue(String) - Method in class org.intermine.web.logic.bag.WebJobInput
Only used in the portal when we have to link directly to the list upload
setExtraValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput
Sets extra value
setExtraValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of extraValue
setExtraValue(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
An extra value, such as an organism, for use in lookup constraints.
setExtraValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm
Set an extra value
setExtraValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Sets the extra values
setFavourite(String, String, boolean) - Method in class org.intermine.dwr.AjaxServices
Creates a favourite Tag for the given templateName
setFetchFields(boolean, Set<FieldDescriptor>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
Sets variables which determines which fields are prefetched.
setField(Object) - Method in class org.intermine.api.results.ResultElement
Set the field value
setFieldExporter(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the class name of the FieldExporter to use when this field is viewed.
setFieldExpr(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the JSTL expression for this field which will be evaluated in the request context when the JSP is viewed.
setFieldToAlias(FromElement, Map<String, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
 
setFieldValue(Object, String, Object) - Static method in class org.intermine.util.DynamicUtil
Sets the value of a public or protected Field of an Object given the field name.
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.PermanentToken
 
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.SavedBag
 
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.SavedQuery
 
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.Tag
 
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.TemplateSummary
 
setFieldValue(String, Object) - Method in class org.intermine.api.userprofile.UserProfile
 
setFieldValue(String, Object) - Method in interface org.intermine.model.FastPathObject
Sets the value of a field by name.
setFieldValue(String, Object) - Method in class org.intermine.model.fulldata.Attribute
 
setFieldValue(String, Object) - Method in class org.intermine.model.fulldata.Item
 
setFieldValue(String, Object) - Method in class org.intermine.model.fulldata.Reference
 
setFieldValue(String, Object) - Method in class org.intermine.model.fulldata.ReferenceList
 
setFieldValue(String, Object) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the value of a field by name.
setFile(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set a file name to load from
setFile(String) - Method in class org.intermine.task.FullXmlConverterTask
Set a file name to load from
setFileName(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the name of the file to write to.
setFileName(String) - Method in class org.intermine.web.task.ProfileReadTask
Set the name of the file to read from.
setFileName(String) - Method in class org.intermine.web.task.ProfileWriteTask
Set the name of the file to write to.
setFileName(String) - Method in class org.intermine.web.task.TemplateTrackReadTask
Set the name of the file to read from.
setFileName(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask
Set the name of the file to write to.
setFileName(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content disposition filename.
setFilter(String) - Method in class org.intermine.web.logic.widget.EnrichmentWidget
 
setFilter(String) - Method in class org.intermine.web.logic.widget.GraphWidget
 
setFilter(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setFilter(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setFilterLabel(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setFilterLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setFilters(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setFilters(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
builds, runs query.
setFormat(String) - Method in class org.intermine.web.struts.CSVExportForm
Set the format.
setFormat(Format) - Method in class org.intermine.webservice.server.WebService
For very picky services, you can just set it yourself, and say "s****w you requester".
setFormFile(FormFile) - Method in class org.intermine.web.struts.BuildBagForm
Set the FormFile.
setFormFile(FormFile) - Method in class org.intermine.web.struts.ImportXMLForm
Set the FormFile.
setFull(boolean) - Method in class org.intermine.task.AnalyseDbTask
Set true if a VACUUM FULL ANALYSE required
setGeneratedClassesAvailable(boolean) - Method in class org.intermine.metadata.Model
Sets if generated classes are available.
setGlobalSearchRepository(ServletContext, SearchRepository) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the SearchRepository for global (public) objects in the servlet context.
setGraphType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setGzippedContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets gzip content type ("application/octet-stream")
setGzippedHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for gzipped output.
setHeaderAttributes(String, Integer) - Method in class org.intermine.webservice.server.query.QueryToListService
Sets the header attributes map on the current output object.
setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Output
Sets header attributes that are displayed for example in xml header.
setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.StreamedOutput
Sets header attributes that are displayed for example in xml header.
setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.QueryResultService
Set the header attributes of the output based on the values of the PathQuery
setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.TableRowService
 
setHide(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
If set to true, do not display field on report page.
setHighlight(String) - Method in class org.intermine.web.struts.WidgetForm
 
setHTMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets HTML content type.
setIconImage(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the icon Image
setId(Integer) - Method in class org.intermine.api.userprofile.PermanentToken
 
setId(Integer) - Method in class org.intermine.api.userprofile.SavedBag
 
setId(Integer) - Method in class org.intermine.api.userprofile.SavedQuery
 
setId(Integer) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setId(Integer) - Method in class org.intermine.api.userprofile.Tag
 
setId(Integer) - Method in class org.intermine.api.userprofile.TemplateSummary
 
setId(Integer) - Method in class org.intermine.api.userprofile.UserProfile
 
setId(Integer) - Method in class org.intermine.model.fulldata.Item
 
setId(Integer) - Method in interface org.intermine.model.InterMineFastPathObject
Setter for the ID field.
setId(Integer) - Method in interface org.intermine.model.InterMineObject
Setter for the ID field.
setId(Integer) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the ID value
setId(String) - Method in class org.intermine.web.logic.config.TableExportConfig
Set the id of this TableExportConfig
setId(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setId(String) - Method in class org.intermine.web.registry.model.Instance
 
setId(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Sets element id.
setIdentifier(String) - Method in class org.intermine.api.beans.ObjectDetails
 
setIdentifier(String) - Method in class org.intermine.model.fulldata.Item
 
setIdentifier(String) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Set identifier
setIdentifier(String) - Method in class org.intermine.web.uri.InterMineLUI
Set the identifier
setIdentifier(String) - Method in class org.intermine.xml.full.Item
Set the identifier of this item.
setIds(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setIgnore(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set a comma separated list of template names to ignore - i.e.
setIgnoreDuplicates(boolean) - Method in interface org.intermine.dataloader.IntegrationWriter
Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the value of ignoreDuplicates for the IntegrationWriter.
setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the value of ignoreDuplicates for the IntegrationWriter
setIgnoreDuplicates(boolean) - Method in class org.intermine.task.DirectDataLoaderTask
Set the value of ignoreDuplicates for the IntegrationWriter
setImage(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
Set
setImmutable() - Method in class org.intermine.objectstore.query.Results
Tells this Results object that it is being put into a cache, so it needs to be made immutable to prevent threads stomping on each other and changing settings.
setImplementations(String) - Method in class org.intermine.model.fulldata.Item
 
setImplementations(String) - Method in class org.intermine.xml.full.Item
Set the "implements" of this item.
setIncludeHeaders(boolean) - Method in class org.intermine.web.struts.TableExportForm
Set the includeHeaders flag.
setIndex(int) - Method in class org.intermine.api.results.Column
Sets the value of index
setInputModelFile(File) - Method in class org.intermine.task.ModelMergerTask
Set the model to add additions to.
setInstance(Instance) - Method in class org.intermine.web.registry.model.RegistryResponse
 
setIntegrationWriter(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the IntegrationWriter.
setIntegrationWriter(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the IntegrationWriter.
setIntegrationWriterAlias(String) - Method in class org.intermine.task.DirectDataLoaderTask
Set the IntegrationWriter.
setInterMineAPI(ServletContext, InterMineAPI) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the InterMineAPI in the servlet context.
setIntermineVersion(String) - Method in class org.intermine.web.registry.model.Instance
 
setIntroText(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the introduction text
setInvite(String) - Method in class org.intermine.web.struts.InvitationForm
 
setIsProduction(boolean) - Method in class org.intermine.web.registry.model.Instance
 
setItem(Item) - Method in class org.intermine.model.fulldata.Attribute
 
setItem(Item) - Method in class org.intermine.model.fulldata.Reference
 
setItem(Item) - Method in class org.intermine.model.fulldata.ReferenceList
 
setJavaClass(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the Java class name of the controller for this displayer.
setJoinType(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setJSONContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content type to "application/json"
setJSONHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the response header and content type for json output
setJSONHeader(HttpServletResponse, String, boolean) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the response header and content type for json output
setJSONPContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content type to "text/javascript"
setJSONPHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the response header and content type for jsonp output
setJSONSchemaContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets the content type to "application/schema+json"
setJSONSchemaHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Set the header for a JSON-schema response.
setJspName(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the name of the JSP associated with this displayer.
setKeyFieldNames(List<String>) - Method in class org.intermine.api.profile.InterMineBag
Set the keyFieldNames
setKeystoreFile(String) - Method in class org.intermine.web.task.KeyStoreTask
Bean-style setter for keystoreFile, as per ant spec.
setKeyToRetreive(String) - Method in class org.intermine.task.RetrieveMetadataTask
Set a key to retrieve from database.
setLabel(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the label for this field-configuration.
setLabel(String) - Method in class org.intermine.web.logic.config.Type
Set the label property.
setLabel(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the label of the constraint.
setLabel(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setLargeImage(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the webapp relative path to the large image.
setLastTimeUpdated(String) - Method in class org.intermine.web.registry.model.Instance
 
setLayout(String) - Method in class org.intermine.web.logic.template.TemplateResultInput
 
setLayout(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
 
setLdr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setLevel(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
setLimit(int) - Method in class org.intermine.objectstore.query.Query
Sets the LIMIT parameter for this query - note that this is only honoured in a subquery.
setLimit(Integer) - Method in class org.intermine.webservice.server.WebServiceInput
Sets maximum of returned results.
setLimitOffset(int, int) - Method in class org.intermine.sql.query.Query
Sets the LIMIT and OFFSET numbers for this query.
setLineLength(Integer) - Method in class org.intermine.web.logic.config.InlineListConfig
Sets the amount of entries to show based on their total length
setLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setLink(String) - Method in class org.intermine.web.struts.WidgetForm
 
setLinkRedirect(String) - Method in class org.intermine.api.results.ResultElement
 
setListId(Integer) - Method in class org.intermine.webservice.server.lists.ListUploadService
Sets the id of the list on the header attributes.
setListLeft(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setListPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setListRight(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setListsButton(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setListSize(Integer) - Method in class org.intermine.webservice.server.lists.ListUploadService
Sets the size of the list on the header attributes.
setLocalAccount(boolean) - Method in class org.intermine.api.userprofile.UserProfile
 
setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Set the log writer
setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Not implemented.
setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the logBeforeExecute configuration option.
setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the logBeforeExecute configuration option.
setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the logEverything configuration option.
setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the logEverything configuration option.
setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the logExplains configuration option.
setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the logExplains configuration option.
setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Allows the log table name to be set in this objectstore.
setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Not implemented.
setLoopQueryOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of loopQueryOp
setLoopQueryValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of loopQueryValue
setMailinglist(boolean) - Method in class org.intermine.web.struts.CreateAccountForm
 
setMaintainerEmail(String) - Method in class org.intermine.web.registry.model.Instance
 
setMaintainerGithubUrl(String) - Method in class org.intermine.web.registry.model.Instance
 
setMaintainerOrgName(String) - Method in class org.intermine.web.registry.model.Instance
 
setMaintainerUrl(String) - Method in class org.intermine.web.registry.model.Instance
 
setMainTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Set main title(s) path(s) for the object, e.g.: symbol, primaryIdentifier => eve FBgn0000606
setMatchIDs(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the encoded match ids.
setMatchOnFirst(boolean) - Method in class org.intermine.api.bag.BagQueryConfig
If flag is true, bagqueryrunner queries for identifier until match is found, returning only that first matching record.
setMaterialisedCollection(Collection<E>) - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets the collection with a new materialised collection.
setMax(int) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the maximum possible number of rows in the results.
setMax(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setMax(String) - Method in class org.intermine.web.struts.WidgetForm
 
setMaxP(double) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setMaxQueryParseTime(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Set the maximum time in milliseconds that the optimiser should spend parsing a query from SQL string to an org.intermine.sql.Query object.
setMessage(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
setMessage(String) - Method in class org.intermine.web.struts.ContactForm
 
setMethod(String) - Method in class org.intermine.task.StaticMethodTask
Name of method to call.
setMin(int) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the minimum possible number of rows in the results.
setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Set the cutoff value used to decide if a bag should be put in a table.
setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Set the cutoff value used to decide if a bag should be put in a table.
setMineId(Integer) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Sets Intermine unique object id
setMinRows(int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
Set the minimum row count for precomputed queries.
setMinRows(Integer) - Method in class org.intermine.task.PrecomputeTask
Set the minimum row count for precomputed queries.
setMinRows(Integer) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the minimum row count for precomputed queries.
setMode(String) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Sets the optimiser mode of operation.
setModel(String) - Method in class org.intermine.task.AnalyseDbTask
Set model name, must be set if class name specified
setModel(String) - Method in class org.intermine.task.BuildDbTask
Sets the model
setModel(String) - Method in class org.intermine.task.ModelOutputTask
Set the model to be used.
setModel(Model) - Method in class org.intermine.metadata.ClassDescriptor
Set the model for this ClassDescriptor, this is only be called once and will throw an Exception if called again.
setModel(Model) - Method in class org.intermine.pathquery.Node
Attach the model.
setModel(Model) - Method in class org.intermine.web.logic.query.MetadataNode
 
setModel(Model) - Method in class org.intermine.xml.full.Item
Set the Model to use when checking calls to the other set methods
setModelName(String) - Method in class org.intermine.task.ConverterTask
Set the target model name
setModelName(String) - Method in class org.intermine.task.StoreMetadataTask
Sets the model name
setMonkey(String) - Method in class org.intermine.web.struts.ContactForm
 
setMultiValueAttribute(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of multiValueAttribute, a string representing the values selected by the user separated by a comma.
setMultiValueAttribute(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set the multivalueattribute
setMultivalues(List<String>) - Method in class org.intermine.web.logic.template.ConstraintInput
Set multivalues
setMultiValues(String, String[]) - Method in class org.intermine.web.struts.TemplateForm
Set a multiselect attribute value
setMultiValues(Map<String, String[]>) - Method in class org.intermine.web.struts.TemplateForm
Set the multiValues
setName(String) - Method in class org.intermine.api.beans.ObjectDetails
 
setName(String) - Method in class org.intermine.api.profile.InterMineBag
Set the value of name
setName(String) - Method in class org.intermine.api.template.ApiTemplate
 
setName(String) - Method in class org.intermine.api.userprofile.SavedBag
 
setName(String) - Method in class org.intermine.model.fulldata.Attribute
 
setName(String) - Method in class org.intermine.model.fulldata.Reference
 
setName(String) - Method in class org.intermine.model.fulldata.ReferenceList
 
setName(String) - Method in class org.intermine.template.TemplateQuery
Sets the query short name.
setName(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the data set name.
setName(String) - Method in class org.intermine.web.logic.aspects.AspectSource
Set the source name.
setName(String) - Method in class org.intermine.web.logic.template.TemplateResultInput
Sets template name.
setName(String) - Method in class org.intermine.web.registry.model.Instance
 
setName(String) - Method in class org.intermine.web.struts.ContactForm
 
setName(String) - Method in class org.intermine.web.struts.TemplateForm
Set the template name.
setName(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
 
setName(String) - Method in class org.intermine.xml.full.Attribute
Set the name of this field
setName(String) - Method in class org.intermine.xml.full.Reference
Set the name of this field
setName(String) - Method in class org.intermine.xml.full.ReferenceList
Set the name of this field.
setNamespace(String) - Method in class org.intermine.web.registry.model.Instance
 
setNameSpace(String) - Method in class org.intermine.webservice.server.WebService
Set the default name-space for configuration property look-ups.
setNeighbours(List<String>) - Method in class org.intermine.web.registry.model.Instance
 
setNewBagName(String) - Method in class org.intermine.api.bag.operations.BagOperation
 
setNewBagName(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Set the bag name.
setNewBagName(String) - Method in class org.intermine.web.struts.ModifyBagForm
Set the new bag name.
setNewBagName(String) - Method in class org.intermine.web.struts.SaveBagForm
Sets the value of newBagName
setNewBagType(String) - Method in class org.intermine.web.struts.TriageBagForm
Set the new bag name.
setNewpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm
The new password
setNewpassword(String) - Method in class org.intermine.web.struts.PasswordResetForm
Sets the value of newpassword.
setNewpassword2(String) - Method in class org.intermine.web.struts.ChangePasswordForm
New password verification
setNewpassword2(String) - Method in class org.intermine.web.struts.PasswordResetForm
Sets the value of newpassword2.
setNextEnabled(boolean) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setNextUniqueNumber(long) - Static method in class org.intermine.metadata.StringUtil
Sets the number that is used to generate the next uniqueString.
setNoCache(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets that the result must not be cached.
setNoCacheEnforced(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets enforced no-cache headers to completely disable cache for this response.
setNoExplain() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Sets this LazyCollection to bypass the explain check in ObjectStore.execute().
setNoExplain() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets this LazyCollection to bypass the explain check in ObjectStore.execute().
setNoExplain() - Method in class org.intermine.objectstore.query.Results
Sets this Results object to bypass the explain check in ObjectStore.execute().
setNoOptimise() - Method in interface org.intermine.objectstore.proxy.LazyCollection
Sets this LazyCollection to bypass the optimiser
setNoOptimise() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Sets this LazyCollection to bypass the optimiser
setNoOptimise() - Method in class org.intermine.objectstore.query.Results
Sets this Results object to bypass the optimiser.
setNoPrefetch() - Method in class org.intermine.objectstore.query.Results
Tells this Results object to never do any background prefetching.
setNoResultsMessage(String) - Method in class org.intermine.web.tags.table.TableTag
 
setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.HTMLWidget
 
setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.Widget
 
setNullConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the null/not null constraint.
setNullConstraint(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set a nullConstraint
setNullConstraint(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
Set the nullConstraint
setNumberOfMainTitlesToShow(Integer) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
How many main titles to show in the main title
setNumberOpt(String) - Method in class org.intermine.web.struts.WidgetForm
 
setOAuth2Providers(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the set of supported OAuth2 providers to use.
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.PermanentToken
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.SavedBag
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.SavedQuery
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.Tag
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.TemplateSummary
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.api.userprofile.UserProfile
 
setoBJECT(String[], ObjectStore) - Method in class org.intermine.model.fulldata.Item
 
setoBJECT(String[], ObjectStore) - Method in interface org.intermine.model.InterMineObject
Sets the values of the fields to the values in the given split NotXml.
setoBJECT(String[], ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the values of the fields to the values in the given split NotXml.
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.PermanentToken
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.SavedBag
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.SavedQuery
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.Tag
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.TemplateSummary
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.api.userprofile.UserProfile
 
setoBJECT(String, ObjectStore) - Method in class org.intermine.model.fulldata.Item
 
setoBJECT(String, ObjectStore) - Method in interface org.intermine.model.InterMineObject
Sets the values of the fields to the values in the given NotXml.
setoBJECT(String, ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference
Sets the values of the fields to the values in the given NotXml.
setObjectId(Integer) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
Set imObj ID for the object (taken from the first valid imObj id for this row)
setObjectIdentifier(String) - Method in class org.intermine.api.userprofile.Tag
 
setObjects(Set<ObjectDetails>) - Method in class org.intermine.api.beans.PartnerLink
 
setObjectStore(ObjectStore) - Method in class org.intermine.objectstore.translating.Translator
Set this Translator's ObjectStore.
setObjectStore(ObjectStore) - Method in class org.intermine.task.CreateIndexesTask
Set the ObjectStore to use.
setObjectStore(ObjectStore) - Method in class org.intermine.web.task.CreateSearchIndexTask
Set the object store.
setObjectStoreAlias(String) - Method in class org.intermine.task.PrecomputeTask
 
setObjectStoreAlias(String) - Method in class org.intermine.web.task.EvictOrphansTask
Bean-style setter so that any can do its stuff.
setOldModelLocation(String) - Method in class org.intermine.web.task.ModelUpdateTask
Set the location of the previous model.
setOldpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm
The old password
setOnClick(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
 
setOpenByDefault(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set whether this field should be uncollapsed if sectionOnRight is true.
setOpened(boolean) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Sets new state of disclosure.
setOpenIdProviders(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the set of supported Open-ID providers to use.
setOperationButton(String) - Method in class org.intermine.web.struts.SaveBagForm
 
setOperator(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the operator, "and" or "or"
setOptions(String) - Method in class org.intermine.web.task.KeyStoreTask
Bean-style setter for optionsFile, as per ant spec.
setOptionsTileName(String) - Method in class org.intermine.web.logic.config.TableExportConfig
Set the optionsTileName of this TableExportConfig
setOrCheckClass(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Set the class, or if one is already set on the map, check that this one is valid for it.
setOrCheckClassAndId(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Sets the basic information (class and objectId) on the jsonMap provided.
setOrCheckId(ResultElement, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
Set the id, or if one is already set, check that it matches the one on the map.
setOrganisms(List<String>) - Method in class org.intermine.web.registry.model.Instance
 
