All Classes Interface Summary Class Summary Enum Summary Exception Summary
| Class |
Description |
| AbstractConstraint |
An abstract representation of an item that can be present in the WHERE or HAVING
sections of an SQL query.
|
| AbstractHelper |
A class that can be extended to easily create RangeHelpers for a particular type.
|
| AbstractListService |
Base class for list services.
|
| AbstractQueryService |
A base class for query services.
|
| AbstractTable |
An abstract representation of an item that can be present in the FROM section of an
SQL query.
|
| AbstractTracker |
Abstract interface for creating trackers objects.
|
| AbstractValue |
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.
|
| AcceptanceTestTask |
A Task to run acceptance tests, configurable from a file.
|
| AddColumnAction |
AddColumnAction adds new column to existing WebTable that should be displayed.
|
| AdditionalConverter |
Represents an additional converter config
|
| AddToBagAction |
Action to save a single object o an existing bag.
|
| AjaxServices |
This class contains the methods called through DWR Ajax
|
| AlwaysMap<K,V> |
This is a dumb implementation of a Map.
|
| AlwaysSet<E> |
A Set that always returns true for the contains method.
|
| AnalyseDbTask |
Task to run ANALYSE on a table or whole database.
|
| AnonProfile |
A null-object for profiles for use with the web services.
|
| API |
The interface of the API, abstracted for testing purposes.
|
| ApiJavaController |
|
| ApiPerlController |
|
| ApiTemplate |
This class extends TemplateQuery to provide the features needed by
the API - Lucene indexing and database serialisation.
|
| ArrayFormatter |
Not good practice, but this is how JBrowse wants results, so when in
Rome.
|
| Aspect |
Configuration for a single data set.
|
| AspectBinding |
Routines for unmarshaling Aspect objects from XML.
|
| AspectController |
Contoller for a single data set tile embedded in a page.
|
| AspectSource |
Describes a source of data contributing to some data set.
|
| AspectTagUtil |
Util class for working with aspect tags.
|
| AsymmetricOperationInput |
A list input class for operations that have a left and a right side.
|
| Attribute |
|
| Attribute |
Representation of an Attribute in an object
|
| AttributeDescriptor |
Describes an attribute of a class - i.e.
|
| AttributeLinkURL |
Simple class that parses provided url.
|
| AuthenticatedListService |
A Class that insists on being authenticated.
|
| Authenticator |
The action that bounces the user off to their respective authentication
provider when they want to use them to log-in with OAuth2.
|
| AuthenticatorService |
This service just generates the appropriate link to the oauth2 provider
Similar to the Authenticator class used by struts.
|
| AuthenticatorServlet |
A Servlet for routing requests to the oauth2 AuthenticatorService.
|
| AutoCompleter |
Autocompleter class for initializing and using the autocompletion
|
| AvailableColumnsController |
Controller for availableColumns.tile.
|
| AvailableListsService |
A service to report what lists a user has access to, and some details of
those lists.
|
| AvailableListsServlet |
|
| AvailableServicesServlet |
Report whether a requested service is implementented on this
mine.
|
| AvailableTemplatesService |
Fetch the names of public template queries for use with the Templates web service.
|
| AvailableWidgetsService |
A service for listing the available widgets.
|
| AvailableWidgetsServlet |
Servlet handling requests for information about which widgets are
available.
|
| BadQueryException |
|
| BadRequestException |
The BadRequestException is thrown by service when there is a problem with the request.
|
| BadTemplateException |
Exception thrown when template has invalid name.
|
| BagBuildController |
Controller Action for buildBag.jsp
|
| BagConstraint |
Constrain a QueryClass or QueryEvaluable to be within a bag.
|
| BagConversionHelper |
Utility methods used when converting lists (bags) between types.
|
| BagConverter |
|
| BagDetailsAction |
Action that builds a PagedCollection to view a bag.
|
| BagDetailsController |
|
| BagDoesNotExistException |
Exception thrown when bag is not found.
|
| BagHelper |
Helper methods for bags.
|
| BagManager |
A BagManager provides access to all global and/or user bags and methods to fetch them by
type, etc.
|
| BagNotFound |
|
| BagOperation |
|
| BagOperationException |
|
| BagOperations |
Perform logical operations on bags - combine bags to create new InterMineBags
|
| BagProducer |
Functional interface for BagOperations, so we can be all forward looking.
|
| BagQuery |
A class encapsulating a query used to create a bag from a collection of input identifiers.
|
| BagQueryConfig |
Configuration for BagQuery objects.
|
| BagQueryHandler |
Handler for bag-query.xml files.
|
| BagQueryHelper |
|
| BagQueryResult |
Class to hold the results of querying for a bag of objects.
|
| BagQueryResult.IssueResult |
Simple struct to hold three pieces of information together.
|
| BagQueryRunner |
For a given list of input strings search for objects using default and configured queries for a
particular type.
|
| BagQueryUpgrade |
|
| BagResultCategoryKeyFormatter |
Format a bag query result, grouping by category of issue.
|
| BagResultFormatter |
|
| BagResultOutputKeyFormatter |
Format a bag result grouping by matched object.
|
| BagSet |
A class containing valiud and invalid bags.
|
| BagState |
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 ))
|
| BagUpgradeAction |
An action that prepare a BagQueryResult and save it into the session.
|
| BagUploadConfirmAction |
Action class for saving a bag from the bagUploadConfirm page into the user profile.
|
| BagUploadConfirmController |
Controller for the bagUploadConfirm; retrieve an IDResolutionService job id
|
| BagUploadConfirmForm |
Form for the bagUploadConfirm page.
|
| BagUploadConfirmInlineResultsTable |
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
|
| BagUploadConfirmInlineResultsTableRow |
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.
|
| BagUploadConfirmIssueController |
Controller for the bagUploadConfirmIssue tile.
|
| BagValue |
A class representing a value stored in an InterMineBag.
|
| Base64PublicKeyDecoder |
A public key decoder that reads public keys encoded as base64 strings.
|
| BaseDisclosureTag |
Base tag handler from which are all disclosure tag handlers derived.
|
| BaseEquivalentObjectFetcher |
Class providing methods to look up equivalent objects by primary key in a production
objectstore.
|
| Batch |
A class representing a collection of writes to an SQL database.
|
| BatchingFetcher |
Class providing EquivalentObjectFetcher functionality that batches fetches to improve
performance.
|
| BatchWriter |
An interface representing an object that can flush a TableBatch to an SQL server Connection.
|
| BatchWriterPostgresCopyImpl |
An implementation of the BatchWriter interface that uses PostgreSQL-specific COPY commands.
|
| BatchWriterPreparedStatementImpl |
An implementation of the BatchWriter interface that uses JDBC PreparedStatement addBatch() and
executeBatch() methods.
|
| BatchWriterSimpleImpl |
An implementation of the BatchWriter interface that uses simple JDBC addBatch() and
executeBatch() methods.
|
| BeginAction |
Prepare templates and news to be rendered on home page
|
| BestQuery |
This object is an abstract superclass for a Best Query tracker.
|
| BestQueryException |
An Exception that may be thrown by an BestQuery.
|
| BestQueryExplainer |
Gets the database to explain each Query added and keeps hold of the best one so far.
|
| BestQueryExplainerVerbose |
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.
|
| BestQueryFallback |
Gets the database to explain each Query added and keeps hold of the best one so far.
|
| BestQueryLogger |
Logs each query added.
|
| BestQueryStorer |
Stores each query added.
|
| BGPropertiesCreationService |
Create a new bluegenes property.
|
| BGPropertiesDelationService |
Delete an existing bluegenes property.
|
| BGPropertiesService |
Return all the existing bluegenes property or a specific one
|
| BGPropertiesServlet |
Runs BGProperties related web service.
|
| BGPropertiesUpdateService |
Update an existing bluegenes property.
|
| BioEntityMarkupService |
Serve bioentity markup to be added to the report page
|
| BrandingService |
Serve branding information so that a client can provide a branded
visual experience.
|
| BuildBagAction |
An action that makes a bag from text.
|
| BuildBagForm |
Form bean to represent the inputs needed to create a bag from user input.
|
| BuildDbTask |
Generates and inserts SQL given database name, schema and temporary directory
|
| CacheHoldingArrayList<E> |
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.
|
| CacheMap<K,V> |
This is a Map implementation designed specifically for people intending to create a cache.
|
| Callback |
The controller that handles the requests made after the user has visited their
authorisation provider to log-in.
|
| CallbackService |
The service handles the requests made after the user has visited their
authorisation provider to log-in.
|
| CallbackServlet |
A Servlet for routing requests to the oauth2 CallbackService.
|
| ChangeEvent |
Events that represent changes in something.
|
| ChangePasswordAction |
|
| ChangePasswordForm |
Form bean to represent the inputs needed to change a password from user input.
|
| ChangePasswordService |
Class for changing the password of an existing user
|
| ChangeTableAction |
Implementation of DispatchAction.
|
| ChangeTableSizeAction |
Changes the size of the results displayed.
|
| ChangeTableSizeForm |
Form bean for changing the page size.
|
| CheckForIsNotNullConstraint |
For use with ConstraintHelper.traverseConstraints().
|
| ClassAttributes |
container class to cache class attributes
|
| ClassChooserController |
Gets list of help text blurbs for each class, and passes them on to the display page.
|
| ClassConstraint |
Constrain whether a QueryClass is equal/not equal to another
QueryClass or an example of an object belonging to a
QueryClass.
|
| ClassDescriptor |
Describe a business model class.
|
| ClassKeyHelper |
Methods to read and manage keys for classes.
|
| ClassKeys |
Type alias for classkeys - simplifies matters and prevents mistakes.
|
| ClassKeyServlet |
A Servlet for routing requests to the ClassKeyService.
|
| ClassKeysNotFoundException |
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.
|
| ClassKeysService |
A service to fetch a JSON representation of class keys for all classes in the model.
|
| ClassNameURIIdentifierMapper |
Class to map the class name defined in the core.xml with the identifier used to generate the
InterMineLUI (e.g.
|
| ClassResourceOpener |
Objects that open resources relative to a classpath.
|
| Clob |
Object representing a large String that has been stored in the database.
|
| ClobAccess |
Class used to read a Clob from the ObjectStore.
|
| ClobAccess.ClobAccessSubclassFactory |
Class to provide fast access to the constructor of plugin subclasses of ClobAccess.
|
| CodeService |
A service for generating code based on a query.
|
| CodeServlet |
A servlet for routing requests to the code service.
|
| CodeTranslator |
Translates strings between codes used in ConstraintOp class and abbreviations or
full code names of operations.
|
| CollectionDescriptor |
Describes a field that references a collection of other objects.
|
| CollectionDetailsAction |
Action that creates a table of collection elements for display.
|
| CollectionTableAction |
Action that creates a table of collection elements for display in a table widget.
|
| CollectionUtil |
Utilities for Collections.
|
| Column |
Configuration information for a column in a table
|
| ColumnHeaderStyle |
Enumeration for outer join status.
|
| CombinedIterator<E> |
An Iterator that combines the contents of various other Iterators.
