All Classes

AbstractConstraint AbstractTable AbstractValue AcceptanceTestTask AddColumnAction AddToBagAction AjaxServices AlwaysMap AlwaysSet AnalyseDbTask Aspect AspectBinding AspectController AspectSource AspectTagUtil Attribute AttributeDescriptor AttributeLinkURL AutoCompleter AvailableColumnsController BadRequestException BadRequestException BadRequestException BagBuildController BagConstraint BagConversionHelper BagConverter BagDetailsAction BagDetailsController BagHelper BagManager BagOperations BagQuery BagQueryConfig BagQueryHandler BagQueryHelper BagQueryResult BagQueryRunner BagUploadConfirmAction BagUploadConfirmController BagUploadConfirmForm BagUploadConfirmIssueController BaseDisclosureTag BaseEquivalentObjectFetcher Batch BatchingFetcher BatchWriter BatchWriterPostgresCopyImpl BatchWriterPreparedStatementImpl BatchWriterSimpleImpl BeginAction BenjaminiHochberg BestQuery BestQueryException BestQueryExplainer BestQueryExplainerVerbose BestQueryFallback BestQueryLogger BestQueryStorer BioDBConverter BioDirectoryConverter BioFileConverter BioGridConverter BioJavaFlatFileConverter BioQueries BiosegIndexTask Bonferroni BuildBagAction BuildBagForm BuildDbTask CacheHoldingArrayList CacheMap CalculateLocations ChadoCV ChadoCVFactory ChadoCVTerm ChadoDBConverter ChadoProcessor ChangePasswordAction ChangePasswordForm ChangeTableAction ChangeTableSizeAction ChangeTableSizeForm CheckForIsNotNullConstraint ClassChooserController ClassConstraint ClassDescriptor ClassKeyHelper Clob CodeTranslator CollectionDescriptor CollectionDetailsAction CollectionUtil Column CombinedIterator CompletelyFalseException ConfigAction ConsistentSet Constant Constants Constants Constants Constraint Constraint Constraint ConstraintHelper ConstraintLoad ConstraintOp Constraints ConstraintSet ConstraintSet ConstraintTraverseAction ConstraintValueParser ContactAction ContactForm ContainsConstraint ContentType ConvertBagController ConvertedObjectPair ConverterTask CountTableController CreateAccountAction CreateAccountForm CreateCollectionAction CreateFlankingRegions CreateFlyBaseLinkIns CreateIndexesTask CreateReferences CreateSiteMaps CreateSynonymAction CreateTemplateAction CSVExportForm CSVFormatter CSVHttpExporter CSVRowFormatter CurrentQueryAction CustomPrintWriter Database DatabaseFactory DatabaseSchema DatabaseSchema.Fields DatabaseUtil DatabaseWriter DataChangedException DataConverter DataConverterStoreHook DataLoader DataLoaderHelper DataSetLdr DataSetStoreHook DataTracker DBConverter DBConverterTask DelimitedFileConfiguration DirectDataLoader DirectDataLoaderTask DirectoryConverter DirectoryConverterTask DisclosureBodyTag DisclosureDetailsTag DisclosureHeadTag DisclosureTag DisclosureTitleTag DisplayCollection DisplayConstraint Displayer DisplayField DisplayLookupMessageHandler DisplayObject DisplayObjectFactory DisplayReference DoNothingAction DropPrecomputedTablesTask DummyExplainResult DumpDefaultTemplatesTask DynamicAttributeTask DynamicBean DynamicUtil EditTemplateAction EncloseSubqueryBestQuery EnrichmentWidget EnrichmentWidgetConfig EnrichmentWidgetForm EnrichmentWidgetLdr EntrezOrganismRetriever EntrezPublicationsRetriever EquivalentObjectFetcher EquivalentObjectHints ErrorCorrection ErrorMessageParser ErrorMessagesController ExcelExporter ExcelHttpExporter ExplainResult ExportController Exporter ExporterImpl ExportException ExportHelper ExportOptionsController ExportQueryAction