setOriginalConstraint(PathConstraint) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setOsAlias(String) - Method in class org.intermine.task.StaticMethodTask
Set the os alias.
setOSAlias(String) - Method in class org.intermine.web.task.CreateSearchIndexTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.ProfileReadTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask
Set the alias of the main object store.
setOSAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask
Set the alias of the main object store.
setOsb(ObjectStoreBag) - Method in class org.intermine.api.profile.InterMineBag
Sets the ObjectStoreBag.
setOsbId(int) - Method in class org.intermine.api.userprofile.SavedBag
 
setOsName(String) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
Set the ObjectStore for which to generate the data.
setOsName(String) - Method in class org.intermine.task.AnalyseDbTask
Set the database alias
setOsName(String) - Method in class org.intermine.task.BuildDbTask
Sets the objectstore
setOsName(String) - Method in class org.intermine.task.ConverterTask
Set the objectstore name
setOsName(String) - Method in class org.intermine.task.GenerateUpdateTriggersTask
Sets the os alias.
setOsName(String) - Method in class org.intermine.task.PostProcessorTask
Set the ObjectStore alias.
setOsName(String) - Method in class org.intermine.task.RetrieveMetadataTask
Sets the os alias
setOsName(String) - Method in class org.intermine.task.StoreMetadataTask
Sets the database alias
setOut(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask
Set the output handler.
setOuterInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
 
setOuterJoin(boolean) - Method in class org.intermine.pathquery.Node
Sets whether this should be an outer join.
setOuterJoins(PathQuery, String) - Method in class org.intermine.pathquery.PathQueryHandler
Given a path that may contain ':' characters to represent outer joins, find each : separated segment and set the status for that join to OUTER.
setOuterJoinStatus(String, OuterJoinStatus) - Method in class org.intermine.pathquery.PathQuery
Sets the outer join status of the last part of a given path in this query.
setOutputFile(File) - Method in class org.intermine.task.AcceptanceTestTask
Set the File to write output to
setOutputFile(File) - Method in class org.intermine.task.ModelMergerTask
Path of file to write resulting model to.
setOutputFile(File) - Method in class org.intermine.task.SummariseObjectStoreTask
Set the name of the file to write the summary into
setOverwriting(boolean) - Method in class org.intermine.web.struts.ImportTagsForm
Set the overwriting flag.
setOverwriting(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm
Set the overwriting flag.
setPackageName(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Set the package name NOTE: this method is merely here to make this a Bean.
setPageAndPageSize(int, int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Set the page size and page together.
setPageName(String) - Method in class org.intermine.web.struts.ModifyBagForm
 
setPageName(String) - Method in class org.intermine.web.struts.ModifyTemplateForm
 
setPageSize(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Set the page size of the table
setPageSize(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag
 
setPageSize(String) - Method in class org.intermine.web.struts.ChangeTableSizeForm
Set the page size
setParameterName(String) - Method in class org.intermine.web.logic.template.ConstraintInput
 
setParameters(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
A JSON string representing custom parameters for this displayer.
setParameters(List<?>) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Set the parameters
setPassword(String) - Method in class org.intermine.api.userprofile.UserProfile
 
setPassword(String) - Method in class org.intermine.web.struts.CreateAccountForm
 
setPassword(String) - Method in class org.intermine.web.struts.LoginForm
Sets the value of password
setPassword(String) - Method in class org.intermine.webservice.server.WebServiceInput
 
setPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager
Change a user's password A check should be made prior to this call to ensure a Profile exists
setPassword2(String) - Method in class org.intermine.web.struts.CreateAccountForm
 
setPath(String) - Method in class org.intermine.web.logic.config.InlineListConfig
Path set from WebConfig, ie "probeSets.primaryIdentifier"
setPath(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of path
setPathConstraints(String, List<? super PathConstraint>) - Static method in class org.intermine.web.logic.widget.config.WidgetConfig
Turn a string representing a set of constraints into a list of constraints.
setPathId(String) - Method in class org.intermine.web.logic.template.ConstraintInput
 
setPathQuery(PathQuery) - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
 
setPathsString(String) - Method in class org.intermine.web.struts.TableExportForm
Set the paths string
setPathStrings(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setPerm(String) - Method in class org.intermine.task.GrantTask
The permission to grant: SELECT, INSERT, UPDATE, DELETE, RULE, REFERENCES, TRIGGER, ALL
setPermanentTokens(Set<PermanentToken>) - Method in class org.intermine.api.userprofile.UserProfile
 
setPlacement(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the data category name under which this displayer should appear.
setPlainTextContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets plain text content type.
setPlainTextHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for plain text output.
setPopulationBagName(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
Set the bag's name for reference population
setPopulationCount(int) - Method in class org.intermine.web.logic.widget.Widget
 
setPopulationIds(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setPrecomputePropertiesPath(String) - Method in class org.intermine.task.PrecomputeTask
 
setPreference(Profile, String, String) - Method in class org.intermine.api.profile.PreferencesManager
 
SetPreferencesService - Class in org.intermine.webservice.server.user
A service to set one or more preferences for a user.
SetPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.SetPreferencesService
 
setProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the user profile in the session.
setProfile(Profile) - Method in class org.intermine.api.template.ApiTemplate
Only used on export so we can get the tags related to this template.
setProfileId(Integer) - Method in class org.intermine.api.profile.InterMineBag
Sets the profileId - moves this bag from one profile to another.
setPropertiesOrigins(ServletContext, Map<String, List<String>>) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the origins of the web properties on the servlet context.
setProperty(String, String) - Method in class org.intermine.webservice.server.jbrowse.util.NameSpacedProperties
 
setPropertyName(String) - Method in class org.intermine.web.struts.EditPropertiesForm
Set the property name.
setPropertyValue(String) - Method in class org.intermine.web.struts.EditPropertiesForm
Set the value of the property
setPublicId(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Sets id of object.
setPValue(String) - Method in class org.intermine.web.struts.WidgetForm
 
setQuery(String) - Method in class org.intermine.api.userprofile.SavedQuery
 
setQuery(String) - Method in class org.intermine.task.RunIqlQueryTask
An query string to execute, may be IQL or SQL by format parameter must be set correctly, richard
setQuery(String) - Method in class org.intermine.web.struts.QueryForm
 
setQuery(HttpSession, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Set the current query on the session.
setQueryBuilder(String) - Method in class org.intermine.web.struts.ImportQueriesForm
Set the queryBuilder field.
setQueryClass(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
If the name of a class is set will only load objects of that type.
setQueryInfo(PathQuery, ResultsInfo) - Method in class org.intermine.api.query.WebResultsExecutor
Sets a ResultsInfo entry in the infoCache for a given PathQuery.
setQueryName(String) - Method in class org.intermine.web.struts.SaveQueryForm
Set the query name
setQueryString(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Set the query String NOTE: this method is merely here to make this a Bean.
setRangeConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the range constraint value.
setRangeLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Set the value of rangeLabel
setRangeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setReference(String, String) - Method in class org.intermine.xml.full.Item
Add a reference to this item.
setReference(String, Item) - Method in class org.intermine.xml.full.Item
Add a reference that points to a particular item.
setReferences(Set<Reference>) - Method in class org.intermine.model.fulldata.Item
 
setRefId(String) - Method in class org.intermine.model.fulldata.Reference
 
setRefId(String) - Method in class org.intermine.xml.full.Reference
Set the refId of this field
setRefIds(String) - Method in class org.intermine.model.fulldata.ReferenceList
 
setRefIds(List<String>) - Method in class org.intermine.xml.full.ReferenceList
Set the references in this collection
setReleaseVersion(String) - Method in class org.intermine.web.registry.model.Instance
 
setReplacesFields(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the comma separated list of field names that should not be displayed on the report page when this displayer is used.
setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter
Sets header and content type of result in response.
setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
Sets header and content type of result in response.
setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.TabHttpExporter
Sets header and content type of result in response.
setResultsTable(HttpSession, String, PagedTable) - Static method in class org.intermine.web.logic.session.SessionMethods
 
setReturnToString(String) - Method in class org.intermine.web.struts.LoginForm
Sets the URL to return to if the login is successful.
setRowFormatter(RowFormatter) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
Set the row formatter
setRows(int) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the estimated number of rows in the results.
setRows(List<List<String>>) - Method in class org.intermine.web.tags.table.TableTag
Set table rows.
setRowSpan(Integer) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Set how many rows this identifier spans
setSavedBags(Set<SavedBag>) - Method in class org.intermine.api.userprofile.UserProfile
 
setSavedQuerys(Set<SavedQuery>) - Method in class org.intermine.api.userprofile.UserProfile
 
setSavedTemplateQuery(SavedTemplateQuery) - Method in class org.intermine.api.template.ApiTemplate
Sets the saved template query object.
setSavedTemplateQuerys(Set<SavedTemplateQuery>) - Method in class org.intermine.api.userprofile.UserProfile
 
setSavePopulation(boolean) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
 
setSchemafile(String) - Method in class org.intermine.task.BuildDbTask
Adds the schemafile to be processed.
setScope(String) - Method in class org.intermine.web.struts.TemplateForm
Set the template scope.
setSectionOnRight(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set whether this field should be rendered in its own section on the right side of the page.
setSectionTitle(String) - Method in class org.intermine.web.logic.config.FieldConfig
Set the section title (if sectionOnRight == true).
setSelectable(boolean) - Method in class org.intermine.api.results.Column
Sets the value of selectable
setSelected(boolean) - Method in class org.intermine.web.logic.query.MetadataNode
Sets the value of selected
setSelected(String[]) - Method in class org.intermine.web.struts.ModifyTemplateForm
Sets the selected templates
setSelected(String[]) - Method in class org.intermine.web.struts.WidgetForm
 
setSelectedBagOp(ConstraintOp) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the seletedBagOp
setSelectedBags(String[]) - Method in class org.intermine.web.struts.ModifyBagForm
Sets the selected bags
setSelectedBagValue(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the seletedBagValue returned bye the getSelectedValue if the bag is selected
setSelectedClass(String) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setSelectedElements(String[]) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
Set the list of selectedElements
setSelectedExtraAttribute(String) - Method in class org.intermine.web.struts.WidgetForm
 
setSelectedObjects(String[]) - Method in class org.intermine.web.struts.BagUploadConfirmForm
Sets the ids of the selected objects - ie.
setSelectedObjects(String[]) - Method in class org.intermine.web.struts.SaveBagForm
Sets the selected objects
setSelectedQueries(String[]) - Method in class org.intermine.web.struts.ModifyQueryForm
Sets the selected queries
setSelectionIds(Map<Integer, String>) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setSeriesLabels(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setSeriesPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setSeriesValues(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setSession(HttpSession) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
 
setShowExtraConstraint(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setShowIdentifier(Boolean) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
Set to show the identifier in this row
setShowImmediately(Boolean) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set if we should display the displayer immediately
setShowInHeader(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig
Show this list in the header?
setShowInInlineCollection(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set the showInInlineCollection flag.
setShowInListAnalysisPreviewTable(Boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Specify if we want to show this field for an object in list analysis page table preview
setShowInQB(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Shall we show this field in a QueryBuilder? Ref #355
setShowInResults(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set the showInResults flag.
setShowInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
Set the showInSummary flag.
setShowLinksToObjects(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig
Shall we show links to the objects's report pages?
setShowOnLeft(String) - Method in class org.intermine.web.logic.config.Displayer
 
setSimpleCellId() - Method in class org.intermine.api.results.ResultElement
Set a hopefully unique persistent local id for simple objects.
setSingleton(boolean) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
Sets whether the collection should be a singleton collection, or whether it should be a collection of ResultRows.
setSize(int) - Method in class org.intermine.webservice.server.lists.FlatListFormatter
 
setSize(int) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter
 
setSize(int) - Method in class org.intermine.webservice.server.lists.JSONListFormatter
 
setSize(int) - Method in interface org.intermine.webservice.server.lists.ListFormatter
set the size of the list.
setSource(Integer, String, Source) - Method in class org.intermine.dataloader.DataTracker
Set the Source for a field of an object in the database
setSource(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the ObjectStore that is the data source.
setSource(Source) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
Sets the source of the data, so we know what the primary keys are, and can fetch that extra data.
setSourceName(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the source name, as used by primary key priority config.
setSourceName(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the source name, as used by primary key priority config.
setSourceName(String) - Method in class org.intermine.task.DirectDataLoaderTask
Set the source name, as used by primary key priority config.
setSourceName(String) - Method in class org.intermine.task.FullXmlConverterTask
Set the source name, as used by primary key priority config.
setSourceType(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
Set the source type, as used by primary key priority config.
setSourceType(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set the source type, as used by primary key priority config.
setSourceType(String) - Method in class org.intermine.task.DirectDataLoaderTask
Set the source type, as used by primary key priority config.
setSrc(String) - Method in class org.intermine.web.logic.config.Displayer
Set the source of this displayer
setStart(long) - Method in class org.intermine.objectstore.query.ResultsInfo
Sets the estimated amount of time taken to produce the first row of the results.
setStart(Integer) - Method in class org.intermine.webservice.server.WebServiceInput
Sets from which index should be results returned 1-based.
setStartClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setStartClassDisplay(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
 
setStartingPoints(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the starting point class names as a space seperated list.
setState(String) - Method in class org.intermine.api.userprofile.SavedBag
 
setState(String, Object) - Method in class org.intermine.web.logic.results.WebState
Set attribute.
setState(String, String) - Static method in class org.intermine.dwr.AjaxServices
Set state that should be saved during the session.
setState(BagState) - Method in class org.intermine.api.profile.InterMineBag
Set bag state
setStatus(String) - Method in class org.intermine.web.registry.model.Instance
 
setStatusCode(int) - Method in class org.intermine.web.registry.model.RegistryResponse
 
setStoreHook(DataConverterStoreHook) - Method in class org.intermine.dataconversion.DataConverter
Set a hook for this converter that will be called just before each Item is stored.
setStyle(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Sets element style.
setStyleClass(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
Sets css style class of element.
setSubclass(String) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
Sets the subclass on this path.
setSubclassValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Sets the value of subclassValue
setSubject(String) - Method in class org.intermine.web.struts.ContactForm
 
setSubject(String) - Method in class org.intermine.web.task.IssueTokenTask
Bean-style setter, as per the ant spec.
setSubTitle(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the subtitle.
setSubTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
Set subtitle(s) path(s) for the object, e.g.: organism.shortName => D.
setSummaries(Set<TemplateSummary>) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setSummarise(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the summarise flag.
setSummary(String) - Method in class org.intermine.api.userprofile.TemplateSummary
 
setSuperuser(boolean) - Method in class org.intermine.api.profile.Profile
Set the superuser flag and store it in userprofile database
setSuperuser(boolean) - Method in class org.intermine.api.userprofile.UserProfile
 
setSuperuserPassword(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the superuser's initial password.
setSuperUsers(String[]) - Method in class org.intermine.web.struts.ModifySuperUserForm
Sets the super users
setSwitchable(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setSwitchOff(String, String) - Method in class org.intermine.web.struts.TemplateForm
Set the SwitchOff ability.
setSwitchOffAbility(PathConstraint, SwitchOffAbility) - Method in class org.intermine.template.TemplateQuery
Sets the sbitch-off-ability of a constraint.
setSwitchOffAbility(SwitchOffAbility) - Method in class org.intermine.web.logic.query.DisplayConstraint
Set the switchOffAbility
setTabContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets tab separated values content type.
setTabHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for tab separated values output.
setTable(String) - Method in class org.intermine.web.struts.TableExportForm
Set the table identifier to look up in the servlet context
setTableDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
Set the table displayer for this Type
setTableid(String) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
 
setTagName(String) - Method in class org.intermine.api.userprofile.Tag
 
setTags(Set<Tag>) - Method in class org.intermine.api.userprofile.UserProfile
 
setTempdir(File) - Method in class org.intermine.task.BuildDbTask
Sets the directory for temporary files including sql output
setTemplate(SavedTemplateQuery) - Method in class org.intermine.api.userprofile.TemplateSummary
 
setTemplateButton(String) - Method in class org.intermine.web.struts.ModifyTemplateForm
 
setTemplateLabel(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
Set the template label.
setTemplateQuery(String) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setTemplatesummary(List<Object>) - Method in class org.intermine.web.logic.query.DisplayConstraint
 
setTemplatesXml(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the templates xml file.
setText(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
Set
setText(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the query string
setTextToFind(String) - Method in class org.intermine.web.struts.FindInListForm
 
setThreshold(int) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
This sets the threshold above which a temp table will be used for deletes.
setTileName(String) - Method in class org.intermine.web.logic.aspects.Aspect
Set the name of the tile/page to embed in the centre of the data set homepage.
setTimeLimit(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
Sets the optimiser's maximum effort time, in milliseconds.
settings - Variable in class org.intermine.sql.Database
 
setTitle(String) - Method in class org.intermine.api.template.ApiTemplate
 
setTitle(String) - Method in class org.intermine.pathquery.PathQuery
Sets the name of the query.
setTitle(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setTitle(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
 
setTitle(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
Set the title
setToggledElements(Map<String, Boolean>) - Method in class org.intermine.web.logic.results.WebState
Sets map of ids and its state.
setToken(String) - Method in class org.intermine.api.userprofile.PermanentToken
 
setToken(String) - Method in class org.intermine.web.struts.PasswordResetForm
Sets the value of token.
setToken(String) - Method in class org.intermine.web.task.VerifyTokenTask
Bean-style setter for token, as per ant spec.
setTrackQueue(Queue<Track>) - Method in class org.intermine.api.tracker.AbstractTracker
Set the queue of tracks
setTreatColNames(boolean) - Method in class org.intermine.web.tags.table.TableTag
 
setTwitter(String) - Method in class org.intermine.web.registry.model.Instance
 
setType(String) - Method in class org.intermine.api.beans.ObjectDetails
 
setType(String) - Method in class org.intermine.api.profile.InterMineBag
 
setType(String) - Method in class org.intermine.api.userprofile.SavedBag
 
setType(String) - Method in class org.intermine.api.userprofile.Tag
 
setType(String) - Method in class org.intermine.pathquery.Node
Set the value of type
setType(String) - Method in class org.intermine.task.ModelOutputTask
Set the type of model output required.
setType(String) - Method in class org.intermine.web.logic.query.MetadataNode
Set the value of type
setType(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the bag type
setType(String) - Method in class org.intermine.web.struts.TableExportForm
Set the type
setType(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
Sets type of tag.
setType(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
Sets object type.
setTypeClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setTypes(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
Set the types this displayer should be used for as a comma separated list of unqualified class names.
setUp() - Method in class org.intermine.task.CreateIndexesTask
Sets up the instance variables
setupDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Sets up the database for storing precomputed tables
setupFieldValues() - Method in class org.intermine.web.logic.results.ReportObject
Setup fieldValues HashMap
setUpPermission(InterMineAPI, ProfileManager.ApiPermission) - Static method in class org.intermine.web.logic.profile.LoginHandler
Does whatever needs to be done to a permissions object to get it ready for a life cyle in a web service request.
setUpProfile(HttpSession, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler
Initialises a profile for the current user based on their user name and password.
setUpProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
Sets up a profile ready for a session in InterMine.
setUrl(String) - Method in class org.intermine.web.logic.aspects.AspectSource
Set the URL to source website.
setUrl(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
Set
setUrl(String) - Method in class org.intermine.web.registry.model.Instance
 
setUseBagConstraint(String, boolean) - Method in class org.intermine.web.struts.TemplateForm
Set value of useBagConstraint for given constraint key.
setUseJoin(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
 
setUser(String) - Method in class org.intermine.task.GrantTask
Set user to grant permissions to
setUserId(Integer) - Method in class org.intermine.api.profile.Profile
Set the userId
setUsername(String) - Method in class org.intermine.api.userprofile.UserProfile
 
setUsername(String) - Method in class org.intermine.web.struts.CreateAccountForm
 
setUsername(String) - Method in class org.intermine.web.struts.LoginForm
Sets the value of username
setUsername(String) - Method in class org.intermine.web.struts.RequestPasswordForm
Sets the value of username
setUsername(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the account name to laod template to.
setUsername(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the account name to load template to.
setUsername(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the account name to laod template to.
setUserName(String) - Method in class org.intermine.webservice.server.WebServiceInput
 
setUserProfile(UserProfile) - Method in class org.intermine.api.userprofile.PermanentToken
 
setUserProfile(UserProfile) - Method in class org.intermine.api.userprofile.SavedBag
 
setUserProfile(UserProfile) - Method in class org.intermine.api.userprofile.SavedQuery
 
setUserProfile(UserProfile) - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
setUserProfile(UserProfile) - Method in class org.intermine.api.userprofile.Tag
 
setUserProfileAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileReadTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackReadTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask
Set the alias of the userprofile database.
setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask
Set the alias of the userprofile object store.
setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateTrackTableTask
Set the alias of the userprofile object store.
setV(int) - Method in class org.intermine.web.registry.model.Instance
 
setValue(B) - Method in class org.intermine.webservice.server.core.Pair
 
setValue(String) - Method in class org.intermine.model.fulldata.Attribute
 
setValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput
Sets constraint value.
setValue(String) - Method in class org.intermine.xml.full.Attribute
Set the value of this field
setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Sets the verboseQueryLog configuration option.
setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Sets the verboseQueryLog configuration option.
setView(String) - Method in class org.intermine.web.struts.TemplateForm
Set the selected alternative view name.
setViews(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
 
setVisible(boolean) - Method in class org.intermine.api.results.Column
Sets the value of visible
setWebConfig(ServletContext, WebConfig) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the WebConfig into the ServletContext.
setWebConfig(WebConfig) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
 
setWebProperties(ServletContext, Properties) - Static method in class org.intermine.web.logic.session.SessionMethods
Sets the web properties in the session.
setWhichInput(String) - Method in class org.intermine.web.struts.BuildBagForm
Set the method the user used to upload her bag.
setWidgetid(String) - Method in class org.intermine.web.struts.WidgetForm
 
setWidgets(LinkedList) - Method in class org.intermine.web.logic.config.Type
 
setWidgetTitle(String) - Method in class org.intermine.web.struts.WidgetForm
used on results page for description: "results for widget XYZ"
setWriter(PrintWriter) - Method in class org.intermine.webservice.server.output.StreamedOutput
Sets associated writer
setXml(String) - Method in class org.intermine.web.struts.ImportTagsForm
Set the xml.
setXml(String) - Method in class org.intermine.web.struts.ImportXMLForm
Set the xml.
setXml(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
Sets xml query string.
setXMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets XML content type.
setXMLHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
Sets response header and content type for XML output.
setXmlResource(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
Set XML resource name (to load data from classloader).
setXmlResource(String) - Method in class org.intermine.task.FullXmlConverterTask
Set XML resource name (to load data from classloader).
SHA256withRSA - org.intermine.webservice.server.JWTBuilder.Algorithm
SHA256withRSA
SHA384withRSA - org.intermine.webservice.server.JWTBuilder.Algorithm
SHA384withRSA
SHA512withRSA - org.intermine.webservice.server.JWTBuilder.Algorithm
SHA512withRSA
ShadowClass - Interface in org.intermine.model
A root interface for all shadow classes for performance.
shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager
Share the bag given in input with the user which userName input
shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.SharedBagManager
Share the bag given in input with user which userName is given in input To be used ONLY when deserialising the user-profile from XML.
shareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager
Share the bag given in input with user which userName is given in input
shareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Let the recipient gain access to this bag in future uses of the application.
SHARED_BAGS - Static variable in class org.intermine.api.bag.SharedBagManager
the table name
SharedBagBinding - Class in org.intermine.api.xml
Parse the shared bags in XML format
SharedBagBinding() - Constructor for class org.intermine.api.xml.SharedBagBinding
 