|
| Command |
|
| CommandRunner |
|
| Commands |
|
| Commands.Action |
|
| CommutativeOperationInput |
An input class for operations that are commutative.
|
| CompletelyFalseException |
Exception thrown if a Constraint is deemed to be completely false.
|
| Config |
Provide standard JBrowse configuration files (trackList.json and
refSeqs.json) that are required to run a JBrowse instance.
|
| ConfigurableMine |
A sub-interface of Mine to encapsulate the mutable elements of the interface, and not
expose them the the consumer.
|
| ConfigurableWebServiceServlet |
A servlet that can be configured entirely in XML.
|
| ConfigurationException |
An error caused when trying to configure something.
|
| ConsistentSet<E> |
A Set that allows for its member objects to be changed whilst still
belonging to the set.
|
| Constant |
A representation of a constant value in an SQL query.
|
| Constants |
A single constant.
|
| Constants |
Container for ServletContext and Session attribute names used by the webapp
|
| Constraint |
Abstract reperesentation of a query constraint.
|
| Constraint |
A representation of a normal constraint, comparing two AbstractValue objects.
|
| ConstraintHelper |
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 |
Simple object that carries constraint values for other processing.
|
| ConstraintOp |
Operations used in building constraints.
|
| ConstraintOptions |
A bundle of options consumed by the AbstractHelper when generating constraint
sets for a set of ranges.
|
| Constraints |
Builds constraints for the PathQuery.
|
| ConstraintSet |
Groups a series of Constraints together.
|
| ConstraintSet |
A representation of a set of constraints ORed together.
|
| ConstraintTraverseAction |
ConstraintTraverseActions are passed to the traverseConstraints() method.
|
| ConstraintValueParser |
Parser for parsing constraint value.
|
| ConstraintWithBag |
Common interface for BagConstraint and MultipleInBagConstraint defining the getBag() method.
|
| ContactAction |
Action handles submission of user feedback form.
|
| ContactForm |
Form bean representing feedback form.
|
| ContainsConstraint |
Constrain whether a QueryClass is member of a QueryReference or not.
|
| ContentType |
An enumeration of the content-types we know about.
|
| ContextNotInitialisedException |
An error thrown when the InterMineContext object has not been initialised.
|
| ConvertBagController |
|
| ConvertedObjectPair |
A class to represent the mapping between an object before type conversion and the converted
object.
|
| ConverterTask |
Task superclass for invoking converters.
|
| CorrectionCoefficient |
An Interface which defines when/how a correction coefficient can be applied
to the results obtained by a enrichment widget
|
| CountProcessor |
A class that processes counts.
|
| CountTableController |
Start a count in a separate thread of the number of rows in the PagedTable given by the
"resultsTable" request attribute.
|
| CreateAccountAction |
|
| CreateAccountForm |
Form bean to represent the inputs to create a new user account
|
| CreateIndexesTask |
Task to create indexes on a database holding objects conforming to a given model by
reading that model's primary key configuration information.
|
| CreateSearchIndexTask |
Create a keyword search index for a mine.
|
| CreateTemplateAction |
Action to create a new TemplateQuery from current query.
|
| CreationEvent |
A representation of a notification a web searchable object has been created.
|
| CSVExportForm |
A form to hold options for CSV and tab separated output.
|
| CSVFormatter |
Formats data to comma separated data format.
|
| CSVHttpExporter |
Exporter that exports table with results in comma separated format.
|
| CSVRowFormatter |
Row formatter formats line as comma separated strings.
|
| CurrentQueryAction |
Action to display the query builder (if there is a current query) or redirect to
project.sitePrefix.
|
| CustomOAuthProvider |
A representation of an OAuth provider which has been configured
entirely in web-properties.
|
| CustomPrintWriter |
Customized PrintWriter that terminates end of the lines with defined line
separator.
|
| Database |
Class that represents a physical SQL database
|
| DatabaseConnectionException |
Exception thrown on failing to object a database connection.
|
| DatabaseFactory |
Creates Databases
|
| DatabaseSchema |
An object that represents the mapping of a Model onto a relational database.
|
| DatabaseSchema.Fields |
Inner class to hold information on Attributes and References.
|
| DatabaseUtil |
Collection of commonly used Database utilities
|
| DatabaseUtil.Type |
|
| DatabaseWriter |
Writes tab-separated Strings to a database table
|
| DataChangedException |
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.
|
| DataConverter |
Abstract parent class of all DataConverters
|
| DataConverterStoreHook |
A hook that is called immediately before each Item is stored by the DataConverter.
|
| DataLoader |
Loads information from a data source into the InterMine database.
|
| DataLoaderHelper |
Class providing utility methods to help with primary key and data source priority configuration
|
| DataService |
|
| DataSetLdr |
An Interface which defines a frame
in which data can be retrieved, organised and created
to then be passed to a JFreeChart for representation
|
| DataTracker |
Interface providing access to data tracking.
|
| DBConverter |
A DataConverter that reads from a Database and writes to a ItemWriter
|
| DBConverterTask |
Task to call DBConverters.
|
| DecodingException |
The error that indicates we cannot decode something.
|
| DefaultOAuthProvider |
A representation of an OAuth provider which is one of the default
providers provided for end-users.
|
| DelegatedIdentity |
A simple struct class for containing information about a delegated identity.
|
| DeletePreferencesService |
A service that deletes a user's preferences.
|
| DeleteTokensService |
Service which ensures that the authenticating user has no tokens.
|
| DeletionEvent |
A representation of a notification that a websearchable has been deleted.
|
| DeletionToken |
A class representing a deletion token.
|
| DeletionTokenCancellationService |
A service that cancels the profile deletion process by deleting the
token that could be used to complete it.
|
| DeletionTokenInfoService |
A service that retrieves information about a deletion token.
|
| DeletionTokens |
A class that manages deletion tokens for the lifespan of a webapp.
|
| DelimitedFileConfiguration |
This class specifies how the values in a tab or comma separated file should be used to fill in
objects in an ObjectStore.
|
| DeregistrationService |
|
| DeregistrationTokenServlet |
A servlet for routing requests to do with deregistration.
|
| DescriptorUtils |
|
| DevNullMap<K,V> |
An implementation of Map that is totally forgetful.
|
| DirectDataLoader |
A DataLoader with helper methods for creating and storing objects using an IntegrationWriter.
|
| DirectDataLoaderTask |
This task uses a DirectDataLoader to create objects and store them directly into an ObjectStore
using an IntegrationWriter.
|
| DirectoryConverter |
Parent class for DataConverters that read from directories
|
| DirectoryConverterTask |
Initiates retrieval and conversion of data from a source directory.
|
| DisclosureBodyTag |
This class renders disclosureBody tag.
|
| DisclosureDetailsTag |
This class renders disclosureDetails tag.
|
| DisclosureHeadTag |
This class renders disclosureHead tag.
|
| DisclosureTag |
This class renders disclosure tag.
|
| DisclosureTitleTag |
This class renders disclosureTitle tag.
|
| DisplayCollection |
Class to represent a collection field of an object for the webapp
|
| DisplayConstraint |
Representation of a PathQuery constraint for use by JSP pages.
|
| DisplayConstraintFactory |
A class that will help you manufacture instances of DisplayConstraint.
|
| DisplayConstraintHelpMessages |
Class to generate help messages appropriate to a given constraint for display in the QueryBuilder
and template form.
|
| Displayer |
Configuration object describing details of a displayer
|
| DisplayerManager |
Read in and provide access to report page displayers.
|
| DisplayField |
Class to represent a field of an object for the webapp
|
| DisplayLookupMessageHandler |
|
| DisplayPath |
A small wrapper around Path with more jsp-accessible data.
|
| DisplayReference |
Class to represent a reference field of an object for display in the webapp
|
| DropPrecomputedTablesTask |
A Task that drops all precomputed tables in an ObjectStore.
|
| DummyExplainResult |
Subclass of ExplainResult not associated with a database.
|
| DumpDefaultTemplatesTask |
Dump templates and configuration tags.
|
| DuplicateMappingException |
|
| DynamicAttributeTask |
An ant task that provides a method for setting attributes dynamically within a class.
|
| DynamicBean |
Class which represents a generic bean
|
| DynamicUtil |
Utilities to create DynamicBeans
|
| EditPropertiesAction |
A controller to edit the properties of a running application.
|
| EditPropertiesForm |
An overly verbose way of passing parameters back to the controller.
|
| EditTemplateAction |
Action to edit a user template query.
|
| Either<A,B> |
Disjoint type union
|
| Either.Left<A,B> |
|
| Either.Right<A,B> |
|
| EitherVisitor<A,B,T> |
A mapping function capable of accessing a disjoint sum-type (an Either A B).
|
| Emailer |
A class that will send emails to people.
|
| EmailerFactory |
|
| EncloseSubqueryBestQuery |
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.
|
| Endpoint |
|
| EnrichmentCalculation |
Calculate enrichment of an attribute applied to members of a sample that is a subset of a larger
population.
|
| EnrichmentInput |
Define methods to access data an enrichment calculation needs to be provided with.
|
| EnrichmentInputWidgetLdr |
Executes queries and summarises data for a specific EnrichmentWidgetLdr ready for calculation.
|
| EnrichmentJSONProcessor |
|
| EnrichmentOptions |
The type of options that enrichment widgets expect to receive.
|
| EnrichmentResultProcessor |
The type of objects that can process enrichment results for serialisation
to the outside world.
|
| EnrichmentResults |
A container for results from an Enrichment analysis.
|
| EnrichmentWidget |
|
| EnrichmentWidgetConfig |
A description of an enrichment calculation.
|
| EnrichmentWidgetForm |
|
| EnrichmentWidgetImplLdr |
Implement methods to access data an enrichment calculation needs to be provided with.
|
| EnrichmentWidgetResultService |
Web service that returns the result of an enrichment calculation over a list
of objects.
|
| EnrichmentXMLProcessor |
A widget result processor for enrichment results that produces output
as XML.
|
| EquivalentObjectFetcher |
Interface providing methods to look up equivalent objects by primary key in a production
objectstore.
|
| EquivalentObjectHints |
Object for holding hint data for the getEquivalentObjects method in IntegrationWriters.
|
| ErrorCorrection |
See online help docs for detailed description of what error correction is and why we need it.
|
| ErrorCorrection.Strategy |
|
| ErrorMessagesController |
Take the messages stored in the session which are not using ActionMessages or ActionErrors and
put them in the request
|
| EvictOrphansTask |
A task for removing tags that don't point to anything.
|
| ExpiresHeaderFilter |
A Filter that modifies response headers of outgoing pages.
|
| ExplainResult |
Represents a result from an EXPLAIN request to a database.
|
| ExportController |
Controller to initialise for the export.tile
|
| Exporter |
Simple exporter interface.
|
| ExporterImpl |
Simple exporter exporting data as tab separated, comma separated
and so.
|
| ExportException |
Exception thrown if the there is a problem while exporting (eg.
|
| ExportHelper |
Helper methods for exporters.
|
| ExportOptionsController |
Controller for exportOptions.tile
|
| ExportQueryAction |
Export the current query in XML format.
|
| ExportResultsIterator |
An Iterator that produces data in a format suitable for exporting.