ExportResultsIterator ExportTagsAction ExtraQueryTime FastaLoaderTask FastPathObject FavouritesController Field FieldConfig FieldConfigHelper FieldDescriptor FieldExporter FileConverter FileConverterTask FileDirectDataLoaderTask FindInListAction FindInListForm FlushJob FlushJobBatchCommit FlushJobPostgresCopyImpl FlushJobStatementBatchImpl FlushJobUpdateStatistics FlyBaseCDSFastaLoaderTask FlyBaseFeatureFastaLoaderTask FlyBaseIdResolverFactory FlyBaseProcessor FlyBaseUniProtRefsTask FlyBaseUTRFastaLoaderTask FormattedTextParser Formatter ForwardParameters FromElement FullHandler FullParser FullRenderer FullXmlConverter FullXmlConverterTask Function GalaxyController GenesFileProcessor GenesProcessorException GenomeDBConverter GetAttributeAsFileAction GFF3Converter GFF3ConverterTask GFF3Parser GFF3Record GFF3RecordHandler GFF3SeqHandler GFF3Util GoConverter GoPostprocess GotoWebSearchableAction GrantTask GraphCategoryURLGenerator GraphWidget GraphWidgetConfig GridDataSet GridDataSetLdr GridWidget GridWidgetConfig HeaderFilter HeartbeatAction HintingFetcher HintManager HintsController HtmlHeadController HTMLOutput HTMLWidget HTMLWidgetConfig HttpClient HttpConnection HttpExporterBase HttpExportUtil Hypergeometric IdentityMap IdResolver IdResolverFactory IdUpgrader ImportQueriesAction ImportQueriesForm ImportTagsAction ImportTagsForm IncompatibleTypesException IndirectionTableBatch InitialiserPlugin InlineResultsTable InlineTagEditorController InListConstraint InparanoidConverter IntegrationWriter IntegrationWriterAbstractImpl IntegrationWriterDataTrackingImpl IntegrationWriterFactory IntergenicRegionUtil InterMineAction InterMineAPI InterMineBag InterMineBagBinding InterMineBagHandler InterMineDispatchAction InterMineException InterMineExceptionHandler InterMineLookupDispatchAction InterMineModelParser InterMineObject InterMineRequestProcessor InternalErrorException InternalErrorException InternalErrorException InterProConverter IntPresentSet IntronUtil IntToIntMap IqlQuery IqlQueryParser Item ItemFactory ItemHelper ItemToObjectTranslator ItemWriter IteratorIterable JavaModelOutput KeggPathwayConverter Lazy LazyCollection LimitOffsetQuery LinkGeneratorBase LinkInTask ListManager ListService ListsRequestParser ListsService ListsServiceInput ListsServlet LoadDefaultTemplatesTask LoadQueryAction LogicExpression LoginAction LoginController LoginForm LoginHandler LogoutAction LuceneIndex LuceneObjectClass LuceneSearchEngine MailUtils MainHelper MainHelper.CsTreeStructure MainHelper.SummaryConfig MappingUtil MappingUtilChecker MatchingFieldConfigAction MemoryOutput MetaDataException MetadataManager MetadataNode Mine MirandaGFF3RecordHandler MockIdResolverFactory MockItemWriter Model ModelMerger ModelMergerException ModelMergerTask ModelOutputTask ModelParser ModelService ModelService ModelServlet ModEncodeFeatureProcessor ModEncodeMetaDataProcessor ModifyBagAction ModifyBagDetailsAction ModifyBagDetailsForm ModifyBagForm ModifyDetails ModifyQueryAction ModifyQueryChangeAction ModifyQueryForm ModifyTemplateAction ModifyTemplateForm MultiRow MultiRowFirstValue MultiRowLaterValue MultiRowValue MyMineController NameUtil NavigationBarTag NCBIFastaLoaderTask NoContentException NoContentException Node NonOverrideableProperties NotConnectedException NotConstraint NotImplementedException NotXmlParser NotXmlRenderer NullFirstComparator ObjectDescription ObjectDetailsAspectController