Index (InterMine 5.0.0 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
All Classes All Packages

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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