|
| ExportTagsAction |
Export tags.
|
| ExtraQueryTime |
An object that holds information about extra queries run during the ResultsConverter operation.
|
| F<A,B> |
A type for a function from A -> B.
|
| F.Constant<X,R> |
An implementation of a constant function.
|
| FacetListService |
A web service for returning all the facet list
|
| FacetListServlet |
A web service for returning all the facet list
|
| FacetService |
A web service for returning facet related to particular query
|
| FacetServlet |
A web service for returning facet related to particular query
|
| FastPathObject |
A root interface for all objects that can be stored in a InterMine database.
|
| FavouritesController |
Controller for the starTemplate tile.
|
| FeedbackService |
Send feedback from users
|
| FeedbackServlet |
Send feedback from users
|
| Field |
A representation of a field in a table.
|
| FieldConfig |
The webapp configuration for one field of a class.
|
| FieldConfigHelper |
Helper methods for the FieldConfig class.
|
| FieldDescriptor |
Abstract representation of a field within a class - could be an attribute, an
object reference or a collection.
|
| FieldExporter |
An interface implemented by objects that can export the value of a particular.
|
| FileConverter |
Parent class for DataConverters that read from files
|
| FileConverterTask |
Initiates retrieval and conversion of data from a source file.
|
| FileDirectDataLoaderTask |
A DirectDataLoaderTask for files.
|
| FileDownloadAction |
This is a generic action to download file from any given directory.
|
| FilteringResultIterator |
A result iterator that skips things we aren't interested in.
|
| FindInListAction |
Action to search a list for an identifier and then highlight it on the list details page.
|
| FindInListForm |
Form for FindInListAction.
|
| FlatFileFormatter |
A class to define behaviour common to flat files (csv, tsv)
|
| FlatFileWidgetResultProcessor |
A widget result processor that produces results in flat file format (tsv/csv)
|
| FlatListFormatter |
Formats a list into its name.
|
| FlatWidgetProcessor |
|
| FlushJob |
An interface representing a job to be performed when actually flushing data to a database.
|
| FlushJobBatchCommit |
A FlushJob that commits and re-opens a transaction on the database.
|
| FlushJobPostgresCopyImpl |
An implementation of the FlushJob interface that represents a batch created in a Statement.
|
| FlushJobStatementBatchImpl |
An implementation of the FlushJob interface that represents a batch created in a Statement.
|
| FlushJobUpdateStatistics |
An interface representing a job to be performed when actually flushing data to a database.
|
| Format |
|
| FormattedTextParser |
Class for methods and util methods for parsing csv files and others.
|
| Formatter |
Abstract class for formatting result data.
|
| ForseenProblem |
An exception type to plaster over the absence of first-class
continuations in java.
|
| ForwardParameters |
Utility wrapper class for programatically adding parameters to ActionForward paths.
|
| FrictionlessDataPackage |
Exports Frictionless Data Package if the parameter exportDataPackage
is true.
|
| FriendlyMineManager |
Class to manage friendly mines
|
| FromElement |
An element that can appear in the FROM clause of a query
|
| FullHandler |
Extension of DefaultHandler to handle parsing full XML.
|
| FullParser |
Unmarshal XML Full format data into java business objects.
|
| FullRenderer |
Render an object in InterMine Full XML format
|
| FullXmlConverter |
Loads InterMine XML into an items database.
|
| FullXmlConverterTask |
Load InterMine Items XML file(s) into a target items database.
|
| Function |
A representation of a function in an SQL query.
|
| Function<A,B> |
An interface for defining a thing that can take something and return
something else.
|
| GenerateUpdateTriggersTask |
|
| GetAttributeAsFileAction |
Provide an attribute value as a file
|
| GlobalRepository |
A representation of an object that knows how to index global objects, and also how to respond
to changes to those objects.
|
| GotoWebSearchableAction |
Action handles search.
|
| GrantTask |
Task to grant permissions on all tables in a database to a given user.
|
| GraphJSONProcessor |
A widget result processor that produces chart results in JSON.
|
| GraphService |
|
| GraphWidget |
|
| GraphWidgetActionType |
Enumeration for possible actions when create the query for graph widgets.
|
| GraphWidgetConfig |
Configuration object describing details of a graph displayer
|
| GraphWidgetLoader |
The class that does the actual querying for results.
|
| GraphWidgetsServlet |
Servlet running WidgetsService.
|
| GraphXMLProcessor |
A processor for returning results from graph widgets in XML.
|
| HasFromList |
Interface to define the types of things that can have from elements added to them.
|
| HeaderConfigLink |
Will store a link configured through HeaderConfig (WebConfig) and used on report page header
|
| HeaderConfigTitle |
Configuration of an object (Type) header when displayed on report
|
| HeaderFilter |
A Filter that modifies response headers of outgoing pages.
|
| HeartbeatAction |
Takes a parameter "type" with value "webapp" or "query" and prints "OK"
to the client if everything is ok, otherwise something else.
|
| HintingFetcher |
Class providing EquivalentObjectFetcher functionality that makes use of hints to improve
performance.
|
| HomePageMarkupService |
Serve markup to be added to the home page
|
| HtmlHeadController |
Controller for the html head tile.
|
| HtmlListFormatter |
A formatter that represents lists as HTML.
|
| HTMLOutput |
HTMLOutput extends is similar to MemoryOutput, only difference is, that it prints out errors
immediately to output.
|
| HTMLTableFormatter |
A formatter that presents query results as HTML.
|
| HTMLWidget |
Represents a widget with no data, it just diplays the "content" string.
|
| HTMLWidgetConfig |
dummy widget to output html widget
|
| HttpClient |
Very simple http client that downloads data.
|
| HttpExporterBase |
Abstract class with functionality common for all classes implementing TableHttpExporter
interface like getting result from paged table.
|
| HttpExportUtil |
Util for export.
|
| HttpRequester |
A mine requester that makes HTTP requests.
|
| IdentityMap<E> |
This is a dumb implementation of a Map.
|
| IdResolutionService |
|
| IdResolutionServlet |
Route requests for ID resolution.
|
| IDResolver |
|
| IdUpgrader |
Bag object id upgrader - find old objects in a new ObjectStore.
|
| ImportQueriesAction |
Imports query in XML format and forward user to the query builder.
|
| ImportQueriesForm |
Form bean representing query import form.
|
| ImportTagsAction |
Import tags.
|
| ImportTagsForm |
Form bean representing tags import form.
|
| ImportXMLForm |
Form bean representing a generic import form.
|
| IncompatibleTypes |
|
| IncompatibleTypesException |
Exception thrown when given bags are of incompatible types, has methods to set and fetch the
types.
|
| IndexHandler |
Interface for handling indexes.
|
| IndirectionTableBatch |
A class representing all changes to be made to an SQL indirection table.
|
| InitialiserPlugin |
Initialiser for the InterMine web application.
|
| InlineList |
|
| InlineListConfig |
Represents an inline list to be shown on a Report page
|
| InlineListObject |
An individual InterMineObject wrapped in an InlineList Set
|
| InlineResultsTable |
An inline table created from a Collection
This table has one object per row
|
| InlineResultsTableRow |
Provides a wrapper for a row of InlineTableResultElement
|
| InlineTableResultElement |
ResultElement used in an InlineResultsTable
|
| InlineTagEditorController |
Controller for the inline tag editing tile
|
| InListConstraint |
A representation of a constraint where an AbstractValue is IN a list of constants.
|
| Instance |
Pojo class to map the intermine instance retrieved from the registry
|
| IntegrationWriter |
Define methods needed to deal with integration when writing to an ObjectStore.
|
| IntegrationWriterAbstractImpl |
Abstract implementation of ObjectStoreIntegrationWriter.
|
| IntegrationWriterDataTrackingImpl |
Priority-based implementation of IntegrationWriter.
|
| IntegrationWriterFactory |
Produce IntegrationWriters
|
| InterMineAction |
An InterMine specific version of Action.
|
| InterMineAPI |
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.
|
| InterMineBag |
An object that represents a bag of objects in our database for the webapp.
|
| InterMineBagBinding |
Parse InterMineIdBags in XML format
|
| InterMineBagHandler |
A handler for turning XML bags data into an InterMineIdBag.
|
| InterMineContext |
A context object that doesn't require the session.
|
| InterMineDispatchAction |
An InterMine specific version of DispatchAction.
|
| InterMineException |
An Exception that may be thrown by client facing parts
of InterMine code.
|
| InterMineExceptionHandler |
InterMine implementation of the Struts ExceptionHandler
|
| InterMineFastPathObject |
A root interface for all objects that can be stored in a InterMine database.
|
| InterMineLinkGenerator |
Helper class for intermine links generated on report and list pages
|
| InterMineLinkGenerator |
Helper class for intermine links generated on report and list pages
|
| InterMineLookupDispatchAction |
An InterMine specific version of LookupDispatchAction.
|
| InterMineLUI |
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
|
| InterMineLUIConverter |
This class converts an intermineID into a InterMineLUI
or a InterMineLUI into an intermineID.
|
| InterMineModelParser |
Parse InterMine metadata XML to produce an InterMine Model
|
| InterMineObject |
A root interface for all objects that can be stored in a InterMine database.
|
| InterMineRequestProcessor |
A RequestProcessor that sends you back to the start if your session isn't valid.
|
| InterMineResultsContainer |
container to hold results for a reference query and associated iterator
|
| InternalBagOperationException |
Exceptions that are the fault of underlying infrastructure, and not the way the
classes themselves were used.
|
| Intersection |
|
| IntHelper |
|
| IntPresentSet |
This is a set of ints.
|
| IntToIntMap |
This is a map that maps from int to int.
|
| InvalidBag |
A class representing a bag that is invalid because it does not conform to the current model.
|
| InvalidPermanentURLException |
Thrown to indicate that the http request is not a permanent URL
The valid patters is: domain/context/classname:identifier
(e.g.
|
| InvalidQueryException |
A class representing a failure to generate the code for a query because
the query is invalid.
|
| InvitationAction |
Action that processes invitations.
|
| InvitationForm |
A form that contains the information for requests that invite users to share resources.
|
| InvitationHandler |
|
| IqlLexer |
|
| IqlParser |
|
| IqlQuery |
OQL representation of an object-based Query
|
| IqlQueryParser |
Parser for the InterMine dialect of OQL (IQL)
|
| IqlTokenTypes |
|
| ISO8601DateFormat |
A date formatter for the ISO8601 date format.
|
| IssueTokenTask |
A task that will issue a signed JWT token for the current configuration.
|
| Item |
|
| Item |
Representation of an object
|
| ItemFactory |
ItemFactory class
|
| ItemHelper |
Class providing Item utility methods
|
| ItemToObjectTranslator |
Translator that translates fulldata Items to business objects
|
| ItemWriter |
Stores Items in something - an objectstore or otherwise.
|
| IteratorIterable<T> |
This is an Iterable that returns a given Iterator.
|
| JaccardIndexService |
A service to compare the given list to all other available lists using the Jaccard Index
|
| JaccardIndexServlet |
|
| JavaModelOutput |
Maps InterMine metadata to Java source files
|
| Job |
|
| Job.JobStatus |
|
| JobInput |
|
| JobJanitor |
Wake up once a minute and evict old completed jobs.