SharedBagHandler - Class in org.intermine.api.xml
Handle parsing of shared bags
SharedBagHandler(List<Map<String, String>>) - Constructor for class org.intermine.api.xml.SharedBagHandler
Constructor
SharedBagManager - Class in org.intermine.api.bag
Singleton manager class for shared bags.
SharingBagUsersController - Class in org.intermine.web.struts
Controller for the inline tag editing tile
SharingBagUsersController() - Constructor for class org.intermine.web.struts.SharingBagUsersController
 
SharingInvite - Class in org.intermine.api.bag
A representation of an invitation to share a resource.
SharingInvite(InterMineBag, String) - Constructor for class org.intermine.api.bag.SharingInvite
Constructor.
SharingInvite(InterMineBag, String, String) - Constructor for class org.intermine.api.bag.SharingInvite
Constructor.
SharingInvite(InterMineBag, String, String, Date, Date, Boolean) - Constructor for class org.intermine.api.bag.SharingInvite
Constructor.
SharingInvite.IntermediateRepresentation - Class in org.intermine.api.bag
A structure for holding data we read from the DB.
SharingInvite.NotFoundException - Exception in org.intermine.api.bag
Exception thrown when we can't find a shared invitation.
shouldCancelQuery() - Method in interface org.intermine.web.logic.query.QueryMonitor
Called intermittently while a query is run providing an opportunity to cancel the query.
shouldCancelQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Return true if tickle has not been called in a period of time greater than the timeout value.
shouldSavePopulation() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
showColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't hide columns any more
shuffle(Map<String, V>, int) - Static method in class org.intermine.web.logic.WebUtil
takes a map and puts it in random order also shortens the list to be map.size() = max
shutdown() - Method in class org.intermine.api.tracker.TrackerDelegate
Called from ShutdownHook.
shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
Called by the ShutdownHook on shutdown.
shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Called by the StatsShutdownHook on shutdown
shutdown() - Method in class org.intermine.sql.Database
Logs stuff
shutdown() - Method in interface org.intermine.util.Shutdownable
Shuts down an instance.
shutdown() - Static method in class org.intermine.util.ShutdownHook
Performs the shutdown.
shutdown() - Method in class org.intermine.web.context.InterMineContext
Send the signal that shutdown is happening - try and release resources.
Shutdownable - Interface in org.intermine.util
An interface for any object that can be shut down by the ShutdownHook.
ShutdownHook - Class in org.intermine.util
This class provides a "shutdown" service to other classes.
SIMPLE_VALUE - org.intermine.template.TemplateValue.ValueType
a simple value, like a string
SimpleConstraint - Class in org.intermine.objectstore.query
Represents a constraint between two QueryEvaluable types.
SimpleConstraint(QueryEvaluable, ConstraintOp) - Constructor for class org.intermine.objectstore.query.SimpleConstraint
Construct a Constraint.
SimpleConstraint(QueryEvaluable, ConstraintOp, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.SimpleConstraint
Construct a Constraint.
simpleConstraintToString(SqlGenerator.State, StringBuffer, SimpleConstraint, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a SimpleConstraint object into a String suitable for putting in an SQL query.
simpleCreateObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil
Create a new object given a class, which may be an interface.
SINGLE - org.intermine.api.searchengine.KeywordSearchFacetType
single value per document
SingleTemplateService - Class in org.intermine.webservice.server.template
Service that responds with a single template.
SingleTemplateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.SingleTemplateService
 
SINGLETON - Static variable in class org.intermine.util.NullFirstComparator
Publicly-accessible instance
SingletonResults - Class in org.intermine.objectstore.query
This class is equivalent to a Result object with ResultRows consisting only of single items
SingletonResults(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.SingletonResults
Constructor for a SingletonResults object
SingletonResults(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.SingletonResults
Constructor for a SingletonResults object, given a ResultsBatches object.
singletonResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
size - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
size() - Method in class org.intermine.api.profile.StorableBag
Returns the number of elements in the bag.
size() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
size() - Method in class org.intermine.api.results.WebResults
size() - Method in class org.intermine.api.search.SearchResults
 
size() - Method in class org.intermine.objectstore.proxy.ProxyCollection
Gets the number of elements in this collection
size() - Method in class org.intermine.objectstore.query.Results
Gets the number of results rows in this Results object
size() - Method in class org.intermine.util.AlwaysMap
size() - Method in class org.intermine.util.ConsistentSet
Return the number of elements in this Set.
size() - Method in class org.intermine.util.IdentityMap
size() - Method in class org.intermine.util.IntPresentSet
Returns the number of ints present.
size() - Method in class org.intermine.util.IntToIntMap
Returns the number of mappings to non-minus-one ints present.
size() - Method in class org.intermine.util.PseudoSet
size() - Method in class org.intermine.util.ReferenceMap
size(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
Gets the number of results rows in this Results object.
SIZE - Static variable in class org.intermine.objectstore.query.ResultsInfo
Denotes that the result of getRows() is the known size of the results.
sizeOfArray(Object[]) - Static method in class org.intermine.sql.writebatch.TableBatch
Calculates the size of an array, in bytes.
sizeOfList(List<Object[]>) - Static method in class org.intermine.sql.writebatch.TableBatch
Calculates the size of a List of arrays, in bytes.
SKELETON - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
skeletons - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
SKIP_BUILDER_PARAMETER - Static variable in class org.intermine.web.struts.TemplateAction
Name of skipBuilder parameter
SoftReferenceMap<K,​V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
SoftReferenceMap() - Constructor for class org.intermine.util.SoftReferenceMap
 
SolrClientManager - Class in org.intermine.api.searchengine.solr
Singleton class to create one instance of Solr Client
SolrIndexHandler - Class in org.intermine.api.searchengine.solr
Solr Implementation of IndexHandler
SolrIndexHandler() - Constructor for class org.intermine.api.searchengine.solr.SolrIndexHandler
 
SolrKeywordSearchHandler - Class in org.intermine.api.searchengine.solr
Solr implementation of KeywordSearchHandler
SolrKeywordSearchHandler() - Constructor for class org.intermine.api.searchengine.solr.SolrKeywordSearchHandler
 
SolrObjectHandler - Class in org.intermine.api.searchengine.solr
Thread to fetch all intermineobjects (with exceptions) from database, create a solr document for them, add references (if applicable) and put the final document in the indexing queue
SortableMap<K extends java.lang.Comparable<K>,​V extends java.lang.Comparable<V>> - Class in org.intermine.web.logic
SortableMap extends a LinkedHashMap with some useful sorting features.
SortableMap() - Constructor for class org.intermine.web.logic.SortableMap
Default constructor.
SortableMap(Map<K, V>) - Constructor for class org.intermine.web.logic.SortableMap
Create new SortableMap based on the given Map.
sortConstraints(List<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery
A method to sort constraints by a given lists, provided to allow TemplateQuery to set a specific sort order that will be preserved in a round-trip to XML.
sortKeys() - Method in class org.intermine.web.logic.SortableMap
Sort this map ascending on keys in natural order (default).
sortKeys(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap
Sort this map on keys.
sortMap(Map<String, BigDecimal>) - Static method in class org.intermine.web.logic.widget.ErrorCorrection
Sort the map by values.
sortValues() - Method in class org.intermine.web.logic.SortableMap
Sort this map ascending on values in natural order (default).
sortValues(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap
Sort this map on values.
source - Variable in class org.intermine.dataloader.BatchingFetcher
 
source - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
Source - Class in org.intermine.dataloader
Represents a data source, by name and skeleton status.
Source(String) - Constructor for class org.intermine.dataloader.Source
Create a new source object with no type information that isn't a skeleton
Source(String, boolean) - Constructor for class org.intermine.dataloader.Source
Create a new source object with no type information.
Source(String, String) - Constructor for class org.intermine.dataloader.Source
Create a new source object that isn't a skeleton.
Source(String, String, boolean) - Constructor for class org.intermine.dataloader.Source
Create a new source object.
SOURCE - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
sourceKeys - Static variable in class org.intermine.dataloader.DataLoaderHelper
 
sourceName - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
sourceName - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
sourceName - Variable in class org.intermine.task.DirectDataLoaderTask
 
sourceName - Variable in class org.intermine.task.FullXmlConverterTask
 
SourcePriorityComparator - Class in org.intermine.dataloader
Comparator, that compares two InterMineObjects, with reference to a particular FieldDescriptor for priority.
SourcePriorityComparator(DataTracker, Class<? extends InterMineObject>, String, Source, InterMineObject, IntPresentSet, IntegrationWriterAbstractImpl, Source, Source, PriorityConfig) - Constructor for class org.intermine.dataloader.SourcePriorityComparator
Constructs a new Comparator for comparing objects for priority for a given field.
sourceToString(Source) - Method in class org.intermine.dataloader.DataTracker
Converts a Source to a source name.
sourceType - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
SPACE_SPLITTER - Static variable in class org.intermine.pathquery.PathQuery
A Pattern that finds spaces in a String.
split(String, String) - Static method in class org.intermine.metadata.StringUtil
Returns a list of tokens delimited by delim in String str.
split(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression
Takes a List of collections of String variables and returns a List of the same length, containing sections of the LogicExpression with those variables in.
spliterator() - Method in class org.intermine.objectstore.query.SingletonResults
 
SPLITTER - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
A Pattern that will find delimiters.
sql() - Method in class org.intermine.sql.query.SqlParser
 
sql(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
sql_statement() - Method in class org.intermine.sql.query.SqlParser
 
sql_statement(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
SQL_STATEMENT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
sqlCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
 
SqlGenerator - Class in org.intermine.objectstore.intermine
Code to generate an sql statement from a Query object.
SqlGenerator.State - Class in org.intermine.objectstore.intermine
Internal representation of the State of the query as it is built up.
SqlLexer - Class in org.intermine.sql.query
 
SqlLexer(InputBuffer) - Constructor for class org.intermine.sql.query.SqlLexer
 
SqlLexer(LexerSharedInputState) - Constructor for class org.intermine.sql.query.SqlLexer
 
SqlLexer(InputStream) - Constructor for class org.intermine.sql.query.SqlLexer
 
SqlLexer(Reader) - Constructor for class org.intermine.sql.query.SqlLexer
 
SQLOperation<T> - Class in org.intermine.objectstore.intermine
A functional interface (oh, please come Java 8 - you cannot come soon enough) to help manage out-of-control boilerplate-itis in SQL code.
SQLOperation() - Constructor for class org.intermine.objectstore.intermine.SQLOperation
 
SqlParser - Class in org.intermine.sql.query
 
SqlParser(ParserSharedInputState) - Constructor for class org.intermine.sql.query.SqlParser
 
SqlParser(TokenBuffer) - Constructor for class org.intermine.sql.query.SqlParser
 
SqlParser(TokenBuffer, int) - Constructor for class org.intermine.sql.query.SqlParser
 
SqlParser(TokenStream) - Constructor for class org.intermine.sql.query.SqlParser
 
SqlParser(TokenStream, int) - Constructor for class org.intermine.sql.query.SqlParser
 
SQLStringable - Interface in org.intermine.sql.query
An interface for all classes that implement the getSQLString method.
SqlTokenTypes - Interface in org.intermine.sql.query
 
SqlTreeParser - Class in org.intermine.sql.query
 
SqlTreeParser() - Constructor for class org.intermine.sql.query.SqlTreeParser
 
StandardHttpExporter - Class in org.intermine.web.logic.export.http
Abstract class implementing functionality common for exporters exporting table in simple format like comma separated format.
StandardHttpExporter() - Constructor for class org.intermine.web.logic.export.http.StandardHttpExporter
Constructor.
start - Variable in class org.intermine.dataconversion.FullXmlConverter
 
start - Variable in class org.intermine.objectstore.query.OverlapRange
 
start - Variable in class org.intermine.objectstore.query.ResultsInfo
 
start - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
start - Variable in class org.intermine.sql.query.ExplainResult
 
START_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
Name of start parameter that determines index of first returned result.
START_PATHS - Static variable in class org.intermine.web.struts.InterMineRequestProcessor
Paths that can be used as initial pages ie.
start_rule() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
start_rule() - Method in class org.intermine.sql.query.SqlParser
 
start_rule(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
startClass - Variable in class org.intermine.web.logic.widget.WidgetLdr
 
startContainsClass(String) - Method in class org.intermine.pathquery.Path
Return true if the first element in the path has the class given in input as type
startDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler
 
startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.BagQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.InvitationHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.PreferencesHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.TagHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.InterMineBagHandler
InvalidBag
startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SavedQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SharedBagHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.pathquery.PathQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.template.xml.TemplateQueryHandler
startElement(String, String, String, Attributes) - Method in class org.intermine.webservice.server.ServiceListingHandler
 
startElement(String, String, String, Attributes) - Method in class org.intermine.xml.full.FullHandler
startListening() - Method in class org.intermine.api.search.SearchRepository
Begin listening for events on the items of interest.
startPagedTableCount(PageTableQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods
Start a query running in the background that will return the row count of the collection.
startQuery(QueryMonitor, HttpSession, MessageResources, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Start the current query running in the background, then return.
startQueryCount(QueryCountQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods
Start a query running in the background that will return the row count of the query argument.
startQueryWithTimeout(HttpServletRequest, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
Start the given query running in the background, then return, with a default timeout.
startTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Put query builder in template building mode.
state - Variable in class org.intermine.api.userprofile.SavedBag
 
State() - Constructor for class org.intermine.objectstore.intermine.SqlGenerator.State
Constructor
StaticMethodTask - Class in org.intermine.task
Given a class name and method name, just invokes a static method.
StaticMethodTask() - Constructor for class org.intermine.task.StaticMethodTask
 
stats - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
 
stats(Command) - Method in class org.intermine.webservice.server.jbrowse.CommandRunner
 
STATS - org.intermine.webservice.server.jbrowse.Commands.Action
stats
statsBagTableTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsConTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsEstTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsExeTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsGenTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
statsOptTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
StatusDictionary - Class in org.intermine.webservice.server
HTTP status code dictionary.
STDDEV - Static variable in class org.intermine.objectstore.query.QueryFunction
Sample standard deviation of a number of rows
STDDEV - Static variable in class org.intermine.sql.query.Function
STDDEV operator - takes one operand
stm - Variable in class org.intermine.api.tracker.xml.TrackHandler
 
stop() - Method in class org.intermine.webservice.server.idresolution.JobJanitor
Let others tell us to stop.
stopListening() - Method in class org.intermine.api.search.SearchRepository
Stop listening for events
stopTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
Bring the query builder out of template building mode and discard any unfinished template building.
StorableBag - Class in org.intermine.api.profile
Base class for representations of user's collections of objects stored in a database.
StorableBag() - Constructor for class org.intermine.api.profile.StorableBag
 
store(Object) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Store an object in this ObjectStore, delegates to internal ObjectStoreWriter.
store(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Store an object in this ObjectStore.
store(Object) - Method in interface org.intermine.objectstore.ObjectStoreWriter
Store an object in this ObjectStore.
store(Connection) - Method in interface org.intermine.api.tracker.track.Track
Save into the table the track object representing the user activity
store(Connection) - Method in class org.intermine.api.tracker.track.TrackAbstract
 
store(Collection<Item>) - Method in class org.intermine.dataconversion.DataConverter
Store a Collection of XMl Items
store(FastPathObject) - Method in class org.intermine.dataloader.DirectDataLoader
Store an object using the IntegrationWriter, buffering writes so that integration queries and database writes can be run in batches.
store(FastPathObject, Source, Source) - Method in interface org.intermine.dataloader.IntegrationWriter
Stores the given object in the objectstore.
store(FastPathObject, Source, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Stores the given object in the objectstore.
store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
Stores the given object in the objectstore.
store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
Stores the given object in the objectstore.
store(Attribute, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Attribute after setting its item id.
store(Attribute, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Attribute after setting its item id.
store(Attribute, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Attribute after setting its item id.
store(Item) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Item and all its associated attributes, references, and referencelists.
store(Item) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Item and all its associated attributes, references, and referencelists.
store(Item) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Item and all its associated attributes, references, and referencelists.
store(ReferenceList, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given ReferenceList after setting its item id.
store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given ReferenceList after setting its item id.
store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given ReferenceList after setting its item id.
store(Reference, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Reference after setting its item id.
store(Reference, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Reference after setting its item id.
store(Reference, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Reference after setting its item id.
store(Database, String, String) - Static method in class org.intermine.modelproduction.MetadataManager
Store a (key, value) pair in the metadata table of the database
store(Attribute, Integer) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML Attribute
store(Item) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML Item
store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML ReferenceList
store(Reference, Integer) - Method in class org.intermine.dataconversion.DataConverter
Store a single XML Reference
storeAll(Collection<Item>) - Method in interface org.intermine.dataconversion.ItemWriter
Stores the given Collection of Items and all their associated attributes, references, and referencelists.
storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.MockItemWriter
Stores the given Collection of Items and all their associated attributes, references, and referencelists.
storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
Stores the given Collection of Items and all their associated attributes, references, and referencelists.
storeBinary(Database, String, byte[]) - Static method in class org.intermine.modelproduction.MetadataManager
Store a binary (key, value) pair in the metadata table of the database
storeException(HttpServletRequest, String, ActionMessage, ActionForward, String) - Method in class org.intermine.web.struts.InterMineExceptionHandler
Default implementation for handling an ActionMessage generated from an Exception during Action delegation.
storeInvites(Profile) - Method in class org.intermine.api.bag.InvitationHandler
 
storeLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
Returns an OutputStream object with which to write a large binary value to the database.
StoreMetadataTask - Class in org.intermine.task
Store model metadata to a database
StoreMetadataTask() - Constructor for class org.intermine.task.StoreMetadataTask
 
storeSavedBag() - Method in class org.intermine.api.profile.StorableBag
Perform the actual insertion of data into the userprofile database.
storeTrack(Track) - Method in class org.intermine.api.tracker.AbstractTracker
Save into the table the track object representing the user activity
storeTrack(Track) - Method in interface org.intermine.api.tracker.Tracker
Save into the table a Track
storeWithConnection(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Performs store with a given Connection.
StreamedOutput - Class in org.intermine.webservice.server.output
Immediately as the data or error messages are added they are streamed via http connection.
StreamedOutput(PrintWriter, Formatter) - Constructor for class org.intermine.webservice.server.output.StreamedOutput
Constructor.
StreamedOutput(PrintWriter, Formatter, String) - Constructor for class org.intermine.webservice.server.output.StreamedOutput
Constructor.
STRICT_NOT_EQUALS - Static variable in class org.intermine.metadata.ConstraintOp
Require that the two arguments are not equal
STRING_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
 