ObjectDetailsController ObjectDetailsInListController ObjectDetailsTemplateController ObjectPipe ObjectStore ObjectStoreAbstractImpl ObjectStoreBag ObjectStoreBagCombination ObjectStoreBagsForObject ObjectStoreDataLoader ObjectStoreDataLoaderTask ObjectStoreException ObjectStoreFactory ObjectStoreFastCollectionsForTranslatorImpl ObjectStoreFastCollectionsImpl ObjectStoreInterMineImpl ObjectStoreItemWriter ObjectStoreLimitReachedException ObjectStorePassthruImpl ObjectStoreQueryDurationException ObjectStoreSafeImpl ObjectStoreSummary ObjectStoreTranslatingImpl ObjectStoreWriter ObjectStoreWriterFactory ObjectStoreWriterInterMineImpl ObjectTrailController ObjectTrailController.TrailElement ObjectViewController OboConverter OboConverterTask OboParser OboRelation OboTerm OboTermSynonym OboToModel OboTypeDefinition OMIMConverter OptimiserCache OptimiserCache.DateAndSequence OptimiserCacheLine OptimiserMappingChecker OrderDescending OrderDescending OrganismData OrganismRepository OrthologueLinkManager Output OverlapConstraint OverlapRange OverlapUtil OverlapViewTask PagedTable PageOutOfRangeException PageTableQueryMonitor ParallelBatchingFetcher ParallelPrecomputer ParallelPrecomputer.Job ParseValueException PasswordHasher PasswordResetAction PasswordResetController PasswordResetForm Path PathException PathExpressionField PathNode PathQuery PathQueryAPI PathQueryBinding PathQueryBuilder PathQueryExecutor PathQueryHandler PathQueryHelper PathQueryResultHelper PathQueryUtil PathUtil PdbConverter PerformanceTester PkQueryIdUpgrader PollQueryAction PortalHelper PortalQueryAction PostgresByteArrayOutputStream PostgresDataOutputStream PostgresExplainResult PostProcessOperationsTask PostProcessor PostProcessorTask PostProcessUtil PrecomputedTable PrecomputedTableManager PrecomputeTask PrecomputeTemplatesTask PrefetchManager PrimaryKey PrimaryKeyUtil PriorityConfig Profile ProfileAlreadyExistsException ProfileBinding ProfileManager ProfileManagerBinding ProfileReadTask ProfileWriteTask PropertiesUtil ProxyCollection ProxyReference PseudoSet PsiConverter PubMedGeneConverter PubMedReference Query Query Queryable QueryBuilderAction QueryBuilderChange QueryBuilderConstraintController QueryBuilderController QueryBuilderForm QueryBuilderPathsController QueryCast QueryClass QueryClassBag QueryClassSelectAction QueryClassSelectForm QueryCloner QueryCollectionPathExpression QueryCollectionReference QueryCountQueryMonitor QueryCreator QueryEvaluable QueryExpression QueryField QueryForeignKey QueryForGraphAction QueryFunction QueryGenUtil QueryGenUtil.QueryAndClass QueryHelper QueryLogger QueryMonitor QueryMonitorTimeout QueryNode QueryObjectPathExpression QueryObjectReference QueryOptimiser QueryOptimiser.AbstractTableComparator QueryOptimiserContext QueryOptimiserException QueryOrderable QueryPathExpression QueryPathExpressionWithSelect QueryReference QueryResultInput QueryResultLinkGenerator QueryResultRequestParser QueryResultService QueryResultServlet QuerySelectable QueryService QueryService.QueryRequest QueryValue QuickSearchAction QuickSearchController QuickSearchForm ReallyFlatIterator Reference ReferenceDescriptor ReferenceList ReferenceMap ReferenceMap.ReferenceWithKey ReferencesFileProcessor ReferencesProcessorException RendererComparator Request Request.RequestType RequestImpl RequestPasswordAction RequestPasswordForm RequestUtil ResourceNotFoundException ResourceNotFoundException