|
| JobRemovalService |
|
| JobResultsService |
|
| JobStatusService |
|
| JSONCountFormatter |
A formatter that presents count results as JSON.
|
| JSONDataTableRowIterator |
|
| JSONDataTableRowResultProcessor |
A result processor for result rows.
|
| JSONFormatter |
Base class for formatters that process JSON data.
|
| JSONFormattingException |
|
| JSONListFormatter |
|
| JSONObjectFormatter |
|
| JSONObjResultProcessor |
|
| JSONQueryHandler |
Handle parsing JSON queries and template queries
|
| JSONResultFormatter |
|
| JSONResultProcessor |
An class that defines the basic methods for processing JSON results.
|
| JSONResultsIterator |
A class to to produce a sequence of JSONObjects from a set of database rows.
|
| JSONRowFormatter |
|
| JSONRowIterator |
|
| JSONRowResultProcessor |
A result processor for result rows.
|
| JSONRowResultProcessor.Verbosity |
|
| JSONService |
A Service that has specialisations for supplying JSON.
|
| JSONSummaryProcessor |
A processor for summary results in JSON format.
|
| JSONTableFormatter |
|
| JSONTableResultProcessor |
|
| JSONUserFormatter |
A formatter that knows how to format a user in JSON
|
| JSONWidgetProcessor |
|
| JSStrings |
|
| JWTBuilder |
A class that encapsulates the logic required to generate JWT tokens
for users.
|
| JWTBuilder.Algorithm |
The signing algorithms this builder supports.
|
| JWTVerifier |
A class to encapsulate the logic for verifying identity claims as represented as JWTs
(JSON Web Tokens).
|
| JWTVerifier.Verification |
The result of a successful verification.
|
| JWTVerifier.VerificationError |
An error that declares that something has gone wrong when trying to
verify a JWT.
|
| KeyDecoder |
Classes that can decode public keys from strings.
|
| KeyFormatException |
|
| KeySearchTrack |
|
| KeySearchTracker |
|
| KeySigner |
Issue certificates for keys we trust.
|
| KeySourceException |
Errors encountered when using a PublicKeySource
|
| KeyStoreBuilder |
Build a key store from some options and possibly a keystore file.
|
| KeyStorePublicKeySource |
A public key store that reads keys from a key store.
|
| KeyStoreTask |
Base task for tasks that require a key store.
|
| KeywordSearchFacet<E> |
container for one faceting field, the current faceting value and the list of
possible items
|
| KeywordSearchFacetData |
container class for a facet field and its settings
|
| KeywordSearchFacetType |
type of faceting to use
see http://snaprojects.jira.com/wiki/display/BOBO/Create+a+Browse+Index
|
| KeywordSearchHandler |
Interface for handling indexes.
|
| KeywordSearchPropertiesManager |
A manager class to handle all the configuration properties from keyword_search.properties file
|
| KeywordSearchResult |
Container for a single result row from the keyword search
|
| KeywordSearchResultContainer<E> |
Container for individual Keyword Search Result
The document type has been given as generic type.
|
| KeywordSearchResults |
A class that wraps both a collection of hits and a collection of facets.
|
| KeywordSearchResultsController |
Controller for keyword search.
|
| LabelsSummaryAction |
An action that presents how all the labels configured for classes and their
top-level fields appear.
|
| Lazy |
Class which uses an ObjectStore to perform lazy fetching of data
|
| LazyCollection<E> |
Class which uses an ObjectStore to perform lazy fetching of data
|
| LimitedMap<K,V> |
A caching map that drops its eldest entries if the map grows beyond a certain size.
|
| LimitOffsetQuery |
A class specifically for use with the OptimiserCache, designed to split a SQL string into
its functional part, and the limit and offset.
|
| LinkGeneratorBase |
Base class for link generators.
|
| LinkRedirectManager |
Class to manage external links.
|
| ListAppendService |
|
| ListBuildMode |
|
| ListCreationInput |
Class representing the input to a list creation request.
|
| ListDeletionService |
A service for deleting lists from the user-profile database.
|
| ListDifferenceService |
A service for performing a symmetric difference operation on a collection
of lists.
|
| ListFormatter |
The common interface for formatters that know how to format lists.
|
| ListFunctions |
Similar to Apache CollectionUtils - but with Generics.
|
| ListInput |
Class representing input to a list service request.
|
| ListIntersectionService |
A service that intersects one or more lists.
|
| ListMaker<T> |
The type of things that can make lists.
|
| ListMakerService |
A base class for all list services that create lists.
|
| ListManager |
Manager of public lists used by web service.
|
| ListOperationService |
A base class for services that perform operations on lists.
|
| ListRenameInput |
Class for encapsulating the input to a list rename request.
|
| ListRenameService |
A service for renaming lists.
|
| ListRenameServlet |
|
| ListResolutionService |
|
| ListResolutionServlet |
Route requests for list resolution.
|
| ListServiceUtils |
Utility functions for dealing with list requests.
|
| ListShareCreationService |
|
| ListShareDeletionService |
|
| ListShareDetailsService |
|
| ListShareServlet |
|
| ListSharingInvitationAcceptanceService |
|
| ListSharingInvitationDeletionService |
|
| ListSharingInvitationDetailsService |
|
| ListSharingInvitationService |
Invite a user to share a list.
|
| ListSharingInvitationServlet |
|
| ListsRequestParser |
Request processor for ListsService that process request, validates it and returns
parsed input as a parameter object.
|
| ListsService |
Web service that returns all public lists (bags) that contain object with
specified id.
|
| ListsServiceInput |
ListsServiceInput is parameter object representing parameters for ListService web service.
|
| ListSubtractionService |
A service for subtracting one group of lists from another group of lists to produce a new
list.
|
| ListTagAddingService |
A service for adding tags to a list.
|
| ListTagRemovalService |
A service for removing tags from a list.
|
| ListTagsController |
Controller for tag display tile on the lists page
|
| ListTagService |
A service for getting the tags of a list.
|
| ListTrack |
Class to represent the track for the lists objects.
|
| ListTrackBinding |
|
| ListTracker |
|
| ListTrackerEvent |
|
| ListUnionService |
A class for exposing creating unions of lists as a resource.
|
| ListUpdateService |
A service for updating list descriptions.
|
| ListUpgradingService |
A service for upgrading lists after a new build.
|
| ListUpgradingServlet |
|
| ListUploadService |
A class to create a new list with via a set of identifiers uploaded by a user.
|
| LoadBagValuesTask |
Task to load bagvalues table in the userprofile database.
|
| LoadDefaultTemplatesTask |
Load template queries form an XML file into a given user profile.
|
| LoadQueryAction |
Implementation of Action that sets the current Query for
the session from some random XML the user has passed in, and maybe executes it.
|
| LoadTemplateAction |
Implementation of Action that runs a template
|
| LocalMine |
A mine that refers to the local application instance.
|
| LogicExpression |
In memory representation of constraint logic expression.
|
| LogicLexer |
|
| LogicParser |
|
| LogicTokenTypes |
|
| LoginAction |
Action to handle button presses on the main tile
|
| LoginController |
Controller for the login page.
|
| LoginForm |
The main form, using for editing constraints
|
| LoginHandler |
|
| LoginService |
Login service which authenticates an existing user, given username and password
and attaches the anonymously created lists to it.
|
| LoginServlet |
Runs the login service
|
| LoginTrack |
|
| LoginTrackBinding |
|
| LoginTracker |
Class for tracking when the users log into their accounts.
|
| LogoutAction |
Action that invalidates the user session effectively logging the user out of
intermine.
|
| LogoutService |
Logout service which invalidates the token assigned to the user logging out
It requires token authentication
|
| LogoutServlet |
Runs the logout service
|
| LookupTokeniser |
Class for tokenising identifier input.
|
| MailAction |
The type of objects that can send themselves with an Emailer.
|
| MailDaemon |
An runnable that will send emails delivered over a concurrent queue.
|
| MailUtils |
Mail utilities for the webapp.
|
| MainHelper |
Helper methods for main controller and main action
|
| MainHelper.RangeConfig |
|
| MainHelper.SummaryConfig |
Controls access to configuration information on which fields should be summarised as a count
of occurrences.
|
| MapListener<K,V> |
|
| MappingUtil |
Useful utilities to do with mappings.
|
| MappingUtilChecker<T> |
Interface providing the capability to check partial mappings for validity for the MappingUtil.
|
| MassTaggingEvent |
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.
|
| MemoryOutput |
Implementation of Output that saves data to memory.
|
| MemoryQueryStore |
An in-memory implementation of a query store.
|
| MessageFormat |
|
| MetaDataException |
An Exception that may be thrown if metadata is in an invalid state.
|
| MetadataManager |
Class to handle persistence of an intermine objectstore's metadata to the objectstore's database
|
| MetadataManager.LargeObjectInputStream |
Class providing an InputStream interface to read a value from the database.
|
| MetadataManager.LargeObjectOutputStream |
OutputStream class that writes to a large object in the database.
|
| MetadataNode |
Node used in displaying metadata
|
| MigrationMapping |
A simple record that contains mapping information about the old id of a user.
|
| Mine |
The type of objects that represent InterMine instances.
|
| MineRequester |
The type of objects that can request data from mines.
|
| MinimalJsonIterator |
|
| MissingParameterException |
|
| MockItemWriter |
Mimic behaviour of an ItemWriter but actually store Items in a Map rather than
an ObjectStoreWriter
|
| Model |
Represents a named business model, makes available metadata for each class
within model.
|
| ModelBrowserHelper |
Static class holding methods for managing the model browser in the query builder.
|
| ModelBrowserHelper.NodeBuilder |
An object that will descend through the model and build a tree of metadata nodes.
|
| ModelFactory |
A class that loads a model given a name.
|
| ModelFileMerger |
Methods for merging a model from a list of files.
|
| ModelMerger |
Merge model additions into a source model to produce a new larger model.
|
| ModelMergerException |
An Exception that may be thrown by ModelMerger methods.
|
| ModelMergerTask |
Task to merge a single additions file into an intermine XML model.
|
| ModelOutputTask |
Creates and runs a ModelOutput process to generate java or config files.
|
| ModelParser |
Common interface for parsing source models into InterMine model format.
|
| ModelParserException |
An Exception that may be thrown by ModelMerger methods.
|
| ModelService |
Web service that returns a serialised representation of the data model.
|
| ModelServlet |
Runs ModelService web service.
|
| ModelUpdate |
Update savedquery, savedtemplatequery and savedbag when the model has been changed
|
| ModelUpdateTask |
Task updating savedquery, savedtemplatequery and savedbag in the userprofile (identified by
the userProfileAlias) when the model has been changed
|
| ModifyBagAction |
Implementation of Action to modify bags
|
| ModifyBagDetailsAction |
|
| ModifyBagDetailsForm |
|
| ModifyBagForm |
Form bean to used in combining bags
|
| ModifyDetails |
Action to handle events related to displaying Report templates and displayers
|
| ModifyQueryAction |
Action that results from a button press on the user profile page.