StringConstructor - Class in org.intermine.model
A CharSequence object representing a String constructed out of a sequence of other Strings.
StringConstructor() - Constructor for class org.intermine.model.StringConstructor
Main constructor - creates an empty object.
StringHelper - Class in org.intermine.api.query.range
 
StringHelper() - Constructor for class org.intermine.api.query.range.StringHelper
 
StringTableExporter - Class in org.intermine.web.logic.export.string
Simple exporter exporting table of strings.
StringTableExporter(PrintWriter, RowFormatter) - Constructor for class org.intermine.web.logic.export.string.StringTableExporter
Constructor.
stringToObject(Class<?>, String) - Static method in class org.intermine.metadata.TypeUtil
Returns an object for a given String.
stringToSource(String) - Method in class org.intermine.dataloader.DataTracker
Converts a string sourcename to a Source.
stringToSource(String, String) - Method in class org.intermine.dataloader.DataTracker
Converts a string sourcename to a Source if the type is known.
StringUtil - Class in org.intermine.metadata
Collection of commonly used String utilities
StringUtil.LineWrappedString - Class in org.intermine.metadata
Class for returning multiple values from the wrapLines method.
stripStart(String, Properties) - Static method in class org.intermine.metadata.Util
Strips the given string off the keys of the given Properties, and returns a new set of properties.
stripStart(String, Properties) - Static method in class org.intermine.util.PropertiesUtil
Strips the given string off the keys of the given Properties, and returns a new set of properties.
STRPOS - Static variable in class org.intermine.sql.query.Function
STRPOS operator - takes two operands.
SUB - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
A subtitle.
SUBCLASSES - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute, Map from unqualified type name to list of subclass names.
subclassValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
subIter - Variable in class org.intermine.api.results.ExportResultsIterator
 
subList(int, int) - Method in class org.intermine.objectstore.query.Results
subMap - Variable in class org.intermine.util.ReferenceMap
 
SubMenuController - Class in org.intermine.web.struts
Controller for the submenu at the top of every page
SubMenuController() - Constructor for class org.intermine.web.struts.SubMenuController
 
submit(BagQueryRunner, JobInput) - Method in class org.intermine.api.idresolution.IDResolver
 
submit(BagQueryUpgrade) - Method in class org.intermine.api.idresolution.IDResolver
 
subquery - Variable in class org.intermine.objectstore.query.SubqueryConstraint
 
subquery - Variable in class org.intermine.objectstore.query.SubqueryExistsConstraint
 
subquery() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
subquery() - Method in class org.intermine.sql.query.SqlParser
 
subquery(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
SubQuery - Class in org.intermine.sql.query
A representation of a subquery that can be present in the FROM section of an SQL query.
SubQuery(Query, String) - Constructor for class org.intermine.sql.query.SubQuery
Constructor for this SubQuery object.
SUBQUERY - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SUBQUERY - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
subquery_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
subquery_constraint() - Method in class org.intermine.sql.query.SqlParser
 
subquery_constraint(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
SUBQUERY_CONSTRAINT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SUBQUERY_CONSTRAINT - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
subquery_exists_constraint() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
SUBQUERY_EXISTS_CONSTRAINT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
subquery_limit() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
SUBQUERY_LIMIT - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
SubqueryConstraint - Class in org.intermine.objectstore.query
Constrain a QueryClass or QueryEvaluable to be within the select list of a given subquery.
SubqueryConstraint(QueryClass, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint
Construct a SubqueryConstraint with a QueryClass
SubqueryConstraint(QueryEvaluable, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint
Construct a SubqueryConstraint with a QueryEvaluable
SubQueryConstraint - Class in org.intermine.sql.query
A representation of a constraint where an AbstractValue is IN the results of a Query.
SubQueryConstraint(AbstractValue, Query) - Constructor for class org.intermine.sql.query.SubQueryConstraint
Constructor for SubQueryConstraint object.
subqueryConstraintToString(SqlGenerator.State, StringBuffer, SubqueryConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a SubqueryConstraint object into a String suitable for putting in an SQL query.
SubqueryExistsConstraint - Class in org.intermine.objectstore.query
Check if there are any rows in the subquery
SubqueryExistsConstraint(ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryExistsConstraint
Construct a SubqueryExistsConstraint
subqueryExistsConstraintToString(SqlGenerator.State, StringBuffer, SubqueryExistsConstraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Converts a SubqueryExistsConstraint object into a String suitable for putting in an SQL query.
subscribe(String, Properties) - Static method in class org.intermine.util.MailUtils
Subscribe the given email address to the mailing list specified in the mine config file
subscribeToList(String) - Method in class org.intermine.util.Emailer
Subscribe a user to a mailing list.
subscribeToList(String) - Method in class org.intermine.web.context.NullMailer
 
subsegment(int, int) - Method in class org.intermine.webservice.server.jbrowse.Segment
 
subSequence - Variable in class org.intermine.objectstore.query.ClobAccess
 
subSequence(int, int) - Method in class org.intermine.model.StringConstructor
subSequence(int, int) - Method in class org.intermine.objectstore.query.ClobAccess
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).
subSequence(int, int) - Method in class org.intermine.objectstore.query.PendingClob
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to end (exclusive).
SUBSTR - Static variable in class org.intermine.sql.query.Function
SUBSTR operator - takes two or three operands.
SUBSTRING - Static variable in class org.intermine.objectstore.query.QueryExpression
Substring of specified length from index in string
SubTable - Class in org.intermine.webservice.server.core
A class that represents a table nested within a cell in another table.
SubTable(Path, List<Path>, List<List<Either<ResultCell, SubTable>>>) - Constructor for class org.intermine.webservice.server.core.SubTable
Construct a sub table.
subtabs - Variable in class org.intermine.web.logic.results.WebState
 
subtract(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
Create a bag that contains the union of the bags provided minus the intersection of those bags.
SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical substraction.
SUBTRACT - Static variable in class org.intermine.objectstore.query.QueryExpression
Subtraction of two numeric fields
SUBTRACT_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput
Things to subtract
SUCCESS - org.intermine.api.idresolution.Job.JobStatus
job has completed successfully
SUM - Static variable in class org.intermine.objectstore.query.QueryFunction
Sum of a number of rows
SUM - Static variable in class org.intermine.sql.query.Function
SUM(v) aggregate function - takes one operand.
summaries - Variable in class org.intermine.api.userprofile.SavedTemplateQuery
 
summarise(String) - Method in class org.intermine.dwr.AjaxServices
Summarises the given template query.
summarise(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
Populates the possibleValues data for a given TemplateQuery from the os.
summariseAsOccurrences(String) - Static method in class org.intermine.api.query.MainHelper.SummaryConfig
Returns whether the given field name is configured to be summarised as a count of occurrences.
SummariseObjectStoreTask - Class in org.intermine.task
Summarise an ObjectStore into a particular properties file.
SummariseObjectStoreTask() - Constructor for class org.intermine.task.SummariseObjectStoreTask
 
summariseQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
 
summariseQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Returns the results for a summary for a column in a PathQuery.
summariseQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
Summarise a query.
SummariseTemplatesAction - Class in org.intermine.web.struts
Action to summarise all templates.
SummariseTemplatesAction() - Constructor for class org.intermine.web.struts.SummariseTemplatesAction
 
summary - Variable in class org.intermine.api.userprofile.TemplateSummary
 
summaryBatchSize - Variable in class org.intermine.api.query.QueryExecutor
 
summaryCallCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
SummaryConstraint - Class in org.intermine.web.logic.querybuilder
Representation of a PathQuery constraint with additional information for display in the QueryBuilder summary section.
SummaryConstraint(PathConstraint, String, boolean, String, String) - Constructor for class org.intermine.web.logic.querybuilder.SummaryConstraint
Construct with the underlying PathConstraint and additional details from the PathQuery.
summaryCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
SummaryPath - Class in org.intermine.web.logic.querybuilder
Representation of a query path with additional information for display in the QueryBulder summary section.
SummaryPath(Path, boolean, boolean) - Constructor for class org.intermine.web.logic.querybuilder.SummaryPath
Construct a summary path with details of whether the path is locked and/or forced to be an inner join.
SummaryService - Class in org.intermine.webservice.server
Serve up the paths used to summarise each class.
SummaryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SummaryService
Constructor
SummaryServlet - Class in org.intermine.webservice.server
Returns a summary field information.
SummaryServlet() - Constructor for class org.intermine.webservice.server.SummaryServlet
 
summaryTimes - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
 
superuser - Variable in class org.intermine.api.userprofile.UserProfile
 
superUsers - Variable in class org.intermine.web.struts.ModifySuperUserForm
 
SURROUND - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
swapColumns(int, int) - Method in class org.intermine.web.logic.results.PagedTable
Deprecated.
Swap 2 columns
swapColumns(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
Deprecated.
as we don't move columns any more
switchable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
SwitchOffAbility - Enum in org.intermine.template
Enumeration for describing the configuration on constraints on a TemplateQuery that determines whether a user is allowed to switch off a constraint, and if so what state it is in.
SymmetricDifference - Class in org.intermine.api.bag.operations
 
SymmetricDifference(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.SymmetricDifference
 
SynchronisedIterator<E> - Class in org.intermine.util
An Iterator that passes through to an underlying Iterator, synchronising all calls.
SynchronisedIterator(Iterator<E>) - Constructor for class org.intermine.util.SynchronisedIterator
Constructs a SynchronisedIterator from an Iterator.
synchroniseWithDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
Synchronise with the underlying database
SystemTemplatesService - Class in org.intermine.webservice.server.template
Fetch the names of public template queries tagged with "im:converter" for use with the System Templates web service.
SystemTemplatesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.SystemTemplatesService
Constructor.

T

TabFormatter - Class in org.intermine.webservice.server.output
Formats data to tab separated data format.
TabFormatter() - Constructor for class org.intermine.webservice.server.output.TabFormatter
Constructor.
TabFormatter(boolean) - Constructor for class org.intermine.webservice.server.output.TabFormatter
Construct, specifying whether or not to quote.
TabHttpExporter - Class in org.intermine.web.logic.export.http
Exporter that exports table with results in tab format.
TabHttpExporter() - Constructor for class org.intermine.web.logic.export.http.TabHttpExporter
Constructor.
table - Variable in class org.intermine.sql.logging.DatabaseWriter
 
table - Variable in class org.intermine.sql.query.Field
 
table() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
table() - Method in class org.intermine.sql.query.SqlParser
 
table(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
Table - Class in org.intermine.sql.query
A representation of a table that can be present in the FROM section of an SQL query.
Table - Interface in org.intermine.sql.writebatch
An interface representing all changes to be made to an SQL table of some sort.
Table(String) - Constructor for class org.intermine.sql.query.Table
Constructor for this Table object, without an alias.
Table(String, String) - Constructor for class org.intermine.sql.query.Table
Constructor for this Table object.
TABLE - org.intermine.webservice.server.Format
JSON Table format constant
TABLE - org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
There is the table type, that produces boring tables of boring data.
TABLE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
TABLE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
table_alias() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
table_alias() - Method in class org.intermine.sql.query.SqlParser
 
table_alias(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
TABLE_ALIAS - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
TABLE_ALIAS - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
TABLE_INDEX - Static variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
TABLE_MAP - Static variable in class org.intermine.web.logic.Constants
Session attribute that holds cache of table identifiers to PagedTable objects.
table_name() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
table_name() - Method in class org.intermine.sql.query.SqlParser
 
table_name(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
TABLE_NAME - Static variable in class org.intermine.api.bag.SharingInvite
The DB table that holds the invitations
TABLE_NAME - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
TABLE_NAME - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
TableBatch - Class in org.intermine.sql.writebatch
A class representing all changes to be made to an SQL table.
TableBatch() - Constructor for class org.intermine.sql.writebatch.TableBatch
Constructor for this class.
TableCell - Class in org.intermine.webservice.server.core
A representation of a table cell.
TableCell(FastPathObject, Path, boolean) - Constructor for class org.intermine.webservice.server.core.TableCell
Construct a table cell.
TableCell(Path) - Constructor for class org.intermine.webservice.server.core.TableCell
Construct a table cell for a null value.
TableCellFormatter - Class in org.intermine.webservice.server.output
A formatter that will render a table cell.
TableCellFormatter(InterMineAPI) - Constructor for class org.intermine.webservice.server.output.TableCellFormatter
 
TableController - Class in org.intermine.web.struts
Implementation of TilesAction.
TableController() - Constructor for class org.intermine.web.struts.TableController
 
tableCount - Variable in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
 
tableExists(Connection, String) - Static method in class org.intermine.sql.DatabaseUtil
Tests if a table exists in the database
TableExportAction - Class in org.intermine.web.struts
Implementation of Action that allows the user to export a PagedTable to a file.
TableExportAction() - Constructor for class org.intermine.web.struts.TableExportAction
 
TableExportConfig - Class in org.intermine.web.logic.config
Configuration information for exporting.
TableExportConfig() - Constructor for class org.intermine.web.logic.config.TableExportConfig
 
TableExporterFactory - Class in org.intermine.web.logic.export.http
Factory class that creates and registers TableHttpExporter classes.
TableExporterFactory(WebConfig) - Constructor for class org.intermine.web.logic.export.http.TableExporterFactory
Constructor.
TableExportForm - Class in org.intermine.web.struts
Form to hold options for exporting.
TableExportForm() - Constructor for class org.intermine.web.struts.TableExportForm
Constructor
TableHttpExporter - Interface in org.intermine.web.logic.export.http
Implemented by objects that can export PagedTable.
TableJSONProcessor - Class in org.intermine.webservice.server.widget
Class to process the result returned by a table widgets in JSON format
TableJSONProcessor() - Constructor for class org.intermine.webservice.server.widget.TableJSONProcessor
 
tableNameForId(Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns the table name used by the ID fetch query.
tablenamesCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
 
TableRowIterator - Class in org.intermine.webservice.server.core
A class for iterating over rows of results returned from the object store in a way that is very similar in shape to the raw results, but more tractable and more easily serialised and handled in other places.
TableRowIterator(PathQuery, Query, Results, Map<String, QuerySelectable>, Page, InterMineAPI) - Constructor for class org.intermine.webservice.server.core.TableRowIterator
Constructor.
TableRowService - Class in org.intermine.webservice.server.query.result
A service that produces results in nested rows for use in tables.
TableRowService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.result.TableRowService
 
tablesAltered - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
TableTag - Class in org.intermine.web.tags.table
Class rendering html table.
TableTag() - Constructor for class org.intermine.web.tags.table.TableTag
 
tableToCollections - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
tableToColNameArray - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
tableToInfo - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
 
TableWidget - Class in org.intermine.web.logic.widget
A table widget gets the values for a given path for all the items in a list.
TableWidget(TableWidgetConfig, InterMineBag, ObjectStore, String) - Constructor for class org.intermine.web.logic.widget.TableWidget
 
TableWidgetConfig - Class in org.intermine.web.logic.widget.config
 
TableWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.TableWidgetConfig
 
TableWidgetLdr - Class in org.intermine.web.logic.widget
 
TableWidgetLdr(WidgetConfig, InterMineBag, ObjectStore, String) - Constructor for class org.intermine.web.logic.widget.TableWidgetLdr
This class loads and formats the data for the count table widgets in the bag details page
TableWidgetService - Class in org.intermine.webservice.server.widget
Web service that returns a table widget for a given list.
TableWidgetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.TableWidgetService
Construct a TableWidgetService
TableWidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet running WidgetsService.
TableWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.TableWidgetsServlet
 
TableXMLProcessor - Class in org.intermine.webservice.server.widget
Class to process the result returned by a table widgets into a XML format
TabRowFormatter - Class in org.intermine.web.logic.export.rowformatters
Row formatter formats line as tab separated strings.
TabRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.TabRowFormatter
Constructor.
Tag - Class in org.intermine.api.userprofile
 
Tag() - Constructor for class org.intermine.api.userprofile.Tag
 
TagBinding - Class in org.intermine.api.xml
Convert Tags from the Profile to and from XML
TagBinding() - Constructor for class org.intermine.api.xml.TagBinding
 
TagChecker - Interface in org.intermine.api.profile
An interface for checking the validity of tags.
TagException(String) - Constructor for exception org.intermine.api.profile.TagManager.TagException
Constructor.
TagFilter - Class in org.intermine.api.search
Class for filtering web-searchables based on their tags.
TagFilter(Collection<String>, Profile, String) - Constructor for class org.intermine.api.search.TagFilter
Constructor
Taggable - Interface in org.intermine.api.profile
An interface for items that may have tags stored for them in the user profile database.
TaggingEvent - Class in org.intermine.api.search
A representation of a notification that a tag has been changed on a web-searchable item.
TaggingEvent(WebSearchable, String, TaggingEvent.TagChange) - Constructor for class org.intermine.api.search.TaggingEvent
Constructor.
TaggingEvent.TagChange - Enum in org.intermine.api.search
The possible actions that this event can represent.
TagHandler - Class in org.intermine.api.profile
Extension of PathQueryHandler to handle parsing TemplateQueries
TagHandler(String, Set) - Constructor for class org.intermine.api.profile.TagHandler
Constructor
TagHandler(ProfileManager, String) - Constructor for class org.intermine.api.profile.TagHandler
Constructor
tagManager - Variable in class org.intermine.api.search.SearchRepository
 
TagManager - Class in org.intermine.api.profile
Manager class for tags.
TagManager(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.TagManager
Constructor.
TagManager.TagException - Exception in org.intermine.api.profile
Class for reporting exceptions from tag manipulation actions.
TagManager.TagNameException - Exception in org.intermine.api.profile
Class for representing errors due to the use of illegal tag names.
TagManager.TagNamePermissionException - Exception in org.intermine.api.profile
Class for representing errors due to the restricted nature of some tags.
TagManagerFactory - Class in org.intermine.api.profile
Factory class for creating TagManager objects.
TagManagerFactory(ProfileManager) - Constructor for class org.intermine.api.profile.TagManagerFactory
Constructor.
TagManagerFactory(ObjectStoreWriter) - Constructor for class org.intermine.api.profile.TagManagerFactory
Constructor.
TagMapper - Class in org.intermine.api.profile
A class that handles transforming a list of tags into a list of strings of different types.
TagMapper.Field - Enum in org.intermine.api.profile
The valid fields that can be read from a tag
tagName - Variable in class org.intermine.api.search.TaggingEvent
 
tagName - Variable in class org.intermine.api.userprofile.Tag
 
TagNameException() - Constructor for exception org.intermine.api.profile.TagManager.TagNameException
Constructor.
TagNamePermissionException() - Constructor for exception org.intermine.api.profile.TagManager.TagNamePermissionException
Constructor.
TagNamePermissionException(String) - Constructor for exception org.intermine.api.profile.TagManager.TagNamePermissionException
Constructor.
TagNames - Class in org.intermine.api.tag
 
tags - Variable in class org.intermine.api.userprofile.UserProfile
 
TAGS_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
Tags to apply
TagTypes - Class in org.intermine.api.tag
Known tag types.
TEMP_SUFFIX - Static variable in class org.intermine.webservice.server.lists.ListInput
A suffix to attach to temporary lists
template - Variable in class org.intermine.api.userprofile.TemplateSummary
 
TEMPLATE - Static variable in class org.intermine.api.tag.TagTypes
Template.
TEMPLATE_ACTION_PATH - Static variable in class org.intermine.web.struts.TemplateAction
path of TemplateAction action
TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
TEMPLATE_BAG_CONSTRAINT - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
TEMPLATE_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of class that tracks templates
TEMPLATE_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
name of table that tracks templates
TemplateAction - Class in org.intermine.web.struts
Action to handle submit from the template page.
TemplateAction() - Constructor for class org.intermine.web.struts.TemplateAction
 
templateButton - Variable in class org.intermine.web.struts.ModifyTemplateForm
 
TemplateComparator - Class in org.intermine.template
Comparator used for ordering templates by title
TemplateComparator() - Constructor for class org.intermine.template.TemplateComparator
 