ResourceNotFoundException ResponseUtil ResultElement ResultElementConverter ResultProcessor ResultRowParser Results ResultsAction ResultsConverter ResultsFlatOuterJoinsImpl ResultsInfo ResultsRow RetrieveMetadataTask Row RowFormatter RowFormatterImpl SaveBagAction SaveBagForm SavedQuery SavedQueryBinding SavedQueryHandler SaveQueryAction SaveQueryForm SAXParser Scope SearchFilterEngine SearchRepository SelectValue SensibleByteArrayOutputStream SequenceProcessor Service ServiceException ServiceException ServiceException ServiceFactory ServiceForbiddenException ServiceForbiddenException ServiceForbiddenException ServiceUnavailableException ServletMethods SessionActivationListener SessionListener SessionMethods SetCollectionCounts SetFieldConfigAction ShadowClass Shutdownable ShutdownHook SimpleConstraint SingletonResults SiteMapTask SOClassNameMapMakerTask SoftReferenceMap SortableMap Source SourcePriorityComparator SqlGenerator SQLStringable StandardHttpExporter StaticMethodTask StatusDictionary StockProcessor StoreMetadataTask StreamedOutput StringConstructor StringTableExporter StringUtil StringUtil.LineWrappedString SubMenuController SubQuery SubqueryConstraint SubQueryConstraint SubqueryExistsConstraint SummariseAllTemplatesAction SummariseObjectStoreTask SynchronisedIterator SynonymUpdater TabFormatter TabHttpExporter Table Table TableBatch TableController TableExportAction TableExportConfig TableExporterFactory TableExportForm TableHelper TableHttpExporter TableTag TableWidget TableWidgetConfig TableWidgetLdr TabLinkPreviewAction TabRowFormatter TabTableResult TagBinding TagChecker TagHandler TagManager TagManagerFactory TagNames TagTypes TempImageLoader TemplateAction TemplateBuildState TemplateComparator TemplateConfigurator TemplateController TemplateForm TemplateHelper TemplateListController TemplateManager TemplateParameter TemplatePopulator TemplatePopulatorException TemplatePrecomputeHelper TemplateQuery TemplateQueryBinding TemplateQueryHandler TemplateResultInput TemplateResultLinkGenerator TemplateResultRequestParser TemplateResultService TemplateResultServlet TemplatesController TemplateService TemplateService.TemplateRequest TemplateSettingsAction TemplateSettingsForm TemplatesExportAction TemplatesImportAction TemplatesImportForm TemplateSummariser TemplateValue TemplateValue.ValueType TextTable TipAction TipController ToolTipGenerator TorqueModelOutput TorqueModelOutputTask TransferSequences Translator TreatStringTag TreeAction TreeController TreeNode TSVFileReaderTask Type TypeConverter TypeUtil TypeUtil.FieldInfo UniprotConfig UniprotConverter UniprotEntry UniProtFastaLoaderTask UniprotFilterTask UniprotKeywordConverter UniprotXmlFilter UnknownTypeValue UpdateOrthologues URLGenerator URLParser URLUtil UserNotFoundException UserTemplateAction Util Version VersionServlet ViewAction ViewChange WeakReferenceHashMap WeakReferenceMap WebConfig WebResults WebResultsExecutor WebSearchable WebSearchableListController WebService WebServiceConstants WebServiceInput WebServiceRequestParser WebState WebTable WebUtil Widget WidgetAction WidgetConfig WidgetForm WidgetHelper WidgetsRequestParser WidgetsService WidgetsServiceInput WidgetsServlet WidgetURLQuery WidgetUtil WormBaseChadoIdResolverFactory WormBaseIdentifiersConverter WormBaseProcessor WriteGFFTask XmlBinding XmlDataLoader XmlDataLoaderTask XMLFormatter XmlHelper XmlUtil XMLValidator XMLValidatorErrorHandler