|
| ModifyQueryChangeAction |
Implementation of Action that modifies a saved query or bag.
|
| ModifyQueryForm |
Form bean to used in combining queries
|
| ModifySuperUserAction |
Implementation of Action to modify superuser role
|
| ModifySuperUserForm |
Form bean used in user admin page
|
| ModifyTemplateAction |
Action that results from a button press on the user profile page.
|
| ModifyTemplateForm |
Form bean used on the saved template form.
|
| MultipleInBagConstraint |
Constraint type requiring any of the given QueryEvaluables to be in a given bag.
|
| MultiRow<E> |
A subclass of ArrayList returned by the ResultsFlatOuterJoinsImpl indicating a row that
can be represented as multiple rows because of collections.
|
| MultiRowFirstValue<E> |
An object representing an entry in a MultiRow - the first instance of this value in a rowspan.
|
| MultiRowLaterValue<E> |
An object representing an entry in a MultiRow - entries other than the first value of the
rowspan.
|
| MultiRowValue<E> |
An object representing an entry in a MultiRow.
|
| MyMineController |
Tiles controller for history tile (page).
|
| Names |
|
| NameSpacedProperties |
Class for simplifying access to sets of namespaces properties.
|
| NameUtil |
Utility methods for naming queries and lists.
|
| NavigationBarTag |
Class implementing rendering of html of navigation bar.
|
| NewDeletionTokenService |
A service that issues a deletion token to a user who intends to
delete their profile.
|
| NewUserService |
Service for creating a new user.
|
| NewUserServlet |
Servlet for handing off requests to the a NewUserService.
|
| NoContent |
|
| NoContentException |
The NoContentException is thrown by a service when the resource requested exists but
has an empty representation.
|
| Node |
Superclass of left and right nodes
|
| NonFatalMetaDataException |
An Exception that may be thrown if metadata is in an invalid state.
|
| NonOverrideableProperties |
Subclass of java.util.Properties that rejects duplicate definitions of a given property.
|
| NonUniqueName |
Exception for non-unique name
|
| NoServiceException |
Exception to throw to signal that there is no service bound to a
particular method on a particular endpoint.
|
| NotAcceptableException |
|
| NotConstraint |
A representation of a constraint that is represented here as the inverse of another Constraint.
|
| NotCurrent |
|
| NotImplementedException |
|
| NotPresentException |
|
| NotXmlParser |
Parses a String suitable for storing in the OBJECT field of database tables into an Object.
|
| NotXmlRenderer |
Render on object into a String suitable for storing in the OBJECT field of database tables.
|
| NullFirstComparator |
A Comparator that uses the natural ordering of elements implementing Comparable, plus null is
allowed and always before all other elements.
|
| NullMailer |
An emailer that doesn't send emails, but does log what it has been asked to do.
|
| OAuthProvider |
A description of an OAuth Provider that we can use as a source
of identity information.
|
| ObjectDescription |
Object class used by DataTracker for data tracking.
|
| ObjectDetails |
An object that describes an object.
|
| ObjectDetailsBeanInfo |
An object that describes the ObjectDetails bean and supports DWR serialization.
|
| ObjectFormatter |
Simpler version of JSONFormatter that doesn't add any
extra information, except in case of error.
|
| ObjectPipe<E> |
This is a rather simple implementation of a queue designed for passing objects from one
Thread to another to form a pipeline.
|
| ObjectRequest |
A generic container for a request for information about an object.
|
| Objects |
Helper class to encapsulate some common logic regarding the use of data objects.
|
| ObjectStore |
Gets the Results of a Query from an underlying store.
|
| ObjectStoreAbstractImpl |
Abstract implementation of the ObjectStore interface.
|
| ObjectStoreBag |
Object representing a collection of objects which have been stored in the database.
|
| ObjectStoreBagCombination |
Object representing a combination of ObjectStoreBags.
|
| ObjectStoreBagsForObject |
Object representing a query to fetch ObjectStoreBag IDs for ObjectStoreBags that contain a
certain value.
|
| ObjectStoreDataLoader |
Loads information from an ObjectStore into the InterMine database.
|
| ObjectStoreDataLoaderTask |
Uses an IntegrationWriter to load data from another ObjectStore.
|
| ObjectStoreException |
An Exception that may be thrown by an ObjectStore indicating a fatal error.
|
| ObjectStoreFactory |
Produce ObjectStores
|
| ObjectStoreFastCollectionsForTranslatorImpl |
Provides an implementation of an objectstore that explicitly materialises all the collections
in the results set it provides, written for the translating objectstore.
|
| ObjectStoreFastCollectionsImpl |
Provides an implementation of an objectstore that explicitly materialises all the collections
in the results set it provides.
|
| ObjectStoreInterMineImpl |
An SQL-backed implementation of the ObjectStore interface.
|
| ObjectStoreItemWriter |
Stores Items in an objectstore.
|
| ObjectStoreLimitReachedException |
An exception that may be thrown by the objectstore, when an access is made outside the allowable
maximum query size.
|
| ObjectStorePassthruImpl |
A generic ObjectStore that passes through every request to an underlying ObjectStore.
|
| ObjectStoreQueryDurationException |
An Exception thrown if the estimated time to complete a query is greater than the maximum
permitted.
|
| ObjectStoreSafeImpl |
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.
|
| ObjectStoreSummary |
A summary of the data in an ObjectStore
|
| ObjectStoreTranslatingImpl |
ObjectStore that transparently translates incoming queries and outgoing objects
|
| ObjectStoreWriter |
Store, update, and delete objects
|
| ObjectStoreWriterFactory |
Produce ObjectStoreWriters
|
| ObjectStoreWriterInterMineImpl |
An SQL-backed implementation of the ObjectStoreWriter interface, backed by
ObjectStoreInterMineImpl.
|
| ObjectTrailController |
Controller for the object trail tile.
|
| ObjectTrailController.TrailElement |
Bean passed to JSP to represent an element in the trail.
|
| ObjectValueContainer |
container class to hold the name and value of an attribute for an object to
be added as a field to the document
|
| ObjectViewController |
Controls display of data in results tables.
|
| OpenIDAuthenticator |
Authenticate requests using OpenID
|
| OptimiserCache |
A class that provides an implementation of a cache for String-based SQL query optimisation.
|
| OptimiserCacheLine |
A class that provides an implementation of a cache line, encapsulating several pieces of data.
|
| OptimiserMappingChecker |
Class for checking partial mappings for validity for the MappingUtil.
|
| OrderDescending |
An element that can appear in the ORDER BY clause of a query, to reverse the order.
|
| OrderDescending |
A representation of an item that can be present in the ORDER BY section of an SQL query, but
ordered descending..
|
| OrderDirection |
An enumeration for the direction of sorting for results.
|
| OrderElement |
An element of the order by list of a PathQuery, containing a path and a direction.
|
| OriginatingEvent |
A representation of a notification that something has happened that originated at a particular
web searchable object.
|
| OuterJoinStatus |
Enumeration for outer join status.
|
| Output |
Abstract class representing an output of a web service.
|
| OverlapConstraint |
Represents a constraint comparing two range values on an object.
|
| OverlapRange |
Represents a range value on an object.
|
| Page |
Parameter class for passing start and limit arguments to
iterators.
|
| PagedTable |
Deprecated.
|
| PageOutOfRangeException |
PageOutOfRangeException class
|
| PageTableQueryMonitor |
An implementation of QueryMonitor that maintains a timeout and remembers which PagedTable it is
monitoring
|
| Pair<A,B> |
A tuple of order two.
|
| ParallelBatchingFetcher |
Class providing EquivalentObjectFetcher functionality that fetches batches of equivalent objects
in parallel to improve performance.
|
| ParallelPrecomputer |
An object that can perform a set of precomputes in parallel.
|
| ParallelPrecomputer.Job |
Class representing a precomputing job to be performed.
|
| ParseValueException |
Exception thrown during parsing constraint value.
|
| PartnerLink |
A bean that contains the information to define a matching set of objects.
|
| PartnerLinkBeanInfo |
An object that describes the PartnerLink bean and supports DWR serialization.
|
| PasswordHasher |
Utility methods for managing hashed passwords
|
| PasswordResetAction |
Action to change a user's password with the authority of a token previously emailed to them.
|
| PasswordResetController |
Controller for the password reset page.
|
| PasswordResetForm |
The form for resetting a password.
|
| Path |
Object to represent a path through an InterMine model.
|
| PathConstraint |
Representation of a constraint in the PathQuery.
|
| PathConstraintAttribute |
Representation of a normal attribute constraint in the PathQuery
|
| PathConstraintBag |
Representation of a constraint to a bag in the PathQuery
|
| PathConstraintIds |
Representation of a constraint to a collection of object ids in a query.
|
| PathConstraintLookup |
Representation of a lookup constraint in the PathQuery
|
| PathConstraintLoop |
Representation of a loop constraint in the PathQuery
|
| PathConstraintMultitype |
A constraint that restricts a path to inhabiting one of a list of types.
|
| PathConstraintMultiValue |
Representation of a constraint to a collection of values in a query.
|
| PathConstraintNull |
Representation of a null attribute constraint in the PathQuery
|
| PathConstraintRange |
A constraint that restrict a path to a particular relationship with a set of ranges.
|
| PathConstraintSubclass |
Representation of a subclass constraint in the PathQuery.
|
| PathException |
An Exception thrown if there is a problem in the Path class.
|
| PathExpressionField |
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.
|
| PathLengthComparator |
|
| PathQuery |
Class to represent a path-based query.
|
| PathQueryAPI |
Provides methods to obtain PathQueryExecutors and WebResultsExecutors
|
| PathQueryBinding |
Convert PathQueries to and from XML or JSON
|
| PathQueryBuilder |
PathQueryBuilder builds PathQuery object from xml and validates it.
|
| PathQueryBuilderForJSONObj |
|
| PathQueryExecutor |
Executes path query and returns results in form suitable for export or web
services.
|
| PathQueryHandler |
Extension of DefaultHandler to handle parsing PathQuery objects
|
| PathQueryResultHelper |
Helper for everything related to PathQueryResults
|
| PathQueryUpdate |
Class for updating a pathquery with a new model
|
| PathUtil |
Utility methods for Paths
|
| PendingClob |
Subclass of ClobAccess that contains data to be written to the database instead of access to data
already in the database.
|
| PerformanceTester |
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.
|
| PermanentToken |
|
| PermanentURIHelper |
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
|
| PermanentURLFilter |
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.
|
| PermanentURLService |
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
|
| PermaTokenDeletionService |
Does what it says on the tin.
|
| PermaTokenInfoService |
|
| PermaTokens |
|
| PermaTokensServlet |
|
| PkQueryIdUpgrader |
Bag object id upgrader that uses the primary keys to find the objects in the new ObjectStore.
|
| PlainFormatter |
Simplest possible formatting.
|
| PollQueryAction |
Repeatedly poll the status of a running query and forward client to appropriate page
each time.
|
| PopulationInfo |
Container for size and extra attribute (e.g.
|
| PortalHelper |
Util methods for the portal
|
| PortalQueryAction |
The portal query action handles links into flymine from external sites.