TemplateController - Class in org.intermine.web.struts
Controller for the template tile.
TemplateController() - Constructor for class org.intermine.web.struts.TemplateController
 
templateExecutions - Variable in class org.intermine.api.tracker.TemplatesExecutionMap
 
TemplateForm - Class in org.intermine.web.struts
Form to handle input from the template page
TemplateForm() - Constructor for class org.intermine.web.struts.TemplateForm
Constructor
templateFormToTemplateValues(TemplateForm, TemplateQuery) - Method in class org.intermine.web.struts.TemplateAction
The method returns a map of TemplateValue for each editable constraint.
TemplateHelper - Class in org.intermine.api.template
Static helper routines related to templates.
templateIsPublic(TemplateQuery, InterMineAPI, Profile) - Static method in class org.intermine.web.struts.WebserviceCodeGenAction
Utility function to determine whether the template is publicly accessible.
templateLabel - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
TemplateListAppendService - Class in org.intermine.webservice.server.template
A class to append items from a set of template results to a list.
TemplateListAppendService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateListAppendService
Constructor.
TemplateListAppendServlet - Class in org.intermine.webservice.server.template
Runs the query-to-list service to run queries and save them as lists.
TemplateListAppendServlet() - Constructor for class org.intermine.webservice.server.template.TemplateListAppendServlet
 
TemplateListController - Class in org.intermine.web.struts
Controller for the template list tile.
TemplateListController() - Constructor for class org.intermine.web.struts.TemplateListController
 
templateManager - Variable in class org.intermine.api.InterMineAPI
 
TemplateManager - Class in org.intermine.api.template
A TemplateManager provides access to all global and/or user templates and methods to fetch them by type, etc.
TemplateManager(Profile) - Constructor for class org.intermine.api.template.TemplateManager
The TemplateManager references the super user profile to fetch global templates.
TemplateManager(Profile, TemplateTracker) - Constructor for class org.intermine.api.template.TemplateManager
The TemplateManager references the super user profile to fetch global templates.
templateMapToXml(Map<String, TemplateQuery>, int) - Static method in class org.intermine.api.template.TemplateHelper
Given a Map of TemplateQueries (mapping from template name to TemplateQuery) return a string containing each template seriaised as XML.
TemplatePopulator - Class in org.intermine.api.template
Configures original template.
TemplatePopulatorException - Exception in org.intermine.template
Exception thrown when errors occur populating a template query with values.
TemplatePopulatorException(String) - Constructor for exception org.intermine.template.TemplatePopulatorException
Constructs an TemplatePopulatorException with the specified detail message.
TemplatePopulatorException(String, Throwable) - Constructor for exception org.intermine.template.TemplatePopulatorException
Constructs an TemplatePopulatorException with the specified detail message and nested throwable.
TemplatePopulatorException(Throwable) - Constructor for exception org.intermine.template.TemplatePopulatorException
Constructs an TemplatePopulatorException with the specified nested throwable.
TemplatePrecomputeHelper - Class in org.intermine.api.template
Helper class providing methods for precomputing and summarising TemplateQuery objects.
TemplateProblemsController - Class in org.intermine.web.struts
Called before templateProblems.jsp
TemplateProblemsController() - Constructor for class org.intermine.web.struts.TemplateProblemsController
 
templateQuery - Variable in class org.intermine.api.userprofile.SavedTemplateQuery
 
TemplateQuery - Class in org.intermine.template
A template query, which consists of a PathQuery, description, category, short name.
TemplateQuery(String, String, String, PathQuery) - Constructor for class org.intermine.template.TemplateQuery
Construct a new instance of TemplateQuery.
TemplateQuery(TemplateQuery) - Constructor for class org.intermine.template.TemplateQuery
Copy constructor.
TemplateQueryBinding - Class in org.intermine.template.xml
Convert PathQueries to and from XML
TemplateQueryBinding() - Constructor for class org.intermine.template.xml.TemplateQueryBinding
 
TemplateQueryHandler - Class in org.intermine.template.xml
Extension of PathQueryHandler to handle parsing TemplateQueries
TemplateQueryHandler(Map<String, TemplateQuery>, int) - Constructor for class org.intermine.template.xml.TemplateQueryHandler
Constructor
TemplateQueryUpdate - Class in org.intermine.api.profile
A class to update template queries to match a new Data model.
TemplateQueryUpdate(ApiTemplate, Model) - Constructor for class org.intermine.api.profile.TemplateQueryUpdate
Constructor.
TemplateRemovalService - Class in org.intermine.webservice.server.template
A service that deletes templates.
TemplateRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateRemovalService
 
TemplateResultInput - Class in org.intermine.web.logic.template
TemplateResultInput is parameter object representing parameters for TemplateResultService web service.
TemplateResultInput() - Constructor for class org.intermine.web.logic.template.TemplateResultInput
 
TemplateResultLinkGenerator - Class in org.intermine.webservice.server.template.result
Class that implements generating links of TemplateResultService web service.
TemplateResultLinkGenerator() - Constructor for class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
 
TemplateResultRequestParser - Class in org.intermine.webservice.server.template.result
Processes service request.
TemplateResultRequestParser(HttpServletRequest) - Constructor for class org.intermine.webservice.server.template.result.TemplateResultRequestParser
TemplateResultRequestProcessor constructor.
TemplateResultService - Class in org.intermine.webservice.server.template.result
Web service that returns results of public template constrained with values in request.
TemplateResultService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.result.TemplateResultService
Construct with an InterMineAPI.
TemplateResultServlet - Class in org.intermine.webservice.server.template.result
Runs TemplateResultService web service.
TemplateResultServlet() - Constructor for class org.intermine.webservice.server.template.result.TemplateResultServlet
 
Templates - Class in org.intermine.web.logic.template
A utility class with static methods for dealing with templates.
TEMPLATES_PARAMETER - Static variable in class org.intermine.webservice.server.template.TemplateUploadService
The key for the templates parameter
Templates.TemplateValueParseException - Exception in org.intermine.web.logic.template
An exception that we throw when we can't parse a template.
TemplatesController - Class in org.intermine.web.struts
Tiles controller for templates tile (page).
TemplatesController() - Constructor for class org.intermine.web.struts.TemplatesController
 
TemplateSettingsForm - Class in org.intermine.web.struts
Form used when building a template.
TemplateSettingsForm() - Constructor for class org.intermine.web.struts.TemplateSettingsForm
 
TemplatesExecutionMap - Class in org.intermine.api.tracker
Class for saving the template executions into the memory.
TemplatesExecutionMap() - Constructor for class org.intermine.api.tracker.TemplatesExecutionMap
 
TemplatesExportAction - Class in org.intermine.web.struts
Exports templates to XML.
TemplatesExportAction() - Constructor for class org.intermine.web.struts.TemplatesExportAction
 
TemplatesImportAction - Class in org.intermine.web.struts
Imports templates in XML format.
TemplatesImportAction() - Constructor for class org.intermine.web.struts.TemplatesImportAction
 
TemplatesImportForm - Class in org.intermine.web.struts
Form bean representing template import form.
TemplatesImportForm() - Constructor for class org.intermine.web.struts.TemplatesImportForm
 
templateSummariser - Variable in class org.intermine.api.InterMineAPI
 
TemplateSummariser - Class in org.intermine.api.template
This class manages summaries of possible values for editable constraints for template queries.
TemplateSummariser(ObjectStore, ObjectStoreWriter, ObjectStoreSummary) - Constructor for class org.intermine.api.template.TemplateSummariser
Construct a TemplateSummariser.
TemplateSummary - Class in org.intermine.api.userprofile
 
TemplateSummary() - Constructor for class org.intermine.api.userprofile.TemplateSummary
 
TemplateTagAddingService - Class in org.intermine.webservice.server.template
A service for adding tags to a template.
TemplateTagAddingService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateTagAddingService
Constructor.
TemplateTagRemovalService - Class in org.intermine.webservice.server.template
A service for removing tags from a template.
TemplateTagRemovalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateTagRemovalService
Constructor.
TemplateTagService - Class in org.intermine.webservice.server.template
A service for getting the tags of a template.
TemplateTagService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateTagService
Constructor.
TemplateToListService - Class in org.intermine.webservice.server.template
A service for turning the results of a template query into a list.
TemplateToListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateToListService
Constructor
TemplateToListServlet - Class in org.intermine.webservice.server.template
Runs the template-to-list service to run templates and save them as lists.
TemplateToListServlet() - Constructor for class org.intermine.webservice.server.template.TemplateToListServlet
 
TemplateTrack - Class in org.intermine.api.tracker.track
Class to represent the track for the templates objects.
TemplateTrack(String, String, String) - Constructor for class org.intermine.api.tracker.track.TemplateTrack
Create a template track
TemplateTrack(String, String, String, Timestamp) - Constructor for class org.intermine.api.tracker.track.TemplateTrack
Create a template track
TEMPLATETRACK - Static variable in class org.intermine.api.tracker.xml.TemplateTrackBinding
label for XML
TemplateTrackBinding - Class in org.intermine.api.tracker.xml
Code for reading and writing template tracks as XML.
TemplateTracker - Class in org.intermine.api.tracker
Class for tracking the templates execution by the users.
TemplateTracker(Queue<Track>) - Constructor for class org.intermine.api.tracker.TemplateTracker
 
TemplateTrackReadTask - Class in org.intermine.web.task
Task to read an templatetrack XML file of a webapp and saved into the userprofile database.
TemplateTrackReadTask() - Constructor for class org.intermine.web.task.TemplateTrackReadTask
 
TEMPLATETRACKS - Static variable in class org.intermine.api.tracker.xml.TemplateTrackBinding
label for XML
TemplateTrackWriteTask - Class in org.intermine.web.task
Task to write an XML file of template track contained in the user profile database.
TemplateTrackWriteTask() - Constructor for class org.intermine.web.task.TemplateTrackWriteTask
 
TemplateUploadService - Class in org.intermine.webservice.server.template
A service to enable templates to be uploaded.
TemplateUploadService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.TemplateUploadService
Constructor.
TemplateUploadServlet - Class in org.intermine.webservice.server.template
Runs the Template Upload Service to handle user template uploads.
TemplateUploadServlet() - Constructor for class org.intermine.webservice.server.template.TemplateUploadServlet
 
TemplateValue - Class in org.intermine.template
A TemplateValue represents the value for an editable constraint of a template query and details about what is being constrained.
TemplateValue(PathConstraint, ConstraintOp, String, TemplateValue.ValueType, String, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Construct with the details of what we are constraining and the value.
TemplateValue(PathConstraint, ConstraintOp, String, TemplateValue.ValueType, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Construct with the details of what we are constraining and the value.
TemplateValue(PathConstraint, ConstraintOp, TemplateValue.ValueType, List<String>, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Construct with the details of what we are constraining and values.
TemplateValue(PathConstraint, ConstraintOp, TemplateValue.ValueType, SwitchOffAbility) - Constructor for class org.intermine.template.TemplateValue
Constructor.Construct with details of what we are constraining, but without the value.
TemplateValue.ValueType - Enum in org.intermine.template
Possible values for TemplateValue type.
TemplateValueParseException(String) - Constructor for exception org.intermine.web.logic.template.Templates.TemplateValueParseException
Construct an exception with a message
TEN - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
TEN_THOUSAND - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
terseClass(String) - Static method in class org.intermine.metadata.ClassDescriptor
Strips everything before the last dot out of a String.
TEST_STRING - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
text - org.intermine.sql.DatabaseUtil.Type
text
TEXT - org.intermine.webservice.server.Format
Plain Text
TextTable - Class in org.intermine.metadata
A utility class for generating multi-column aligned text tables.
TextTable(boolean, boolean, boolean) - Constructor for class org.intermine.metadata.TextTable
Creates a new TextTable object, with or without column separating lines.
TextUtil - Class in org.intermine.api.util
 
then(Function<T, R>) - Method in class org.intermine.webservice.server.core.EitherVisitor
Compose this visitor with a function which consumes the output of this visitor.
thing() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
THOUSAND - Static variable in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
 
THREAD_COUNT - Static variable in class org.intermine.task.PrecomputeTask
 
throwBestQueryException(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
Throws an exception.
throwBestQueryException(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
Throws an exception.
tickle() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
Tell this object to continue returning false from shouldCancelQuery.
tickleCount - Variable in class org.intermine.web.logic.query.QueryMonitorTimeout
number of tickles.
time - Variable in class org.intermine.dataconversion.FullXmlConverter
 
timeLimit - Variable in class org.intermine.sql.precompute.BestQueryExplainer
 
times - Variable in class org.intermine.dataconversion.FullXmlConverter
 
timeSpentExecute - Variable in class org.intermine.dataloader.BatchingFetcher
 
timeSpentPrefetchEquiv - Variable in class org.intermine.dataloader.BatchingFetcher
 
timeSpentPrefetchTracker - Variable in class org.intermine.dataloader.BatchingFetcher
 
timeSpentRecursing - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
 
timestamp - org.intermine.sql.DatabaseUtil.Type
timestampe
timestamp - Variable in class org.intermine.api.tracker.track.TrackAbstract
 
TO_UPGRADE - org.intermine.api.profile.BagState
 
toAdditionsXML() - Method in class org.intermine.metadata.Model
Used to generate the SO additions file
toArray() - Method in class org.intermine.util.PseudoSet
toArray(T[]) - Method in class org.intermine.util.PseudoSet
toIntegers(Collection<String>) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Convert a set of Strings to a set of Integers using identifierToId()
toItems(Collection<FastPathObject>, Model) - Static method in class org.intermine.xml.full.FullRenderer
Convert a collection of Objects to Item format.
toJson() - Method in class org.intermine.pathquery.PathQuery
Convert this PathQuery to a JSON serialisation.
toJson(boolean) - Method in class org.intermine.pathquery.PathQuery
Convert this PathQuery to a JSON serialisation.
toJson(boolean, Date) - Method in class org.intermine.pathquery.PathQuery
Convert this PathQuery to a JSON serialisation.
toJson(Date) - Method in class org.intermine.pathquery.PathQuery
Convert this PathQuery to a JSON serialisation.
toJSON() - Method in class org.intermine.template.TemplateQuery
Returns a JSON string representation of the template query.
toJSON(ResultCell) - Method in class org.intermine.webservice.server.output.TableCellFormatter
Get the JSONObject that represents each cell in the results row
toJsonAST() - Method in class org.intermine.metadata.Model
Returns a data structure suitable for serialisation, eg.
toJSONString() - Method in class org.intermine.metadata.AttributeDescriptor
Return the JSON representation of this object.
toJSONString() - Method in class org.intermine.metadata.ClassDescriptor
 
toJSONString() - Method in class org.intermine.metadata.FieldDescriptor
Return the JSON representation of this object.
toJSONString() - Method in class org.intermine.metadata.ReferenceDescriptor
Return the JSON representation of this object.
token - Variable in class org.intermine.api.userprofile.PermanentToken
 
token - Variable in class org.intermine.web.struts.PasswordResetForm
 
tokenFactory - Variable in class org.intermine.webservice.server.user.NewDeletionTokenService
 
tokenHasMoreUses(String) - Method in class org.intermine.api.profile.ProfileManager
Return whether the token given in input is suitable for using in the future.
tokenise(String) - Method in class org.intermine.api.query.LookupTokeniser
Transform an input string into a list of identifiers.
tokenize(String) - Static method in class org.intermine.metadata.StringUtil
Returns a list of tokens delimited by whitespace in String str (useful when handling XML)
tokenize(String) - Static method in class org.intermine.metadata.Util
Returns a list of tokens delimited by whitespace in String str (useful when handling XML)
tokenize(String, boolean) - Static method in class org.intermine.metadata.StringUtil
Returns a list of tokens delimited by comma.
tokenize(String, String) - Static method in class org.intermine.metadata.StringUtil
 
TokenService - Class in org.intermine.webservice.server.user
A service that issues new tokens to a user.
TokenService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.TokenService
 
TokenServlet - Class in org.intermine.webservice.server.user
 
TokenServlet() - Constructor for class org.intermine.webservice.server.user.TokenServlet
 
TokensService - Class in org.intermine.webservice.server.user
Service that lets a user inspect their currently active tokens
TokensService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.TokensService
 
toMap(ResultCell) - Method in class org.intermine.webservice.server.output.TableCellFormatter
 
toProperties() - Method in class org.intermine.objectstore.ObjectStoreSummary
Convert this summary to a properties object
toQuery() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Convert to a InterMine query
toRangeString() - Method in class org.intermine.webservice.server.jbrowse.Segment
 
TorqueModelOutput - Class in org.intermine.objectstore.intermine
Map InterMine metadata to a Torque database schema in InterMine format
TorqueModelOutput(DatabaseSchema, File) - Constructor for class org.intermine.objectstore.intermine.TorqueModelOutput
Constructor for this class
TorqueModelOutputTask - Class in org.intermine.objectstore.intermine
Creates and runs a ModelOutput process to generate java or config files.
TorqueModelOutputTask() - Constructor for class org.intermine.objectstore.intermine.TorqueModelOutputTask
 
toSameInitialCase(String, String) - Static method in class org.intermine.metadata.StringUtil
Returns a string with the same initial letter case as the template string
toString() - Method in class org.intermine.api.bag.BagQuery
toString() - Method in class org.intermine.api.bag.SharingInvite
 
toString() - Method in class org.intermine.api.beans.ObjectDetails
 
toString() - Method in class org.intermine.api.beans.PartnerLink
 
toString() - Method in class org.intermine.api.idresolution.ResolutionJob
 
toString() - Method in class org.intermine.api.mines.ObjectRequest
 
toString() - Method in class org.intermine.api.profile.BagValue
 
toString() - Method in class org.intermine.api.profile.InterMineBag
 
toString() - Method in class org.intermine.api.results.Column
toString() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
toString() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
toString() - Method in class org.intermine.api.results.ResultElement
Returns a String representation of the ResultElement.
toString() - Method in class org.intermine.api.search.SearchResult
 
toString() - Method in class org.intermine.api.search.SearchTarget
 
toString() - Method in class org.intermine.api.userprofile.PermanentToken
 
toString() - Method in class org.intermine.api.userprofile.SavedBag
 
toString() - Method in class org.intermine.api.userprofile.SavedQuery
 
toString() - Method in class org.intermine.api.userprofile.SavedTemplateQuery
 
toString() - Method in class org.intermine.api.userprofile.Tag
 
toString() - Method in class org.intermine.api.userprofile.TemplateSummary
 
toString() - Method in class org.intermine.api.userprofile.UserProfile
 
toString() - Method in class org.intermine.dataconversion.MockItemWriter
toString() - Method in class org.intermine.dataloader.Source
toString() - Method in class org.intermine.metadata.AttributeDescriptor
toString() - Method in class org.intermine.metadata.ClassDescriptor
toString() - Method in class org.intermine.metadata.CollectionDescriptor
toString() - Method in class org.intermine.metadata.ConstraintOp
Get the String representation of this ConstraintOp
toString() - Method in class org.intermine.metadata.Model
toString() - Method in class org.intermine.metadata.PrimaryKey
toString() - Method in class org.intermine.metadata.ReferenceDescriptor
toString() - Method in class org.intermine.metadata.TextTable
Returns a text-formatted representation of this table.
toString() - Method in class org.intermine.model.fulldata.Attribute
 
toString() - Method in class org.intermine.model.fulldata.Item
 
toString() - Method in class org.intermine.model.fulldata.Reference
 
toString() - Method in class org.intermine.model.fulldata.ReferenceList
 
toString() - Method in class org.intermine.model.StringConstructor
Returns the String that this object represents - note that this method should be avoided, because it defeats the purpose of keeping the constituent Strings separate in the first place.
toString() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.BagTableToRemove
Returns the SQL statement that will drop the table.
toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
toString() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
toString() - Method in class org.intermine.objectstore.proxy.ProxyCollection
We override this here in order to prevent possible infinite recursion.
toString() - Method in class org.intermine.objectstore.proxy.ProxyReference
toString() - Method in class org.intermine.objectstore.query.ClobAccess
Converts the Clob into a String.
toString() - Method in class org.intermine.objectstore.query.ConstraintSet
toString() - Method in class org.intermine.objectstore.query.ContainsConstraint
toString() - Method in class org.intermine.objectstore.query.iql.IqlQuery
Return a string version of the IqlQuery
toString() - Method in class org.intermine.objectstore.query.OverlapConstraint
toString() - Method in class org.intermine.objectstore.query.OverlapRange
toString() - Method in class org.intermine.objectstore.query.PendingClob
Converts the Clob into a String.
toString() - Method in class org.intermine.objectstore.query.Query
Returns a string representation of this Query object
toString() - Method in class org.intermine.objectstore.query.QueryClass
Returns a String representation.
toString() - Method in class org.intermine.objectstore.query.QueryClassBag
Returns a String representation.
toString() - Method in class org.intermine.objectstore.query.QueryField
Produces a String, for debugging purposes.
toString() - Method in class org.intermine.objectstore.query.QueryObjectReference
toString() - Method in class org.intermine.objectstore.query.QueryValue
toString() - Method in class org.intermine.objectstore.query.Results
 