|
| PossibleValuesService |
A service for retrieving the possible values for a path in the data model.
|
| PossibleValuesServlet |
A servlet for routing requests to the possible values service.
|
| PostgresByteArrayOutputStream |
A subclass of SensibleByteArrayOutputStream that has extra methods useful for reducing the memory
footprint of the Postgres database write operations.
|
| PostgresDataOutputStream |
A subclass of DataOutputStream that has extra methods useful for reducing the memory
footprint of the Postgres database write operations.
|
| PostgresExplainResult |
Subclass of ExplainResult specific to PostgreSQL.
|
| PostProcessor |
Generic defn of a post process step...
|
| PostProcessorTask |
Generic defn of a post process step...
|
| PrecomputedTable |
Represents a Precomputed table in a database.
|
| PrecomputedTableManager |
Manages all the Precomputed tables in a given database.
|
| PrecomputeTask |
A Task that reads a list of queries from a properties file (eg.
|
| PrecomputeTemplatesTask |
A Task that reads a list of queries from a properties file (eg.
|
| Predicate<T> |
The type of functions that test things.
|
| PreferencesHandler |
|
| PreferencesManager |
Class encapsulating the logic for reading user preferences in and out of the DB.
|
| PrefetchManager |
A manager for the prefetch mechanism for the Results object.
|
| PrimaryKey |
Class representing a primary key as a list of field names
|
| PrimaryKeyUtil |
Utility methods for PrimaryKey objects.
|
| PriorityConfig |
Class holding data source priority configuration for a Model.
|
| Producer<T> |
The type of functions that take no input and produce a value.
|
| 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.
|
| ProfileAlreadyExistsException |
Exception thrown when attempting to create a profile element with a name that already exists.
|
| ProfileBinding |
Code for reading and writing Profile objects as XML.
|
| ProfileManager |
Class to manage and persist user profile data such as saved bags
|
| ProfileManager.ApiPermission |
A representation of the level of permissions granted to a user.
|
| ProfileManager.ApiPermission.Level |
The possible permission levels.
|
| ProfileManager.AuthenticationException |
Exception thrown when the authentication fails.
|
| ProfileManagerBinding |
Code for reading and writing ProfileManager objects as XML
|
| ProfileMergeIssues |
The problems that arose when merging two profiles.
|
| ProfileReadTask |
Task to read an XML file of a webapp userprofiles into a userprofile ObjectStore.
|
| ProfileWriteTask |
Task to write an XML file of a webapp userprofile object store.
|
| PropertiesUtil |
Convenience class for working with global properties
|
| PropertyChangeEvent |
A representation of a notification that a property of a web searchable has changed.
|
| ProxyCollection<E> |
Class which holds a reference to a collection in the database
|
| ProxyReference |
Class which holds a reference to an object in the database
|
| PseudoSet<E> |
A Set that does not actually contain objects, but provides useful results for the contains
method.
|
| PswResetService |
Change a user's password with the authority of a token previously emailed to them.
|
| PswResetServlet |
Runs the PswReset service
|
| PublicKeySource |
An object that can provide public keys by name, or all known keys, or a subset of keys.
|
| Queries |
|
| Query |
This class provides an implementation-independent abstract representation of a query
|
| Query |
Represents an SQL query in parsed form.
|
| Queryable |
An interface for an object that has a SELECT list and a WHERE clause, like a Query.
|
| QueryBuilderChange |
Action to handle links on main query builder tile.
|
| QueryBuilderConstraintAction |
Action to handle button presses on the main tile
|
| QueryBuilderConstraintController |
Controller for the main constraint editing tile
|
| QueryBuilderConstraintForm |
The form used for editing QueryBuilder constraints
|
| QueryBuilderController |
Controller for the main query builder tile.
|
| QueryBuilderSummaryController |
Controller for the QueryBuilder summary tile.
|
| QueryBuilderSummaryHelper |
Methods to generate summary information for a PathQuery for use in display of QueryBuilder
summary section.
|
| QueryBuilderViewAction |
Action to run constructed query.
|
| QueryBuilderViewChange |
Action to handle links on view tile
|
| QueryCast |
Represents a type cast in a Query.
|
| QueryClass |
Represents the database extent of a Java class
NOTE - No equals() method is defined for this class and none should be.
|
| QueryClassBag |
An element that can appear in the FROM clause of a query
|
| QueryClassSelectAction |
Implementation of Action that processes
QueryClass selection form.
|
| QueryClassSelectForm |
Form bean for selection of a new query class.
|
| QueryCloner |
This is a static class that provides a method to clone a Query object.
|
| QueryCollectionPathExpression |
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.
|
| QueryCollectionReference |
Represents a field of a QueryClass that is a collection
|
| QueryCountQueryMonitor |
A QueryMonitor that maintains a timeout and is used when counting the number of rows a query
returns.
|
| QueryCreator |
Class that helps build queries or parts of queries for common situations.
|
| QueryEvaluable |
An element that can be evaluated for comparison (one that represents an atomic type)
|
| QueryExecutor |
Common superclass of query executors that holds cache of pathToQueryNode maps per query.
|
| QueryExpression |
Represents an arithmetic or substring expression, analogous to those in SQL
|
| QueryField |
Represents a QueryClass field that is neither a collection or reference to
another business object.
|
| QueryForeignKey |
Represents the ID of a field of a QueryClass that is a business object
|
| QueryForm |
Action form that holds query XML.
|
| QueryFunction |
A QueryFunction represents an aggregate
|
| QueryGenUtil |
Utility methods for paths.
|
| QueryGenUtil.QueryAndClass |
Class to allow returning of two arguments from a method.
|
| QueryHelper |
Static methods to assist with query generation from front end.
|
| QueryListAppendService |
Append items to a list from the results of a query.
|
| QueryListAppendServlet |
Runs the query-to-list service to run queries and save them as lists.
|
| QueryLogger |
Provides a logging facility for a Query
|
| QueryMonitor |
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 |
QueryMonitor that cancels a query after a given timeout period.
|
| QueryNode |
An element that can appear in the SELECT, ORDER BY or GROUP BY clause of a query.
|
| QueryObjectPathExpression |
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.
|
| QueryObjectReference |
Represents a field of a QueryClass that is a business object
|
| QueryOptimiser |
A static class providing the code to optimise a query, given a database (presumably with a table
describing the available precomputed tables).
|
| QueryOptimiser.AbstractTableComparator |
Compares two AbstractTables using their equalsIgnoreAlias() method.
|
| QueryOptimiserContext |
A class describing settings for the optimiser.
|
| QueryOptimiserException |
An Exception that may be thrown by a QueryOptimiser method.
|
| QueryOrderable |
An element that can appear in the ORDER BY clause of a query.
|
| QueryParseTimeoutException |
Exception thrown when parsing a query from SQL string to org.intermine.sql.Query object.
|
| QueryPathExpression |
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 |
A Path Expression that has a Select list.
|
| QueryReference |
Represents a field of a QueryClass that is a non-primitive type.
|
| QueryRemovalService |
A service that removes a saved query from profile's collection of saved queries.
|
| QueryRequestParser |
Processes query request parameters.
|
| QueryResultInput |
QueryServiceInput is parameter object representing parameters for
QueryResultService web service.
|
| QueryResultLinkGenerator |
Class that implements generating links for QueryResultService web service.
|
| QueryResultRequestParser |
Processes service request.
|
| QueryResultService |
Executes query and returns results.
|
| QueryResultServlet |
Servlet that runs QueryResultService.
|
| QueryRetrieverService |
A service that retrieves a stored query by qid.
|
| QuerySelectable |
An element that can appear in the SELECT clause of a query.
|
| QueryStore |
|
| QueryStoreException |
|
| QueryStoreService |
A service that stores a query and associates it with an id.
|
| QueryToListService |
A service for transforming a query, represented as a PathQuery serialised
to XML, to a list.
|
| QueryToListServlet |
Runs the query-to-list service to run queries and save them as lists.
|
| QueryTrack |
|
| QueryTrackBinding |
|
| QueryTracker |
|
| QueryUpdateService |
Same in all respects as the upload service, but this class overwrites queries with the provided
names.
|
| QueryUploadService |
A service to enable queries to be uploaded programmatically.
|
| QueryUploadServlet |
Runs the query Upload Service to handle user query uploads.
|
| QueryValue |
Represents a constant in a Query
|
| QuickSearch |
A service that runs key-word searches.
|
| QuickSearchJSONProcessor |
A class that renders quick search results as JSON.
|
| QuickSearchResultProcessor |
The type of objects that can handle keyword search results.
|
| QuickSearchServlet |
|
| QuickSearchTextProcessor |
A result processor that outputs results as plain text.
|
| QuickSearchXMLProcessor |
A result processor that outputs results as XML.
|
| Range |
|
| RangeHelper |
|
| RateLimitException |
Exception representation for denying service based on rate limits.
|
| RateLimitHistory |
A class for making sure that certain resources don't get hammered.
|
| ReadPreferencesService |
A service for reading the current state of a user's preferences.
|
| ReadWriteJSONService |
Convenience for services that need to combine JSON service behaviour
with strict RW authorisation.
|
| ReallyFlatIterator |
An Iterator that flattens the contents of another Iterator.
|
| Reference |
|
| Reference |
Representation of an Reference in an object
|
| ReferenceDescriptor |
Describes a field that references a single other class (i.e.
|
| ReferenceList |
|
| ReferenceList |
Representation of a field in an object.
|
| ReferenceMap<K,V> |
This is a Map implementation designed specifically for people intending to create a cache.
|
| ReferenceMap.ReferenceWithKey<K> |
Interface for entries in the map.
|
| RegistryResponse |
Pojo class to map the response from the intermine registry
|
| RelativeComplement |
|
| ReleaseEtagFilter |
Return responses tagged with the release version.
|
| RemoteMine |
An object that represents an InterMine application hosted somewhere else.
|
| RendererComparator |
An implementation of Comparator to order pairs of Class objects.
|
| ReportAspectController |
Controller for the reportAspect tile.
|
| ReportController |
New objectDetails.
|
| ReportDisplayer |
Parent class for report displayers that appear on report pages.
|
| ReportDisplayerConfig |
Bean to hold configuration for report displayers.
|
| ReportDisplayerController |
Execute a ReportDisplayer placed on the context.
|
| ReportInList |
Wrapper, mainly to provide size
|
| ReportInListController |
|
| ReportObject |
Object to be displayed on report.do
|
| ReportObjectFactory |
A factory for ReportObjects.
|
| ReportObjectField |
Object field, used in header the summary of ReportObject
|
| ReportTemplateController |
Controller for an inline table created by running a template on a report page.
|
| RequestPasswordAction |
Action to handle button presses RequestPasswordForm
|
| RequestPasswordForm |
Form used to request a password
|
| RequestPswResetService |
This service sends a password change email to the user email address
|
| RequestPswResetServlet |
Runs the RequestPswReset service
|
| RequestSubClassFilter |
Filter to wrap all web service requests in a custom delegating wrapper that
prevents sessions being created.
|
| RequestUtil |
Util methods for HttpServletRequest.