toString() - Method in class org.intermine.objectstore.query.ResultsInfo
toString() - Method in class org.intermine.objectstore.query.SimpleConstraint
toString() - Method in class org.intermine.objectstore.query.UnknownTypeValue
toString() - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
toString() - Method in class org.intermine.pathquery.LogicExpression.Operator
Produce an expression for this branch of the tree.
toString() - Method in class org.intermine.pathquery.LogicExpression
Get the expression as a string.
toString() - Method in class org.intermine.pathquery.LogicExpression.Variable
Just returns the variable name.
toString() - Method in class org.intermine.pathquery.Node
toString() - Method in class org.intermine.pathquery.OrderElement
toString() - Method in class org.intermine.pathquery.Path
Returns a representation of the Path as a String, with class constraint markers.
toString() - Method in class org.intermine.pathquery.PathConstraintAttribute
toString() - Method in class org.intermine.pathquery.PathConstraintBag
toString() - Method in class org.intermine.pathquery.PathConstraintIds
toString() - Method in class org.intermine.pathquery.PathConstraintLookup
toString() - Method in class org.intermine.pathquery.PathConstraintLoop
toString() - Method in class org.intermine.pathquery.PathConstraintMultiValue
toString() - Method in class org.intermine.pathquery.PathConstraintNull
toString() - Method in class org.intermine.pathquery.PathConstraintSubclass
toString() - Method in class org.intermine.pathquery.PathQuery
Converts this object into a rudimentary String format, containing all the data.
toString() - Method in class org.intermine.sql.Database
toString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
toString() - Method in class org.intermine.sql.precompute.PrecomputedTable
toString() - Method in class org.intermine.sql.query.Constant
toString() - Method in class org.intermine.sql.query.Constraint
toString() - Method in class org.intermine.sql.query.ExplainResult
toString() - Method in class org.intermine.sql.query.OrderDescending
toString() - Method in class org.intermine.sql.query.Query
Overrides Object.toString().
toString() - Method in class org.intermine.sql.query.Table
A toString method, which helps us when debugging.
toString() - Method in class org.intermine.template.TemplateQuery
 
toString() - Method in class org.intermine.template.TemplateValue
toString() - Method in class org.intermine.util.AlwaysSet
toString() - Method in class org.intermine.util.IntPresentSet
toString() - Method in class org.intermine.util.IntToIntMap
toString() - Method in class org.intermine.util.ReferenceMap
toString() - Method in class org.intermine.web.logic.config.Displayer
Return an XML String of this Type object
toString() - Method in class org.intermine.web.logic.config.FieldConfig
toString() - Method in class org.intermine.web.logic.config.TableExportConfig
toString() - Method in class org.intermine.web.logic.config.Type
Return an XML String of this Type object
toString() - Method in class org.intermine.web.logic.config.WebConfig
Return an XML String of this WebConfig object
toString() - Method in class org.intermine.web.logic.query.MetadataNode
toString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
Returns a representation of the Path as a String, with class constraint markers.
toString() - Method in class org.intermine.web.logic.results.InlineList
toString() - Method in class org.intermine.web.logic.template.ConstraintInput
 
toString() - Method in class org.intermine.web.logic.TreeNode
toString() - Method in class org.intermine.web.logic.WebUtil.HeadResource
 
toString() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
Return an XML String of this Type object
toString() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
Return an XML String of this Type object
toString() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
 
toString() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
 
toString() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
toString() - Method in class org.intermine.web.tags.table.NavigationBarTag
 
toString() - Method in class org.intermine.web.uri.InterMineLUI
Returns the String which represents the InterMineLUI -> className:identifier
toString() - Method in class org.intermine.webservice.server.core.Either.Left
 
toString() - Method in class org.intermine.webservice.server.core.Either.Right
 
toString() - Method in class org.intermine.webservice.server.core.Pair
 
toString() - Method in class org.intermine.webservice.server.core.SubTable
 
toString() - Method in class org.intermine.webservice.server.core.TableCell
 
toString() - Method in enum org.intermine.webservice.server.Format
 
toString() - Method in class org.intermine.webservice.server.JWTBuilder
 
toString() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
toString() - Method in class org.intermine.xml.full.Item
toString(String) - Method in class org.intermine.web.logic.config.Displayer
Return an XML String of this Type object
toStringNoConstraints() - Method in class org.intermine.pathquery.Path
Returns a representation of the Path as a String, with no class constraint markers.
toStrings(Collection<Integer>) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Convert a set of Integers to a set of String using idToIdentifier()
toStrings(List<Object>) - Method in class org.intermine.pathquery.PathQueryHandler
Convert a List of Objects to a List of Strings using toString
toStringTruncateParameters(int) - Method in class org.intermine.objectstore.query.iql.IqlQuery
Return a string version of the IqlQuery but truncated the parameters (lists of bag contents) to the specified length.
TOTAL - org.intermine.web.logic.widget.GraphWidgetActionType
 
toXml() - Method in class org.intermine.pathquery.PathQuery
Convert a PathQuery to XML, using the default value of PathQuery.USERPROFILE_VERSION
toXml(int) - Method in class org.intermine.pathquery.PathQuery
Convert a PathQuery to XML.
toXml(int) - Method in class org.intermine.template.TemplateQuery
Convert a template query to XML.
TRAC_TICKET_URL_PREFIX - Static variable in class org.intermine.task.AcceptanceTestTask
Prefix of the ticket pages in Trac.
Track - Interface in org.intermine.api.tracker.track
Class representing the track
TrackAbstract - Class in org.intermine.api.tracker.track
Class representing the track
TrackAbstract() - Constructor for class org.intermine.api.tracker.track.TrackAbstract
 
TrackAjaxServices - Class in org.intermine.dwr
 
TrackAjaxServices() - Constructor for class org.intermine.dwr.TrackAjaxServices
Construct a ajax services object that does tracking stuff.
Tracker - Interface in org.intermine.api.tracker
Interface to represent a Tracker, an object tracking the users activities in the webapp into the database
trackerDelegate - Variable in class org.intermine.api.InterMineAPI
 
TrackerDelegate - Class in org.intermine.api.tracker
Intermediate class which decouples the tracker components from the code that uses them.
TrackerDelegate(String[], ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.TrackerDelegate
Create the tracker manager managing the trackers specified in input
TrackerFactory - Class in org.intermine.api.tracker.factory
Factory to instantiate the trackers with the reflection
trackerLogger - Variable in class org.intermine.api.tracker.AbstractTracker
 
TrackerLogger - Class in org.intermine.api.tracker
Runnable object providing insertion into the database.
TrackerLogger(Connection, Queue<Track>) - Constructor for class org.intermine.api.tracker.TrackerLogger
Construct a TrackerLogger for a specific connection and table
trackerLoggerThread - Variable in class org.intermine.api.tracker.TrackerDelegate
 
trackerMissingClasses - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
 
trackers - Variable in class org.intermine.api.tracker.TrackerDelegate
 
TrackerUtil - Class in org.intermine.api.tracker.util
 
TrackHandler - Class in org.intermine.api.tracker.xml
 
TrackHandler(ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.xml.TrackHandler
 
trackKeywordSearch(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the login event
trackList(String, int, ListBuildMode, ListTrackerEvent, Profile, String) - Method in class org.intermine.api.tracker.ListTracker
 
trackListCreation(String, int, ListBuildMode, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the list creation
trackListExecution(String, int, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the list execution
trackLogin(String) - Method in class org.intermine.api.tracker.LoginTracker
Track when the user logs in his account
trackLogin(String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the login event
TrackManagerBinding - Class in org.intermine.api.tracker.xml
Code for reading and writing all tracks objects as XML
TrackManagerHandler - Class in org.intermine.api.tracker.xml
Event handler for the track xml file
TrackManagerHandler(ObjectStoreWriter) - Constructor for class org.intermine.api.tracker.xml.TrackManagerHandler
Create a new TrackHandler
trackQuery(String, Profile, String) - Method in class org.intermine.api.tracker.QueryTracker
 
trackQuery(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the execution of a query (saved or temporary)
trackQueue - Variable in class org.intermine.api.tracker.AbstractTracker
 
trackSearch(String, Profile, String) - Method in class org.intermine.api.tracker.KeySearchTracker
Record the search.
trackTableName - Variable in class org.intermine.api.tracker.AbstractTracker
 
trackTemplate(String, Profile, String) - Method in class org.intermine.api.tracker.TemplateTracker
Store into the database the template execution by the user or if the user is not logged during a specific http session.
trackTemplate(String, Profile, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Store into the database the template execution by the user specified in input
transform(Object) - Method in class org.intermine.api.profile.TagMapper
 
transform(Tag) - Method in class org.intermine.api.profile.TagMapper
Transform a tag into a string of some kind.
translateFromDbObject(Object) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate an object exiting the ObjectStore.
translateFromDbObject(Object) - Method in class org.intermine.objectstore.translating.Translator
Translate an object exiting the ObjectStore.
translateIdToIdentifier(Integer) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate an object id into a native identifier.
translateIdToIdentifier(Integer) - Method in class org.intermine.objectstore.translating.Translator
Translate an object id into a native identifier.
translateQuery(Query) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate a query.
translateQuery(Query) - Method in class org.intermine.objectstore.translating.Translator
Translate a query.
translateToDbObject(Object) - Method in class org.intermine.dataconversion.ItemToObjectTranslator
Translate an object entering the ObjectStore.
translateToDbObject(Object) - Method in class org.intermine.objectstore.translating.Translator
Translate an object entering the ObjectStore.
Translator - Class in org.intermine.objectstore.translating
Interface specifying operations required for inline translation of queries and data objects by a translating ObjectStore.
Translator() - Constructor for class org.intermine.objectstore.translating.Translator
 
traverseConstraint(Constraint, Map<QueryEvaluable, ConstraintSet>) - Method in class org.intermine.api.bag.BagQuery
Finds all BagConstraints in a Constraint, and places the QueryEvaluable and the containing ConstraintSet into the given Map.
traverseConstraints(Constraint, ConstraintTraverseAction) - Static method in class org.intermine.objectstore.query.ConstraintHelper
Traverse the given Constraint tree (ie.
TreatStringTag - Class in org.intermine.web.tags.util
Tag escaping apostrophes, quotes and replacing "\n" with html tag for end of line.
TreatStringTag() - Constructor for class org.intermine.web.tags.util.TreatStringTag
 
TreeAction - Class in org.intermine.web.struts
Implementation of Action that modifies a tree.
TreeAction() - Constructor for class org.intermine.web.struts.TreeAction
 
TreeController - Class in org.intermine.web.struts
Perform initialisation steps for displaying a tree
TreeController() - Constructor for class org.intermine.web.struts.TreeController
 
TreeNode - Class in org.intermine.web.logic
Bean to represent one row in the display of a tree
TreeNode(Object, String, int, boolean, boolean, boolean, List<String>) - Constructor for class org.intermine.web.logic.TreeNode
Constructor
TreeWalker<L> - Class in org.intermine.webservice.server.core
A type alias to reduce type stuttering.
TreeWalker() - Constructor for class org.intermine.webservice.server.core.TreeWalker
 
TriageBagAction - Class in org.intermine.web.struts
An action to handle reparative actions to bags.
TriageBagAction() - Constructor for class org.intermine.web.struts.TriageBagAction
 
TriageBagForm - Class in org.intermine.web.struts
 
TriageBagForm() - Constructor for class org.intermine.web.struts.TriageBagForm
 
trimLeft(String) - Static method in class org.intermine.metadata.StringUtil
trim left space in string
trimSlashes(String) - Static method in class org.intermine.metadata.StringUtil
Trim starting and trailing '/' characters from a string if present.
TRUE - Static variable in class org.intermine.objectstore.query.QueryValue
The true value
TRUNCATED_CLASSES - Static variable in class org.intermine.modelproduction.MetadataManager
The name of the key used to store the truncated classes string.
TSV - org.intermine.webservice.server.Format
Tab-separated-values
TSVFileReaderTask - Class in org.intermine.task
Read a file of tab separated values.
TSVFileReaderTask() - Constructor for class org.intermine.task.TSVFileReaderTask
 
type - Variable in class org.intermine.api.results.Column
 
type - Variable in class org.intermine.api.userprofile.SavedBag
 
type - Variable in class org.intermine.api.userprofile.Tag
 
type - Variable in class org.intermine.metadata.AttributeDescriptor
 
type - Variable in class org.intermine.objectstore.query.QueryReference
 
type - Variable in class org.intermine.task.ModelOutputTask
 
type(String, String) - Static method in class org.intermine.pathquery.Constraints
Creates a constraint for a path to be a particular subclass (type).
Type - Class in org.intermine.web.logic.config
Configuration object for displaying a class
Type - org.intermine.api.profile.TagMapper.Field
The type of this tag
Type() - Constructor for class org.intermine.web.logic.config.Type
 
TYPE_BOOLEAN - Static variable in class org.intermine.objectstore.query.UnknownTypeValue
A value that indicates that the value represents a Boolean.
TYPE_CONVERTED - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the object found when querying using input string needed to be translated.
TYPE_NUMBER - Static variable in class org.intermine.objectstore.query.UnknownTypeValue
A value that indicates that the value represents a number.
TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListInput
The type of the list
TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.lists.ListsRequestParser
Name of parameter with object type.
TYPE_PARAMETER - Static variable in class org.intermine.webservice.server.template.result.TemplateResultService
Name of type parameter
TYPE_STRING - Static variable in class org.intermine.objectstore.query.UnknownTypeValue
A value that indicates that the value represents a String or Date.
typecast() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
typecast() - Method in class org.intermine.sql.query.SqlParser
 
typecast(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
TYPECAST - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
TYPECAST - Static variable in class org.intermine.sql.query.Function
Type casts - takes two operands.
TYPECAST - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
typeConstraintToJson(PathConstraint) - Method in class org.intermine.pathquery.PathQuery
format a type constraint to a JSON representation.
TypeConverter - Class in org.intermine.api.bag
Static helper routines to convert bags between different types.
types - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
 
TYPES - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
The parts that make up a header (main title, sub title)
TypeUtil - Class in org.intermine.metadata
Provides utility methods for working with Java types and reflection
TypeUtil.FieldInfo - Class in org.intermine.metadata
Inner class to hold info on a field.

U

unaccept() - Method in class org.intermine.api.bag.SharingInvite
 
UnauthorizedException - Exception in org.intermine.webservice.server.exceptions
 
UnauthorizedException() - Constructor for exception org.intermine.webservice.server.exceptions.UnauthorizedException
Construct an UnauthorizedException
UnauthorizedException(String) - Constructor for exception org.intermine.webservice.server.exceptions.UnauthorizedException
 
unescape(String) - Static method in class org.intermine.objectstore.query.iql.IqlQueryParser
Unescapes a String, by removing quotes from the beginning and end.
UnhandledFeatureException - Exception in org.intermine.api.query.codegen
Exception representing the failure to encode a feature in the target language.
UnhandledFeatureException() - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception with a default message.
UnhandledFeatureException(String) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception with a given message.
UnhandledFeatureException(String, Throwable) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception when there is a message and a cause
UnhandledFeatureException(Throwable) - Constructor for exception org.intermine.api.query.codegen.UnhandledFeatureException
Create an exception when there is something to blame.
union(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
Create a bag that is the UNION of all the bags provided, if the union is the empty set then don't create the new bag - if bags are of incompatible types or are all empty.
Union - Class in org.intermine.api.bag.operations
 
Union(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.Union
 
UNION - Static variable in class org.intermine.api.bag.BagOperations
Constant representing logical union.
UNION - Static variable in class org.intermine.objectstore.query.ObjectStoreBagCombination
Constant representing a UNION operation
UNIQUE_INTEGER_SEQUENCE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
The name of the SEQUENCE in the database to use when generating unique integers in getUniqueInteger().
UNIQUE_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
Common keys
uniqueColumnValues(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
Get the the total number of unique column values for a given path in the context of a given query.
uniqueString() - Static method in class org.intermine.metadata.StringUtil
Returns a String that is different every time
UNIX_SEPARATOR - Static variable in interface org.intermine.web.logic.export.Exporter
Unix line separator only LF
UNKNOWN - org.intermine.webservice.server.Format
The Unknown format
UNKNOWN - org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
And there is a catch-all type, in case someone goes ahead and creates a new type.
UnknownBagTypeException - Exception in org.intermine.api.bag
Exception thrown when given attempting to create a bag for a type that isn't in the model, this can happen when reading bags from a userprofile database and the data model has changed.
UnknownBagTypeException(String) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException
Constructs an IncompatibleBagTypesException with the specified detail message.
UnknownBagTypeException(String, Throwable) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException
Constructs an IncompatibleBagTypesException with the specified detail message and nested throwable.
UnknownBagTypeException(Throwable) - Constructor for exception org.intermine.api.bag.UnknownBagTypeException
Constructs an IncompatibleBagTypesException with the specified nested throwable.
UnknownTypeValue - Class in org.intermine.objectstore.query
Represents a value with an unknown type.
UnknownTypeValue(String) - Constructor for class org.intermine.objectstore.query.UnknownTypeValue
Constructor.
unmarhsal(InputStream) - Static method in class org.intermine.web.logic.aspects.AspectBinding
Read data set configuration from an input stream.
unmarshal(InputStream) - Method in class org.intermine.util.XmlBinding
Unmarshal an XML file to an object.
unmarshal(Reader) - Static method in class org.intermine.web.logic.aspects.AspectBinding
Read in data set configuration from XML.
unmarshal(Reader, Integer) - Static method in class org.intermine.api.xml.SharedBagBinding
Parse saved queries from a Reader.
unmarshal(Reader, Map, int) - Static method in class org.intermine.api.xml.SavedQueryBinding
Parse TemplateQuerys from XML
unmarshal(Reader, ProfileManager, String, String, Set<Tag>, ObjectStoreWriter, int) - Static method in class org.intermine.api.xml.ProfileBinding
Read a Profile from an XML stream Reader.
unmarshal(Reader, ProfileManager, ObjectStoreWriter) - Static method in class org.intermine.api.xml.ProfileManagerBinding
Read a ProfileManager from an XML stream Reader.
unmarshal(Reader, ProfileManager, ObjectStoreWriter, boolean) - Static method in class org.intermine.api.xml.ProfileManagerBinding
Read a ProfileManager from an XML stream Reader
unmarshal(Reader, ObjectStoreWriter) - Static method in class org.intermine.api.tracker.xml.TemplateTrackBinding
Read the template tracks from an XML stream Reader.
unmarshal(Reader, ObjectStoreWriter, ObjectStoreWriter, Integer) - Static method in class org.intermine.api.xml.InterMineBagBinding
Parse saved queries from a Reader
unmarshal(ProfileManager, String, Reader) - Method in class org.intermine.api.xml.TagBinding
Parse Tags from XML and write them to the userprofile object store
unmarshalJSONPathQueries(Reader, Model) - Static method in class org.intermine.pathquery.PathQueryBinding
Parse PathQueries from JSON
unmarshalJSONPathQuery(Model, String) - Static method in class org.intermine.pathquery.PathQueryBinding
Parse PathQuery from JSON
unmarshalJSONTemplates(Reader, Model) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Parse TemplateQueries from JSON.
unmarshalPathQueries(Reader, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Parse PathQueries from XML.
unmarshalPathQueries(Reader, int, Model) - Static method in class org.intermine.pathquery.PathQueryBinding
Parse PathQueries from XML, declaring which model should be used in preference to the default model retrieved by Model::getInstanceByName.
unmarshalPathQuery(Reader, int) - Static method in class org.intermine.pathquery.PathQueryBinding
Parses PathQuery from XML.
unmarshalPathQuery(Reader, int, Model) - Static method in class org.intermine.pathquery.PathQueryBinding
Parses a PathQuery from XML, declaring which model should be used in preference to the default model retrieved by Model::getInstanceByName.
unmarshalTemplates(Reader, int) - Static method in class org.intermine.template.xml.TemplateQueryBinding
Parse TemplateQueries from XML.
unqualifiedName(String) - Static method in class org.intermine.metadata.TypeUtil
Returns the unqualified class name from a fully qualified class name
unqualifiedName(String) - Static method in class org.intermine.metadata.Util
Returns the unqualified class name from a fully qualified class name
unsafe_function() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
unsafe_function() - Method in class org.intermine.sql.query.SqlParser
 
unsafe_function(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
UNSAFE_FUNCTION - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
UNSAFE_FUNCTION - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
unshareAllBagsFromUser(Profile, Profile) - Method in class org.intermine.api.bag.SharedBagManager
Stop sharing all bags owned by the given user which have been shared with the given recipient.
unshareBagWithAllUsers(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager
Delete the sharing between the bag and all the users sharing the bag.
unshareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager
Unshare the bag with the user given in input
unshareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager
Delete the sharing between the user and the bag given in input
unshareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
Un-share the bag with the user given in input
unverbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Deprecated.
ajaxVerbosify is used instead
uosw - Variable in class org.intermine.api.bag.SharedBagManager
 
uosw - Variable in class org.intermine.api.profile.ProfileManager
 
upcast(Map<String, TemplateQuery>) - Static method in class org.intermine.api.template.TemplateHelper
Transform a map of templates into a map of API templates.
update() - Method in class org.intermine.api.profile.ModelUpdate
Update bags, savedquery and savedtemplatequery if class has been renamed -> update type bags, update savedquery and savedtemplatequery if a field has been renamed -> update savedquery and savedtemplatequery if class has been deleted -> delete bags with that type
update(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
Update the path query
updateBagDescription(String, String) - Method in class org.intermine.api.profile.Profile
Update the description of bag.
updateBagType(String, String) - Method in class org.intermine.api.profile.Profile
Update the type of bag.
updateColumnValue(Connection, String, String, Object) - Static method in class org.intermine.sql.DatabaseUtil
Set the default value in a column for all values.
updateColumnValue(Database, String, String, Object) - Static method in class org.intermine.sql.DatabaseUtil
Set the default value in a column for all values where the current value is null.
updateConstraints(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
Update the constraint with the renamed classes or/and fields
updateConstraints(Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.TemplateQueryUpdate
 
UpdateListTablesTask - Class in org.intermine.web.task
Task that rename the column 'intermine_current' into 'intermine_state' in savedbag table (from boolean to text) and add the column 'extra' (and its value) in the bagvalues table
UpdateListTablesTask() - Constructor for class org.intermine.web.task.UpdateListTablesTask
 
updatePopulationQuery(Query, Query, QueryField) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Update the annotated population query given in input using the queryfield specific for the correction
updateQueryToPathToQueryNode(Query, Map<String, QuerySelectable>) - Method in class org.intermine.api.query.QueryExecutor
Update the map to query queryToPathToQueryNode
updateQueryWithCorrectionCoefficient(Query, QueryClass) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
Update the query, given in input, with the field associated with the correction coefficient and return a query field.
updateReferredQueryAndTemplate() - Method in class org.intermine.api.profile.ModelUpdate
Update savedquery and savedtemplatequery when they reeferring to renamed classes or fields
updateStatistics(Map<String, Integer>, Connection) - Method in interface org.intermine.sql.writebatch.BatchWriter
Updates the per-table statistics held in this object, and may tell the SQL database to update its statistics using the supplied Connection.
updateStatistics(Map<String, Integer>, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Updates the per-table statistics held in this object, and may tell the SQL database to update its statistics using the supplied Connection.
updateTemplate(String, String) - Method in class org.intermine.dwr.AjaxServices
Update with the value given in input the field of the previous template saved into the session
updateTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile
Update an existing template, throw exceptions when template doesn't exist.
updateTemplateName(String, String) - Method in class org.intermine.api.tracker.TrackerDelegate
Update the template name value into the database
updateTemplateName(String, String, Connection) - Method in class org.intermine.api.tracker.TemplateTracker
Update the template name value into the database
UpdateTrackTableTask - Class in org.intermine.web.task
Task to modify the type of the column 'timestamp' in the templatetrack table in the userprofile database.
UpdateTrackTableTask() - Constructor for class org.intermine.web.task.UpdateTrackTableTask
 
updateTypeBag() - Method in class org.intermine.api.profile.ModelUpdate
Update the type to all bags having as a type one of the classes renamed
updateUserRepositoryWithSharedBags() - Method in class org.intermine.api.profile.Profile
Update the user repository with the sharedbags
updateUserRepositoryWithSharedBags() - Method in class org.intermine.api.search.UserRepository
Update the user repository with the shared bags
UpgradeBagList - Class in org.intermine.web.logic.profile
Runnable object providing upgrading osbag_int table.
UpgradeBagList(Profile, BagQueryRunner) - Constructor for class org.intermine.web.logic.profile.UpgradeBagList
Constructor
UpgradeJob - Class in org.intermine.api.idresolution
 
UpgradeJob(UUID, BagQueryUpgrade) - Constructor for class org.intermine.api.idresolution.UpgradeJob
 
upgradeOsb(Collection<Integer>, boolean) - Method in class org.intermine.api.profile.InterMineBag
Upgrades the ObjectStoreBag with a new ObjectStoreBag containing the collection of elements given in input
UPGRADING - org.intermine.api.profile.BagState
 
UPGRADING_BAG - Static variable in class org.intermine.web.logic.Constants
Key for the upgrading bag on the session
UPPER - Static variable in class org.intermine.objectstore.query.QueryExpression
Upper case version of the given string
UPPER - Static variable in class org.intermine.sql.query.Function
UPPER operator - takes one operand
URLGenerator - Class in org.intermine.web.util
Class generating useful links like base link: http://localhost:8080/query
URLGenerator(HttpServletRequest) - Constructor for class org.intermine.web.util.URLGenerator
Constructor.
URLUtil - Class in org.intermine.web.util
Util class for URL processing.
USAGE - Static variable in class org.intermine.webservice.server.lists.ListDeletionService
Usage information to help users who provide incorrect input.
USAGE - Static variable in class org.intermine.webservice.server.lists.ListRenameService
Usage information to help users who provide incorrect input.
USAGE - Static variable in class org.intermine.webservice.server.lists.ListUploadService
A usage string to return for bad requests.
useJoin - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
 
user - Variable in class org.intermine.task.GrantTask
 
USER - Static variable in class org.intermine.api.search.Scope
User scope for private bags, templates, etc.
USER_BAGS - Static variable in class org.intermine.api.search.SearchTarget
The search target for user bags
USER_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
The search target for user templates
UserAlreadyShareBagException - Exception in org.intermine.api.profile
Exception thrown when a user already shares the bag.
UserAlreadyShareBagException() - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor
UserAlreadyShareBagException(String) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with message.
UserAlreadyShareBagException(String, Throwable) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with message and throwable
UserAlreadyShareBagException(Throwable) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with throwable
UserAlreadyShareBagException(SavedBag, UserProfile) - Constructor for exception org.intermine.api.profile.UserAlreadyShareBagException
Constructor with the actual objects we are trying to link.
UserDataFormatter - Class in org.intermine.webservice.server.user
A class that processes information about a user into XML.
UserDataFormatter() - Constructor for class org.intermine.webservice.server.user.UserDataFormatter
 
userId - Variable in class org.intermine.api.profile.Profile
 
username - Variable in class org.intermine.api.profile.Profile
 
username - Variable in class org.intermine.api.userprofile.UserProfile
 
username - Variable in class org.intermine.web.struts.CreateAccountForm
 
username - Variable in class org.intermine.web.struts.LoginForm
 
username - Variable in class org.intermine.web.struts.RequestPasswordForm
 
username - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
userName - Variable in class org.intermine.api.tracker.track.TrackAbstract
 
USERNAME - Static variable in class org.intermine.api.util.AnonProfile
The user name of the anonymous user.
USERNAME - Static variable in class org.intermine.web.logic.Constants
The display name of the current user
UserNotFoundException - Exception in org.intermine.api.profile
Exception thrown when user is not found.
UserNotFoundException(String) - Constructor for exception org.intermine.api.profile.UserNotFoundException
Constructor with message.
UserNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.profile.UserNotFoundException
Constructor with message and nested exception.
UserNotFoundException(Throwable) - Constructor for exception org.intermine.api.profile.UserNotFoundException
Constructor with throwable
UserPreferences - Class in org.intermine.api.profile
 
UserPreferences(PreferencesManager, Profile) - Constructor for class org.intermine.api.profile.UserPreferences
 
userProfile - Variable in class org.intermine.api.userprofile.PermanentToken
 
userProfile - Variable in class org.intermine.api.userprofile.SavedBag
 
userProfile - Variable in class org.intermine.api.userprofile.SavedQuery
 
userProfile - Variable in class org.intermine.api.userprofile.SavedTemplateQuery
 
userProfile - Variable in class org.intermine.api.userprofile.Tag
 
UserProfile - Class in org.intermine.api.userprofile
 
UserProfile() - Constructor for class org.intermine.api.userprofile.UserProfile
 
USERPROFILE_VERSION - Static variable in class org.intermine.pathquery.PathQuery
Version number for the userprofile and PathQuery XML format.
userProfileAlias - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
userProfileOS - Variable in class org.intermine.web.task.PrecomputeTemplatesTask
 
UserRepository - Class in org.intermine.api.search
A repository for searching the searchable items of a single user.
UserRepository(Profile) - Constructor for class org.intermine.api.search.UserRepository
Constructor.
UsersController - Class in org.intermine.web.struts
Controller for the users admin page
UsersController() - Constructor for class org.intermine.web.struts.UsersController
 
UserTemplateAction - Class in org.intermine.web.struts
Make some change to a user template.
UserTemplateAction() - Constructor for class org.intermine.web.struts.UserTemplateAction
 
Util - Class in org.intermine.metadata
Generic utility functions.
uuid - org.intermine.sql.DatabaseUtil.Type
uuid

V

v - Variable in class org.intermine.sql.query.SelectValue
 
VALID_OPS - Static variable in class org.intermine.objectstore.query.BagConstraint
List of possible operations
VALID_OPS - Static variable in class org.intermine.objectstore.query.ClassConstraint
Valid operators for this constraint.
VALID_OPS - Static variable in class org.intermine.objectstore.query.ConstraintSet
 
VALID_OPS - Static variable in class org.intermine.objectstore.query.ContainsConstraint
List of possible operations
VALID_OPS - Static variable in class org.intermine.objectstore.query.SubqueryConstraint
 
VALID_OPS - Static variable in class org.intermine.objectstore.query.SubqueryExistsConstraint
 
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintAttribute
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintBag
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintIds
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintLoop
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintMultitype
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintMultiValue
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintNull
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintRange
List of valid ops for this type of constraint
VALID_OPS - Static variable in class org.intermine.pathquery.PathConstraintSubclass
List of valid ops for this type of constraint
VALID_OPS_NULL - Static variable in class org.intermine.objectstore.query.ContainsConstraint
List of possible null operations
VALID_TYPES - Static variable in class org.intermine.metadata.AttributeDescriptor
This is a list of the valid type strings.
validate() - Method in class org.intermine.api.tracker.track.KeySearchTrack
 
validate() - Method in class org.intermine.api.tracker.track.ListTrack
Validate the track before saving into the database
validate() - Method in class org.intermine.api.tracker.track.LoginTrack
Validate the track before saving into the database
validate() - Method in class org.intermine.api.tracker.track.QueryTrack
 
validate() - Method in class org.intermine.api.tracker.track.TemplateTrack
Validate the track before saving into the database
validate() - Method in interface org.intermine.api.tracker.track.Track
Validate the track before saving into the database
validate(String, String) - Method in class org.intermine.webservice.server.query.result.XMLValidator
Validates an XML string according to an XML Schema at a given URL.
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ChangePasswordForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
When there are no other errors, check email address is valid.
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.CreateAccountForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ImportQueriesForm
Call inherited method then check whether xml is valid.
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.LoginForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyQueryForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.ModifyTemplateForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.PasswordResetForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.SaveQueryForm
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplateSettingsForm
 
validate(ActionMapping, HttpServletRequest) - Method in class org.intermine.web.struts.TemplatesImportForm
Call inherited method then check whether xml is valid.
validateBagName(String) - Static method in class org.intermine.dwr.AjaxServices
validate bag upload
validateBagOperations(String, String[], String) - Static method in class org.intermine.dwr.AjaxServices
validation that happens before new bag is saved
validateForGroups(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression
Validates an expression for the given groups of codes, making sure each group is only ANDed together.
validateLookupConstraints() - Method in class org.intermine.template.TemplateQuery
Verify templates don't contain non-editable lookup constraints
validateName(String) - Method in class org.intermine.pathquery.PathQueryHandler
Checks that the query has a name and that there's no name duplicates and appends a number to the name if there is.
validateName(Collection<String>, String) - Static method in class org.intermine.api.util.NameUtil
Checks that the name doesn't already exist and returns a numbered name if it does.
validatePath(String, Model) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
Path should be of the form: Class1 ref1 Class2 ref2 Class3 Where the number of elements is greater than one and an odd number.
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput
 
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.CommutativeOperationInput
 
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.ListInput
Check that the required parameters are there
validateRequiredParams() - Method in class org.intermine.webservice.server.lists.ListRenameInput
 
validateState() - Method in class org.intermine.webservice.server.core.ReadWriteJSONService
 
validateState() - Method in class org.intermine.webservice.server.lists.AuthenticatedListService
 
validateState() - Method in class org.intermine.webservice.server.lists.ListMakerService
 
validateState() - Method in class org.intermine.webservice.server.query.QueryToListService
 
validateState() - Method in class org.intermine.webservice.server.query.QueryUploadService
 
validateState() - Method in class org.intermine.webservice.server.template.TemplateRemovalService
 
validateState() - Method in class org.intermine.webservice.server.template.TemplateUploadService
 
validateState() - Method in class org.intermine.webservice.server.user.DeregistrationService
 
validateState() - Method in class org.intermine.webservice.server.user.NewUserService
 
validateState() - Method in class org.intermine.webservice.server.user.WhoAmIService
 
validateState() - Method in class org.intermine.webservice.server.WebService
Subclasses can put initialisation checks here.
validateWidgetsConfig(Model) - Method in class org.intermine.web.logic.config.WebConfig
Validate the content (the paths) in the widget config
validComparison(Class<?>, ConstraintOp, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
Check whether a comparison is valid i.e.
validOps - Variable in class org.intermine.objectstore.query.OverlapConstraint
 
validOps(Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
Return the list of valid (binary) operator codes given arguments of a specified type
validPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager
Validate a user's password A check should be made prior to this call to ensure a Profile exists
value - Variable in class org.intermine.model.fulldata.Attribute
 
value - Variable in class org.intermine.sql.query.Constant
 
valueConstraintToJson(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
Format a value constraint to a JSON representation.
valueEquals(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
Compare the value of this AbstractValue with another to see if it is equal.
valueMap - Variable in class org.intermine.sql.precompute.PrecomputedTable
 
valueOf(String) - Static method in enum org.intermine.api.idresolution.Job.JobStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.mines.ContentType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.profile.BagState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.profile.ProfileManager.ApiPermission.Level
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.profile.TagMapper.Field
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.search.TaggingEvent.TagChange
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.searchengine.KeywordSearchFacetType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.tracker.util.ListBuildMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.api.tracker.util.ListTrackerEvent
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.pathquery.OrderDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.pathquery.OuterJoinStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.sql.DatabaseUtil.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.template.SwitchOffAbility
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.template.TemplateValue.ValueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.logic.widget.GraphWidgetActionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.struts.oauth2.MessageFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.web.struts.oauth2.ResponseType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.ColumnHeaderStyle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.core.WebServiceServlet.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.Format
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.jbrowse.Commands.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.intermine.api.idresolution.Job.JobStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.mines.ContentType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.profile.BagState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.profile.ProfileManager.ApiPermission.Level
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.profile.TagMapper.Field
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.search.TaggingEvent.TagChange
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.searchengine.KeywordSearchFacetType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.tracker.util.ListBuildMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.api.tracker.util.ListTrackerEvent
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.pathquery.OrderDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.pathquery.OuterJoinStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.sql.DatabaseUtil.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.template.SwitchOffAbility
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.template.TemplateValue.ValueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.intermine.util.AlwaysMap
values() - Method in class org.intermine.util.IdentityMap
values() - Method in class org.intermine.util.ReferenceMap
values() - Static method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.web.logic.widget.GraphWidgetActionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.web.struts.oauth2.MessageFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.web.struts.oauth2.ResponseType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.ColumnHeaderStyle
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.core.WebServiceServlet.Method
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.Format
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.jbrowse.Commands.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.output.JSONRowResultProcessor.Verbosity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.intermine.webservice.server.widget.WidgetProcessorImpl.WidgetType
Returns an array containing the constants of this enum type, in the order they are declared.
VALUES_TEMPLATE - Static variable in class org.intermine.api.config.Constants
returns available queryable values for mine
verboseException(Exception) - Static method in class org.intermine.metadata.Util
Takes an Exception, and returns an Exception of similar type with all available information in the message.
verboseQueryLog - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
verbosify(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyDetails
Deprecated.
ajaxVerbosify is used instead
VERIFICATION_STRATEGY - Static variable in class org.intermine.webservice.server.JWTVerifier
The strategy used to verify tokens
VerificationError(String) - Constructor for exception org.intermine.webservice.server.JWTVerifier.VerificationError
Initialise a new verification error with a message detailing the problem.
verifiedSources - Static variable in class org.intermine.dataloader.DataLoaderHelper
 
verify(String) - Method in class org.intermine.webservice.server.JWTVerifier
Verify this token and return a verification result.
VERIFYAUDIENCE - Static variable in class org.intermine.webservice.server.JWTVerifier
This is the key used to establish whether we should verify the audience.
verifyColumnType(Connection, String, String, int) - Static method in class org.intermine.sql.DatabaseUtil
 
verifyQuery() - Method in class org.intermine.pathquery.PathQuery
Verifies the contents of this query against the model, and for internal integrity.
VerifyTokenTask - Class in org.intermine.web.task
A task to check that a token can be verified.
VerifyTokenTask() - Constructor for class org.intermine.web.task.VerifyTokenTask
 
version - Variable in class org.intermine.pathquery.PathQueryHandler
 
version - Variable in class org.intermine.sql.Database
 
VERSION_PARAMETER - Static variable in class org.intermine.webservice.server.query.QueryUploadService
The key for the version parameter
VERSION_PARAMETER - Static variable in class org.intermine.webservice.server.template.TemplateUploadService
The key for the version parameter
VersionService - Class in org.intermine.webservice.server
Service for returning the version of this service.
VersionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.VersionService
Constructor
VersionServlet - Class in org.intermine.webservice.server
Returns version of the deployed InterMine application.
VersionServlet() - Constructor for class org.intermine.webservice.server.VersionServlet
 
VERTBAR - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
VERTBAR - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
visible - Variable in class org.intermine.api.results.Column
 
visitLeft(A) - Method in class org.intermine.webservice.server.core.EitherVisitor
Override this to access the left hand side.
visitLeft(L) - Method in class org.intermine.webservice.server.core.TreeWalker
 
visitRight(B) - Method in class org.intermine.webservice.server.core.EitherVisitor
Override this to access the right hand side.
visitRight(DisjointRecursiveList<L>) - Method in class org.intermine.webservice.server.core.TreeWalker
 

W

waitForCurrentJobs() - Method in class org.intermine.sql.Database
Blocks until all the current pending jobs are finished.
wantsColumnHeaders() - Method in class org.intermine.webservice.server.WebService
Returns true if the request wants column headers as well as result rows
wantsDataPackage() - Method in class org.intermine.webservice.server.WebService
 
warning(SAXParseException) - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
}
wasSuccessful() - Method in interface org.intermine.api.idresolution.Job
 
wasSuccessful() - Method in class org.intermine.api.idresolution.ResolutionJob
 
wasSuccessful() - Method in class org.intermine.api.idresolution.UpgradeJob
 
WeakReferenceHashMap<K,​V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
WeakReferenceHashMap() - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the default initial capacity (16) and the default load factor (0.75).
WeakReferenceHashMap(int) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the given initial capacity and the default load factor, which is 0.75.
WeakReferenceHashMap(int, float) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the given initial capacity and the given load factor.
WeakReferenceHashMap(String) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new, empty WeakReferenceHashMap with the default initial capacity (16) and the default load factor (0.75), and a name.
WeakReferenceHashMap(Map<K, V>) - Constructor for class org.intermine.util.WeakReferenceHashMap
Constructs a new WeakReferenceHashMap with the same mappings as the specified Map.
WeakReferenceMap<K,​V> - Class in org.intermine.util
This is a Map implementation designed specifically for people intending to create a cache.
WeakReferenceMap() - Constructor for class org.intermine.util.WeakReferenceMap
 
WEB_PROPERTIES - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute used to store web.properties
WEB_SERVICE_VERSION - Static variable in class org.intermine.web.logic.Constants
Current version of the InterMine WebService.
WEB_STATE - Static variable in class org.intermine.web.logic.Constants
Session attribute used to store WebState object.
webConfig - Variable in class org.intermine.web.logic.bag.BagConverter
 
webConfig - Variable in class org.intermine.web.logic.results.InlineResultsTable
 
WebConfig - Class in org.intermine.web.logic.config
Configuration object for web site
WebConfig() - Constructor for class org.intermine.web.logic.config.WebConfig
 