|
| ResolutionJob |
|
| ResourceFinder |
A class for finding resources in the WEB-INF directory at run-time based on patterns.
|
| ResourceNotFoundException |
The ResourceNotFoundException is thrown by a service provider when an attempt is made to
perform an operation upon a resource that cannot be found.
|
| ResourceOpener |
The type of objects that can open resources by names.
|
| ResponseType |
|
| ResponseUtil |
Response util that sets content type and header for various formats and has
util methods for setting headers controlling cache.
|
| RestfulServlet |
|
| ResultCell |
An interface for result cells
|
| ResultElement |
Cell of results table containing information for the parent Object
|
| ResultElementConverter |
|
| ResultProcessor |
Processor of Results object for easy accessing and parsing of results to list of strings.
|
| ResultRowParser |
Interface of parser that parses row of results
to list of strings.
|
| Results |
Results representation as a List of ResultRows.
|
| ResultsAction |
ResultsAction is called before results table is rendered.
|
| ResultsBatches |
Class holding the data batches for the Results object.
|
| ResultsConverter |
Provides a method to convert from SQL ResultSet data to InterMine object-based data.
|
| ResultsFlatOuterJoinsImpl |
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.
|
| ResultsInfo |
Represents a result from the estimate() method of an ObjectStore.
|
| ResultsRow<E> |
|
| RetrieveMetadataTask |
Retrieve the model metadata from a database
|
| Row |
Stores two ints.
|
| RowFormatter |
Interface denoting that object is able format list of objects
to string.
|
| RowFormatterImpl |
Implements RowFormatter interface.
|
| RunIqlQueryTask |
Ant task to read an IQL query from a -Pquery="QUERY" parameter and execute it in the database.
|
| RunQueryAction |
Run a query as passed in directly as XML.
|
| SaveBagAction |
Saves selected items in a new bag or combines with existing bag.
|
| SaveBagForm |
Form bean for the results table and bag creation form.
|
| SavedBag |
|
| SavedQuery |
Container for a saved query.
|
| SavedQuery |
|
| SavedQueryBinding |
Convert SavedQuerys to and from XML
|
| SavedQueryHandler |
Extension of PathQueryHandler to handle parsing SavedQuerys
|
| SavedQueryRetrievalService |
|
| SavedTemplateQuery |
|
| SaveFromIdsToBagAction |
Saves selected items with InterMine ids and a Type in a new bag or combines
with existing bag.
|
| SaveQueryAction |
Implementation of Action that saves a Query from a session.
|
| SaveQueryForm |
Form bean to represent the inputs to the query saving action
|
| SAXParser |
Basic SAX Parser
|
| SAXParser |
Basic SAX Parser
|
| SchemaListService |
Serve up the list of schemata that we have.
|
| SchemaServlet |
Returns a requested schema.
|
| Scope |
Scope constants.
|
| SearchFilterEngine |
Class filtering web searchables according to the associated tags.
|
| SearchRepository |
The base class for search repositories.
|
| SearchResult |
A single item in a set or returned results formed by searching the web-searchable indices with
Lucene.
|
| SearchResults |
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 |
An object for encapsulating the scope and type of object requested from a Lucene search
of the user profile web searchable items.
|
| SearchTrackBinding |
|
| SearchUtils |
The bits of the search infrastructure that belong in the web-package because
they have view dependent logic.
|
| Segment |
Represents an interbase segment.
|
| SelectValue |
Represents an AbstractValue with an alias, suitable for use in the SELECT portion of an SQL
query.
|
| SemanticMarkupFormatter |
Class providing schema/bioschemas markups
|
| SensibleByteArrayOutputStream |
A subclass of ByteArrayOutputStream that behaves a little more sensibly when handling large
writes followed by small writes.
|
| SequenceService |
A service to provide access to substrings of ClobAccess data.
|
| ServiceException |
ServiceException is a base class for all service exceptions.
|
| ServiceForbiddenException |
The ServiceForbiddenException is thrown by a service when an attempt is made to service that
is disabled.
|
| ServiceListingHandler |
|
| ServicesListingsServlet |
Provide a list of all the services available at this mine.
|
| SessionActivationListener |
Added to each session to monitor activation events.
|
| SessionlessRequest |
|
| SessionListener |
Perform InterMine-specific actions when a Session is constructed or destroyed
|
| SessionMethods |
Business logic that interacts with session data.
|
| SessionService |
Open a new 24-hour session.
|
| SetCharacterEncodingFilter |
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.
|
| SetPreferencesService |
A service to set one or more preferences for a user.
|
| ShadowClass |
A root interface for all shadow classes for performance.
|
| SharedBagBinding |
Parse the shared bags in XML format
|
| SharedBagHandler |
Handle parsing of shared bags
|
| SharedBagManager |
Singleton manager class for shared bags.
|
| SharingBagUsersController |
Controller for the inline tag editing tile
|
| SharingInvite |
A representation of an invitation to share a resource.
|
| SharingInvite.IntermediateRepresentation |
A structure for holding data we read from the DB.
|
| SharingInvite.NotFoundException |
Exception thrown when we can't find a shared invitation.
|
| Shutdownable |
An interface for any object that can be shut down by the ShutdownHook.
|
| ShutdownHook |
This class provides a "shutdown" service to other classes.
|
| SimpleConstraint |
Represents a constraint between two QueryEvaluable types.
|
| SingleTemplateService |
Service that responds with a single template.
|
| SingletonResults |
This class is equivalent to a Result object with ResultRows consisting only of single items
|
| SoftReferenceMap<K,V> |
This is a Map implementation designed specifically for people intending to create a cache.
|
| SolrClientManager |
Singleton class to create one instance of Solr Client
|
| SolrIndexHandler |
Solr Implementation of IndexHandler
|
| SolrKeywordSearchHandler |
Solr implementation of KeywordSearchHandler
|
| SolrObjectHandler |
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>> |
SortableMap extends a LinkedHashMap with some useful sorting features.
|
| Source |
Represents a data source, by name and skeleton status.
|
| SourcePriorityComparator |
Comparator, that compares two InterMineObjects, with reference to a particular
FieldDescriptor for priority.
|
| SqlGenerator |
Code to generate an sql statement from a Query object.
|
| SqlGenerator.State |
Internal representation of the State of the query as it is built up.
|
| SqlLexer |
|
| SQLOperation<T> |
A functional interface (oh, please come Java 8 - you cannot come soon
enough) to help manage out-of-control boilerplate-itis in SQL code.
|
| SqlParser |
|
| SQLStringable |
An interface for all classes that implement the getSQLString method.
|
| SqlTokenTypes |
|
| SqlTreeParser |
|
| StandardHttpExporter |
Abstract class implementing functionality common for exporters exporting table in simple format
like comma separated format.
|
| StaticMethodTask |
Given a class name and method name, just invokes a static method.
|
| StatusDictionary |
HTTP status code dictionary.
|
| StorableBag |
Base class for representations of user's collections of objects stored in a database.
|
| StoreMetadataTask |
Store model metadata to a database
|
| StreamedOutput |
Immediately as the data or error messages are added they are streamed via http connection.
|
| StringConstructor |
A CharSequence object representing a String constructed out of a sequence of other Strings.
|
| StringHelper |
|
| StringTableExporter |
Simple exporter exporting table of strings.
|
| StringUtil |
Collection of commonly used String utilities
|
| StringUtil.LineWrappedString |
Class for returning multiple values from the wrapLines method.
|
| SubMenuController |
Controller for the submenu at the top of every page
|
| SubQuery |
A representation of a subquery that can be present in the FROM section of an SQL query.
|
| SubqueryConstraint |
Constrain a QueryClass or QueryEvaluable to be within the select list
of a given subquery.
|
| SubQueryConstraint |
A representation of a constraint where an AbstractValue is IN the results of a Query.
|
| SubqueryExistsConstraint |
Check if there are any rows in the subquery
|
| SubTable |
A class that represents a table nested within a cell in another table.
|
| SummariseObjectStoreTask |
Summarise an ObjectStore into a particular properties file.
|
| SummariseTemplatesAction |
Action to summarise all templates.
|
| SummaryConstraint |
Representation of a PathQuery constraint with additional information for display in the
QueryBuilder summary section.
|
| SummaryPath |
Representation of a query path with additional information for display in the QueryBulder summary
section.
|
| SummaryService |
Serve up the paths used to summarise each class.
|
| SummaryServlet |
Returns a summary field information.
|
| SwitchOffAbility |
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 |
|
| SynchronisedIterator<E> |
An Iterator that passes through to an underlying Iterator, synchronising all calls.
|
| SystemTemplatesService |
Fetch the names of public template queries tagged with "im:converter"
for use with the System Templates web service.
|
| TabFormatter |
Formats data to tab separated data format.
|
| TabHttpExporter |
Exporter that exports table with results in tab format.
|
| Table |
A representation of a table that can be present in the FROM section of an SQL query.
|
| Table |
An interface representing all changes to be made to an SQL table of some sort.
|
| TableBatch |
A class representing all changes to be made to an SQL table.
|
| TableCell |
A representation of a table cell.
|
| TableCellFormatter |
A formatter that will render a table cell.
|
| TableController |
Implementation of TilesAction.
|
| TableExportAction |
Implementation of Action that allows the user to export a
PagedTable to a file.
|
| TableExportConfig |
Configuration information for exporting.
|
| TableExporterFactory |
Factory class that creates and registers TableHttpExporter classes.
|
| TableExportForm |
Form to hold options for exporting.
|
| TableHttpExporter |
Implemented by objects that can export PagedTable.
|
| TableJSONProcessor |
Class to process the result returned by a table widgets in JSON format
|
| TableRowIterator |
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.
|
| TableRowService |
A service that produces results in nested rows for use in tables.
|
| TableTag |
Class rendering html table.
|
| TableWidget |
A table widget gets the values for a given path for all the items in a list.
|
| TableWidgetConfig |
|
| TableWidgetLdr |
|
| TableWidgetService |
Web service that returns a table widget for a given list.
|
| TableWidgetsServlet |
Servlet running WidgetsService.
|
| TableXMLProcessor |
Class to process the result returned by a table widgets into a XML format
|
| TabRowFormatter |
Row formatter formats line as tab separated strings.
|
| Tag |
|
| TagBinding |
Convert Tags from the Profile to and from XML
|
| TagChecker |
An interface for checking the validity of tags.
|
| TagFilter |
Class for filtering web-searchables based on their tags.
|
| Taggable |
An interface for items that may have tags stored for them in the user profile database.
|
| TaggingEvent |
A representation of a notification that a tag has been changed on a web-searchable item.
|
| TaggingEvent.TagChange |
The possible actions that this event can represent.
|
| TagHandler |
Extension of PathQueryHandler to handle parsing TemplateQueries
|
| TagManager |
Manager class for tags.
|
| TagManager.TagException |
Class for reporting exceptions from tag manipulation actions.
|
| TagManager.TagNameException |
Class for representing errors due to the use of illegal tag names.
|
| TagManager.TagNamePermissionException |
Class for representing errors due to the restricted nature of some tags.
|
| TagManagerFactory |
Factory class for creating TagManager objects.
|
| TagMapper |
A class that handles transforming a list of tags into a list of strings of different types.
|
| TagMapper.Field |
The valid fields that can be read from a tag
|
| TagNames |
|
| TagTypes |
Known tag types.
|
| TemplateAction |
Action to handle submit from the template page.
|
| TemplateComparator |
Comparator used for ordering templates by title
|
| TemplateController |
Controller for the template tile.
|
| TemplateForm |
Form to handle input from the template page
|
| TemplateHelper |
Static helper routines related to templates.
|
| TemplateListAppendService |
A class to append items from a set of template results to a
list.
|
| TemplateListAppendServlet |
Runs the query-to-list service to run queries and save them as lists.
|
| TemplateListController |
Controller for the template list tile.
|
| TemplateManager |
A TemplateManager provides access to all global and/or user templates and methods to fetch them
by type, etc.
|
| TemplatePopulator |
Configures original template.
|
| TemplatePopulatorException |
Exception thrown when errors occur populating a template query with values.
|
| TemplatePrecomputeHelper |
Helper class providing methods for precomputing and summarising TemplateQuery objects.
|
| TemplateProblemsController |
Called before templateProblems.jsp
|
| TemplateQuery |
A template query, which consists of a PathQuery, description, category,
short name.
|
| TemplateQueryBinding |
Convert PathQueries to and from XML
|
| TemplateQueryHandler |
Extension of PathQueryHandler to handle parsing TemplateQueries
|
| TemplateQueryUpdate |
A class to update template queries to match a new Data model.
|
| TemplateRemovalService |
A service that deletes templates.
|
| TemplateResultInput |
TemplateResultInput is parameter object representing parameters for
TemplateResultService web service.
|
| TemplateResultLinkGenerator |
Class that implements generating links of TemplateResultService web service.
|
| TemplateResultRequestParser |
Processes service request.
|
| TemplateResultService |
Web service that returns results of public template constrained with values in request.
|
| TemplateResultServlet |
Runs TemplateResultService web service.
|
| Templates |
A utility class with static methods for dealing with templates.
|
| Templates.TemplateValueParseException |
An exception that we throw when we can't parse a template.
|
| TemplatesController |
Tiles controller for templates tile (page).
|
| TemplateSettingsForm |
Form used when building a template.
|
| TemplatesExecutionMap |
Class for saving the template executions into the memory.
|
| TemplatesExportAction |
Exports templates to XML.
|
| TemplatesImportAction |
Imports templates in XML format.
|
| TemplatesImportForm |
Form bean representing template import form.
|
| TemplateSummariser |
This class manages summaries of possible values for editable constraints for template queries.
|
| TemplateSummary |
|
| TemplateTagAddingService |
A service for adding tags to a template.
|
| TemplateTagRemovalService |
A service for removing tags from a template.
|
| TemplateTagService |
A service for getting the tags of a template.
|
| TemplateToListService |
A service for turning the results of a template query into a list.
|
| TemplateToListServlet |
Runs the template-to-list service to run templates and save them as lists.
|
| TemplateTrack |
Class to represent the track for the templates objects.
|
| TemplateTrackBinding |
Code for reading and writing template tracks as XML.
|
| TemplateTracker |
Class for tracking the templates execution by the users.
|
| TemplateTrackReadTask |
Task to read an templatetrack XML file of a webapp and saved into the userprofile database.
|
| TemplateTrackWriteTask |
Task to write an XML file of template track contained in the user profile database.
|
| TemplateUploadService |
A service to enable templates to be uploaded.
|
| TemplateUploadServlet |
Runs the Template Upload Service to handle user template uploads.
|
| TemplateValue |
A TemplateValue represents the value for an editable constraint of a template query and details
about what is being constrained.
|
| TemplateValue.ValueType |
Possible values for TemplateValue type.
|
| TextTable |
A utility class for generating multi-column aligned text tables.
|
| TextUtil |
|
| TokenService |
A service that issues new tokens to a user.
|
| TokenServlet |
|
| TokensService |
Service that lets a user inspect their currently active tokens
|
| TorqueModelOutput |
Map InterMine metadata to a Torque database schema in InterMine format
|
| TorqueModelOutputTask |
Creates and runs a ModelOutput process to generate java or config files.
|
| Track |
Class representing the track
|
| TrackAbstract |
Class representing the track
|
| TrackAjaxServices |
|
| Tracker |
Interface to represent a Tracker, an object tracking the users activities in the webapp
into the database
|
| TrackerDelegate |
Intermediate class which decouples the tracker components from the code that uses them.
|
| TrackerFactory |
Factory to instantiate the trackers with the reflection
|
| TrackerLogger |
Runnable object providing insertion into the database.
|
| TrackerUtil |
|
| TrackHandler |
|
| TrackManagerBinding |
Code for reading and writing all tracks objects as XML
|
| TrackManagerHandler |
Event handler for the track xml file
|
| Translator |
Interface specifying operations required for inline translation of queries and data objects
by a translating ObjectStore.
|
| TreatStringTag |
Tag escaping apostrophes, quotes and replacing "\n" with html tag for end of line.
|
| TreeAction |
Implementation of Action that modifies a tree.
|
| TreeController |
Perform initialisation steps for displaying a tree
|
| TreeNode |
Bean to represent one row in the display of a tree
|
| TreeWalker<L> |
A type alias to reduce type stuttering.
|
| TriageBagAction |
An action to handle reparative actions to bags.
|
| TriageBagForm |
|
| TSVFileReaderTask |
Read a file of tab separated values.
|
| Type |
Configuration object for displaying a class
|
| TypeConverter |
Static helper routines to convert bags between different types.
|
| TypeUtil |
Provides utility methods for working with Java types and reflection
|
| TypeUtil.FieldInfo |
Inner class to hold info on a field.
|
| UnauthorizedException |
|
| UnhandledFeatureException |
Exception representing the failure to encode a feature in the target
language.
|
| Union |
|
| UnknownBagTypeException |
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.
|
| UnknownTypeValue |
Represents a value with an unknown type.
|
| UpdateListTablesTask |
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
|
| UpdateTrackTableTask |
Task to modify the type of the column 'timestamp' in the templatetrack table
in the userprofile database.
|
| UpgradeBagList |
Runnable object providing upgrading osbag_int table.
|
| UpgradeJob |
|
| URLGenerator |
Class generating useful links like base link: http://localhost:8080/query
|
| URLUtil |
Util class for URL processing.
|
| UserAlreadyShareBagException |
Exception thrown when a user already shares the bag.
|
| UserDataFormatter |
A class that processes information about a user into XML.
|
| UserNotFoundException |
Exception thrown when user is not found.
|
| UserPreferences |
|
| UserProfile |
|
| UserRepository |
A repository for searching the searchable items of a single user.
|
| UsersController |
Controller for the users admin page
|
| UserTemplateAction |
Make some change to a user template.
|
| Util |
Generic utility functions.
|
| VerifyTokenTask |
A task to check that a token can be verified.
|
| VersionService |
Service for returning the version of this service.
|
| VersionServlet |
Returns version of the deployed InterMine application.
|
| WeakReferenceHashMap<K,V> |
This is a Map implementation designed specifically for people intending to create a cache.
|
| WeakReferenceMap<K,V> |
This is a Map implementation designed specifically for people intending to create a cache.
|
| WebConfig |
Configuration object for web site
|
| WebJobInput |
|
| WebPropertiesService |
Exports selected web.properties.
|
| WebPropertiesServlet |
Runs WebPropertiesService web service.
|
| WebResults |
The web version of a Results object.
|
| WebResultsExecutor |
Executes a PathQuery and returns a WebResults object, to be used when multi-row
style results are required.
|
| WebSearchable |
An interface implemented by objects that we want to index with Lucene.
|
| WebSearchableListController |
Controller for webSearchableList.tile
|
| WebSearchWatcher |
The interface for describing objects that listen to WebSearchables for events.
|
| WebService |
Base class for web services.
|
| WebserviceCodeGenAction |
Action to handle the web service code generation.
|
| WebserviceCodeGenerator |
Interface for web service code generation.
|
| WebserviceCodeGenInfo |
Class to represent the information used to generate web service source code.
|
| WebServiceConstants |
|
| WebServiceInput |
Base class for input classes used with web services.
|
| WebserviceJavaCodeGenerator |
This Class generates Java source code of web service client for path query and template query.
|
| WebserviceJavaScriptCodeGenerator |
A Class for generating JavaScript that would run a given query.
|
| WebservicePerlCodeGenerator |
This Class generates Perl source code of web service client for path query and template query.
|
| WebservicePythonCodeGenerator |
Class for generating Python code to run a query, using the intermine python library.
|
| WebServiceRequestParser |
Base request parser that is used by advanced web service parsers.
|
| WebserviceRubyCodeGenerator |
|
| WebServiceServlet |
A servlet which can be easily configured to define how to route requests, using
standard RESTful semantics.
|
| WebServiceServlet.Method |
|
| WebState |
This class saves things related to the state of web GUI.
|
| WebTable |
A List that can understand ResultElement objects.
|
| WebUtil |
Utility methods for the web package.
|
| WebUtil.HeadResource |
A bean encapsulating a resource (js or css).
|
| WhoAmIService |
Class for retrieving information about the currently authenticated user.
|
| WhoAmIServlet |
|
| Widget |
A representation of a query using a list tool.
|
| WidgetConfig |
Class representing a Widget Configuration
|
| WidgetConfigUtil |
Utilities for handling the widget configuration
|
| WidgetForm |
|
| WidgetHelper |
An Interface for widget Utils
|
| WidgetLdr |
The class that performs the actual queries for widgets.
|
| WidgetOptions |
The type of options a widget would expect to receive.
|
| WidgetProcessor |
|
| WidgetProcessorImpl |
A base class for Widget Processors
|
| WidgetProcessorImpl.WidgetType |
Of widget types there are several:
|
| WidgetResultProcessor |
Interfaces for classes that are able to process the results that widgets return.
|
| WidgetService |
|
| WidgetsRequestParser |
Request processor for WidgetsService that process request, validates it and returns
parsed input as a parameter object.
|
| WidgetsServiceInput |
WidgetsServiceInput is parameter object representing parameters
for the WidgetsService web service.
|
| WidgetsServiceInput.Builder |
Class to build Inputs for the Widget Service.
|
| WidgetsServlet |
Servlet running WidgetsService.
|
| WidthBucketFunction |
Representation of a call to the Postgresql WIDTH_BUCKET function.
|
| XmlBinding |
Represents an XML mapping - performs XML (un)marshalling of objects/Full Data XML
|
| XmlDataLoader |
Provides a method for unmarshalling XML given source into java
business objects then calls store on each.
|
| XmlDataLoaderTask |
Uses an IntegrationWriter to load data from XML format
|
| XMLFormatter |
Formats data to XML format.
|
| XmlHelper |
Static methods to assist parsing and rendering of XML.
|
| XmlUtil |
General-purpose methods for manipulating URIs and XML schema types
|
| XMLValidator |
XMLValidator is class that validates xml string according an XML Schema at specified url.
|
| XMLValidatorErrorHandler |
|
| XMLWidgetProcessor |
A processor for handling requests for widget metadata.
|