WEBCONFIG - Static variable in class org.intermine.web.logic.Constants
ServletContext attribute used to store the WebConfig object for the Model.
WebJobInput - Class in org.intermine.web.logic.bag
 
WebJobInput(String, Collection<String>, BuildBagForm) - Constructor for class org.intermine.web.logic.bag.WebJobInput
Create a web-job.
WebJobInput(String, Collection<String>, BuildBagForm, boolean) - Constructor for class org.intermine.web.logic.bag.WebJobInput
Create a web-job.
webProperties - Variable in class org.intermine.api.LinkRedirectManager
 
webProperties - Variable in class org.intermine.webservice.server.WebService
The properties this mine was configured with
WebPropertiesService - Class in org.intermine.webservice.server.webproperties
Exports selected web.properties.
WebPropertiesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.webproperties.WebPropertiesService
 
WebPropertiesServlet - Class in org.intermine.webservice.server.webproperties
Runs WebPropertiesService web service.
WebPropertiesServlet() - Constructor for class org.intermine.webservice.server.webproperties.WebPropertiesServlet
 
WebResults - Class in org.intermine.api.results
The web version of a Results object.
WebResults(InterMineAPI, PathQuery, Results, Map<String, QuerySelectable>, Map<String, BagQueryResult>) - Constructor for class org.intermine.api.results.WebResults
Create a new WebResults object.
WebResultsExecutor - Class in org.intermine.api.query
Executes a PathQuery and returns a WebResults object, to be used when multi-row style results are required.
WebResultsExecutor(InterMineAPI, Profile) - Constructor for class org.intermine.api.query.WebResultsExecutor
Constructor with necessary objects to generate an ObjectStore query from a PathQuery and execute it.
WebSearchable - Interface in org.intermine.api.search
An interface implemented by objects that we want to index with Lucene.
WebSearchableListController - Class in org.intermine.web.struts
Controller for webSearchableList.tile
WebSearchableListController() - Constructor for class org.intermine.web.struts.WebSearchableListController
 
WebSearchWatcher - Interface in org.intermine.api.search
The interface for describing objects that listen to WebSearchables for events.
WebService - Class in org.intermine.webservice.server
Base class for web services.
WebService(InterMineAPI) - Constructor for class org.intermine.webservice.server.WebService
Construct the web service with the InterMine API object that gives access to the core InterMine functionality.
WebserviceCodeGenAction - Class in org.intermine.web.struts
Action to handle the web service code generation.
WebserviceCodeGenAction() - Constructor for class org.intermine.web.struts.WebserviceCodeGenAction
 
WebserviceCodeGenerator - Interface in org.intermine.api.query.codegen
Interface for web service code generation.
WebserviceCodeGenInfo - Class in org.intermine.api.query.codegen
Class to represent the information used to generate web service source code.
WebserviceCodeGenInfo(PathQuery, String, String, String, boolean, Profile) - Constructor for class org.intermine.api.query.codegen.WebserviceCodeGenInfo
Constructor.
WebserviceCodeGenInfo(PathQuery, String, String, String, boolean, Profile, String) - Constructor for class org.intermine.api.query.codegen.WebserviceCodeGenInfo
 
WebServiceConstants - Class in org.intermine.webservice.server
 
WebServiceInput - Class in org.intermine.webservice.server
Base class for input classes used with web services.
WebServiceInput() - Constructor for class org.intermine.webservice.server.WebServiceInput
 
WebserviceJavaCodeGenerator - Class in org.intermine.api.query.codegen
This Class generates Java source code of web service client for path query and template query.
WebserviceJavaCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
 
WebserviceJavaScriptCodeGenerator - Class in org.intermine.api.query.codegen
A Class for generating JavaScript that would run a given query.
WebserviceJavaScriptCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator
 
WebservicePerlCodeGenerator - Class in org.intermine.api.query.codegen
This Class generates Perl source code of web service client for path query and template query.
WebservicePerlCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
 
WebservicePythonCodeGenerator - Class in org.intermine.api.query.codegen
Class for generating Python code to run a query, using the intermine python library.
WebservicePythonCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
 
WebServiceRequestParser - Class in org.intermine.webservice.server
Base request parser that is used by advanced web service parsers.
WebServiceRequestParser() - Constructor for class org.intermine.webservice.server.WebServiceRequestParser
 
WebserviceRubyCodeGenerator - Class in org.intermine.api.query.codegen
 
WebserviceRubyCodeGenerator() - Constructor for class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
 
WebServiceServlet - Class in org.intermine.webservice.server.core
A servlet which can be easily configured to define how to route requests, using standard RESTful semantics.
WebServiceServlet() - Constructor for class org.intermine.webservice.server.core.WebServiceServlet
Constructor
WebServiceServlet.Method - Enum in org.intermine.webservice.server.core
 
WebState - Class in org.intermine.web.logic.results
This class saves things related to the state of web GUI.
WebState() - Constructor for class org.intermine.web.logic.results.WebState
 
WebTable - Interface in org.intermine.api.results
A List that can understand ResultElement objects.
WebUtil - Class in org.intermine.web.logic
Utility methods for the web package.
WebUtil.HeadResource - Class in org.intermine.web.logic
A bean encapsulating a resource (js or css).
welcome(String) - Method in class org.intermine.util.Emailer
Welcome a user to the system.
welcome(String) - Method in class org.intermine.web.context.NullMailer
 
welcome(String, Properties) - Static method in class org.intermine.util.MailUtils
Send a welcoming email to an email address
where - Variable in class org.intermine.sql.query.Query
 
where_clause() - Method in class org.intermine.objectstore.query.iql.IqlParser
 
where_clause() - Method in class org.intermine.sql.query.SqlParser
 
where_clause(AST) - Method in class org.intermine.sql.query.SqlTreeParser
 
WHERE_CLAUSE - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
WHERE_CLAUSE - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 
whereHavingSafe(Object, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
Returns an array containing two boolean values.
WHITELIST - Static variable in class org.intermine.webservice.server.JWTVerifier
This is where we get the list of aliases from if the strategy is WHITELIST
WhoAmIService - Class in org.intermine.webservice.server.user
Class for retrieving information about the currently authenticated user.
WhoAmIService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.WhoAmIService
Constructor
WhoAmIServlet - Class in org.intermine.webservice.server.user
 
WhoAmIServlet() - Constructor for class org.intermine.webservice.server.user.WhoAmIServlet
 
Widget - Class in org.intermine.web.logic.widget
A representation of a query using a list tool.
Widget(WidgetConfig) - Constructor for class org.intermine.web.logic.widget.Widget
The constructor
WidgetConfig - Class in org.intermine.web.logic.widget.config
Class representing a Widget Configuration
WidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.WidgetConfig
 
WidgetConfigUtil - Class in org.intermine.web.logic.widget.config
Utilities for handling the widget configuration
WidgetForm - Class in org.intermine.web.struts
 
WidgetForm() - Constructor for class org.intermine.web.struts.WidgetForm
Constructor
WidgetHelper - Interface in org.intermine.web.logic.widget
An Interface for widget Utils
widgetId - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
 
WidgetLdr - Class in org.intermine.web.logic.widget
The class that performs the actual queries for widgets.
WidgetLdr(InterMineBag, ObjectStore, String, WidgetConfig, String) - Constructor for class org.intermine.web.logic.widget.WidgetLdr
 
WidgetOptions - Interface in org.intermine.web.logic.widget
The type of options a widget would expect to receive.
WidgetProcessor - Interface in org.intermine.webservice.server.widget
 
WidgetProcessorImpl - Class in org.intermine.webservice.server.widget
A base class for Widget Processors
WidgetProcessorImpl() - Constructor for class org.intermine.webservice.server.widget.WidgetProcessorImpl
 
WidgetProcessorImpl.WidgetType - Enum in org.intermine.webservice.server.widget
Of widget types there are several:
WidgetResultProcessor - Interface in org.intermine.webservice.server.widget
Interfaces for classes that are able to process the results that widgets return.
WidgetService - Class in org.intermine.webservice.server.widget
 
WidgetService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.WidgetService
Construct the webservice controller.
WidgetsRequestParser - Class in org.intermine.webservice.server.widget
Request processor for WidgetsService that process request, validates it and returns parsed input as a parameter object.
WidgetsRequestParser() - Constructor for class org.intermine.webservice.server.widget.WidgetsRequestParser
ListsRequestProcessor constructor.
WidgetsServiceInput - Class in org.intermine.webservice.server.widget
WidgetsServiceInput is parameter object representing parameters for the WidgetsService web service.
WidgetsServiceInput() - Constructor for class org.intermine.webservice.server.widget.WidgetsServiceInput
 
WidgetsServiceInput.Builder - Class in org.intermine.webservice.server.widget
Class to build Inputs for the Widget Service.
WidgetsServlet - Class in org.intermine.webservice.server.widget
Servlet running WidgetsService.
WidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.WidgetsServlet
 
width - Variable in class org.intermine.sql.query.ExplainResult
 
WIDTH_BUCKET - Static variable in class org.intermine.objectstore.query.QueryFunction
Get the bucket this value would be assigned in an equal-depth histogram.
WidthBucketFunction - Class in org.intermine.objectstore.query
Representation of a call to the Postgresql WIDTH_BUCKET function.
WidthBucketFunction(QueryEvaluable, QueryEvaluable, QueryEvaluable, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.WidthBucketFunction
Constructor.
WILDCARD - Static variable in class org.intermine.api.bag.BagQueryResult
Key of the Map returned by getIssues() when the object found by querying with a wildcard.
wildcardSqlToUser(String) - Static method in class org.intermine.metadata.Util
Deprecated.
I don't think this is used anymore?
wildcardUserToSql(String) - Static method in class org.intermine.metadata.Util
Turn a user supplied wildcard expression with * into an SQL LIKE/NOT LIKE expression with %'s and other special characters.
WINDOWS_SEPARATOR - Static variable in interface org.intermine.web.logic.export.Exporter
Windows line separator CR+LF
withAdditionalProperty(String, Object) - Method in class org.intermine.web.registry.model.Instance
 
withAdditionalProperty(String, Object) - Method in class org.intermine.web.registry.model.RegistryResponse
 
withApiVersion(String) - Method in class org.intermine.web.registry.model.Instance
 
withCreatedAt(String) - Method in class org.intermine.web.registry.model.Instance
 
withDescription(String) - Method in class org.intermine.web.registry.model.Instance
 
withExecutionTime(String) - Method in class org.intermine.web.registry.model.RegistryResponse
 
withId(String) - Method in class org.intermine.web.registry.model.Instance
 
WITHIN - Static variable in class org.intermine.metadata.ConstraintOp
Require that the first argument lie entirely within the second.
withinRange(int) - Method in class org.intermine.webservice.server.core.Page
 
withInstance(Instance) - Method in class org.intermine.web.registry.model.RegistryResponse
 
withIntermineVersion(String) - Method in class org.intermine.web.registry.model.Instance
 
withIsProduction(boolean) - Method in class org.intermine.web.registry.model.Instance
 
withLastTimeUpdated(String) - Method in class org.intermine.web.registry.model.Instance
 
withMaintainerEmail(String) - Method in class org.intermine.web.registry.model.Instance
 
withMaintainerGithubUrl(String) - Method in class org.intermine.web.registry.model.Instance
 
withMaintainerOrgName(String) - Method in class org.intermine.web.registry.model.Instance
 
withMaintainerUrl(String) - Method in class org.intermine.web.registry.model.Instance
 
withName(String) - Method in class org.intermine.web.registry.model.Instance
 
withNamespace(String) - Method in class org.intermine.web.registry.model.Instance
 
withNeighbours(List<String>) - Method in class org.intermine.web.registry.model.Instance
 
withOrganisms(List<String>) - Method in class org.intermine.web.registry.model.Instance
 
withReleaseVersion(String) - Method in class org.intermine.web.registry.model.Instance
 
withStatus(String) - Method in class org.intermine.web.registry.model.Instance
 
withStatusCode(int) - Method in class org.intermine.web.registry.model.RegistryResponse
 
withTwitter(String) - Method in class org.intermine.web.registry.model.Instance
 
withUrl(String) - Method in class org.intermine.web.registry.model.Instance
 
withV(int) - Method in class org.intermine.web.registry.model.Instance
 
wrapLines(String, int, int) - Static method in class org.intermine.metadata.StringUtil
Wraps the given String into several lines and ultimately truncates it with an ellipsis.
wrapLines(String, int, int, int) - Static method in class org.intermine.metadata.StringUtil
Wraps the given String into several lines and ultimately truncates it with an ellipsis.
write(byte[], int, int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
 
write(byte[], int, int) - Method in class org.intermine.util.SensibleByteArrayOutputStream
write(char[], int, int) - Method in class org.intermine.sql.logging.DatabaseWriter
Write a portion of an array to the database
write(int) - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
 
write(int) - Method in class org.intermine.util.SensibleByteArrayOutputStream
write(Connection, Map<String, ? extends Table>, Set<String>) - Method in interface org.intermine.sql.writebatch.BatchWriter
Performs all the processing for flushing a few tables to the connection, and returns a List of jobs to do the actual flushing.
write(Connection, Map<String, ? extends Table>, Set<String>) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
Performs all the processing for flushing a few tables to the connection, and returns a List of jobs to do the actual flushing.
write(Iterator<List<ResultElement>>, Output) - Method in class org.intermine.webservice.server.core.ResultProcessor
Writes results to output.
write(Iterator<List<ResultElement>>, Output) - Method in class org.intermine.webservice.server.output.JSONResultProcessor
 
write(XMLStreamWriter, Profile, ObjectStore) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
Write template-queries and tags elements.
writeCount(int, Output) - Method in class org.intermine.webservice.server.core.CountProcessor
Write the count to the output.
writeDataPackageAttributes() - Method in class org.intermine.webservice.server.query.result.QueryResultService
Writes dataPackageAttributes in the output stream.
writeFooter() - Method in class org.intermine.webservice.server.output.StreamedOutput
Writes footer
writeLargeUTF(String) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream
Writes the given String to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.
writeLargeUTF(Collection<String>) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream
Writes the given Collection of Strings to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.
writeLargeUTF(StringConstructor) - Method in class org.intermine.sql.writebatch.PostgresDataOutputStream
Writes the given StringConstructor to the stream in modified UTF-8 format, following its length in bytes as a four-byte integer.
writeLn(String) - Method in class org.intermine.webservice.server.output.StreamedOutput
 
writePendingClobs(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
Writes the contents of any pending Clobs to the database, and replaces them in the objects with a real ClobAccess object.
writers - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
 
writtenObjects - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
This is a list of the objects in the destination database that we have written to as a non-skeleton.
WS - Static variable in interface org.intermine.objectstore.query.iql.IqlTokenTypes
 
WS - Static variable in interface org.intermine.pathquery.LogicTokenTypes
 
WS - Static variable in interface org.intermine.sql.query.SqlTokenTypes
 

X

xml - Variable in class org.intermine.web.struts.ImportXMLForm
 
xml(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.LoadQueryAction
Load a query from path query XML passed as a request parameter.
XML - org.intermine.api.mines.ContentType
The XML content type
XML - org.intermine.webservice.server.Format
XML
XmlBinding - Class in org.intermine.util
Represents an XML mapping - performs XML (un)marshalling of objects/Full Data XML
XmlBinding(Model) - Constructor for class org.intermine.util.XmlBinding
Constructor
XmlDataLoader - Class in org.intermine.dataloader
Provides a method for unmarshalling XML given source into java business objects then calls store on each.
XmlDataLoader(IntegrationWriter) - Constructor for class org.intermine.dataloader.XmlDataLoader
 
XmlDataLoaderTask - Class in org.intermine.dataloader
Uses an IntegrationWriter to load data from XML format
XmlDataLoaderTask() - Constructor for class org.intermine.dataloader.XmlDataLoaderTask
 
XMLFormatter - Class in org.intermine.webservice.server.output
Formats data to XML format.
XMLFormatter() - Constructor for class org.intermine.webservice.server.output.XMLFormatter
 
XmlHelper - Class in org.intermine.xml
Static methods to assist parsing and rendering of XML.
xmlRes - Variable in class org.intermine.dataloader.XmlDataLoaderTask
 
xmlRes - Variable in class org.intermine.task.FullXmlConverterTask
 
xmlToTemplateMap(String, Map<String, InterMineBag>, int) - Static method in class org.intermine.api.template.TemplateHelper
Parse templates in XML format and return a map from template name to TemplateQuery.
XmlUtil - Class in org.intermine.util
General-purpose methods for manipulating URIs and XML schema types
XMLValidator - Class in org.intermine.webservice.server.query.result
XMLValidator is class that validates xml string according an XML Schema at specified url.
XMLValidator() - Constructor for class org.intermine.webservice.server.query.result.XMLValidator
 
XMLValidatorErrorHandler - Class in org.intermine.webservice.server.query.result
 
XMLValidatorErrorHandler() - Constructor for class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
 
XMLWidgetProcessor - Class in org.intermine.webservice.server.widget
A processor for handling requests for widget metadata.

Y

youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryCast
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in interface org.intermine.objectstore.query.QueryEvaluable
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryExpression
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryField
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryForeignKey
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryFunction
Allows a caller to suggest to this object that it holds a value of a certain type.
youAreType(Class<?>) - Method in class org.intermine.objectstore.query.QueryValue
Allows a caller to suggest to this object that it holds a value of a certain type.

Z

ZERO - Static variable in class org.intermine.web.logic.widget.ErrorCorrection
 
ZERO_PROFILE_VERSION - Static variable in class org.intermine.api.xml.ProfileManagerBinding
Default version of profile if it is not specified.

_

_tokenNames - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenNames - Static variable in class org.intermine.pathquery.LogicParser
 
_tokenNames - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenNames - Static variable in class org.intermine.sql.query.SqlTreeParser
 
_tokenSet_0 - Static variable in class org.intermine.objectstore.query.iql.IqlLexer
 
_tokenSet_0 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_0 - Static variable in class org.intermine.sql.query.SqlLexer
 
_tokenSet_0 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_0 - Static variable in class org.intermine.sql.query.SqlTreeParser
 
_tokenSet_1 - Static variable in class org.intermine.objectstore.query.iql.IqlLexer
 
_tokenSet_1 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_1 - Static variable in class org.intermine.sql.query.SqlLexer
 
_tokenSet_1 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_1 - Static variable in class org.intermine.sql.query.SqlTreeParser
 
_tokenSet_10 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_10 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_100 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_101 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_102 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_103 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_104 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_105 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_106 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_107 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_108 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_109 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_11 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_11 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_110 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_111 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_112 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_113 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_114 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_115 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_12 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_12 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_13 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_13 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_14 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_14 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_15 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_15 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_16 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_16 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_17 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_17 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_18 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_18 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_19 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_19 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_2 - Static variable in class org.intermine.objectstore.query.iql.IqlLexer
 
_tokenSet_2 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_2 - Static variable in class org.intermine.sql.query.SqlLexer
 
_tokenSet_2 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_20 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_20 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_21 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_21 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_22 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_22 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_23 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_23 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_24 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_24 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_25 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_25 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_26 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_26 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_27 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_27 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_28 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_28 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_29 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_29 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_3 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_3 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_30 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_30 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_31 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_31 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_32 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_32 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_33 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_33 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_34 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_34 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_35 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_35 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_36 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_36 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_37 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_37 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_38 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_38 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_39 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_39 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_4 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_4 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_40 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_40 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_41 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_41 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_42 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_42 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_43 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_43 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_44 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_44 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_45 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_45 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_46 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_46 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_47 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_47 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_48 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_48 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_49 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_49 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_5 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_5 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_50 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_50 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_51 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_51 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_52 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_52 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_53 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_53 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_54 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_54 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_55 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_55 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_56 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_56 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_57 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_57 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_58 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_58 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_59 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_59 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_6 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_6 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_60 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_60 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_61 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_61 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_62 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_62 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_63 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_63 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_64 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_64 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_65 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_65 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_66 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_66 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_67 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_67 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_68 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_68 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_69 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_69 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_7 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_7 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_70 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_70 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_71 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_71 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_72 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_72 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_73 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_73 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_74 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_74 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_75 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_75 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_76 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_76 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_77 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_77 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_78 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_78 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_79 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_79 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_8 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_8 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_80 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_80 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_81 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_81 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_82 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_82 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_83 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_83 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_84 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_84 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_85 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_85 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_86 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_86 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_87 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_87 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_88 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_88 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_89 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_9 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_9 - Static variable in class org.intermine.sql.query.SqlParser
 
_tokenSet_90 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_91 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_92 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_93 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_94 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_95 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_96 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_97 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_98 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
_tokenSet_99 - Static variable in class org.intermine.objectstore.query.iql.IqlParser
 
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