Hierarchy For All Packages

Package Hierarchies:

org.intermine, org.intermine.api, org.intermine.api.bag, org.intermine.api.config, org.intermine.api.profile, org.intermine.api.query, org.intermine.api.results, org.intermine.api.results.flatouterjoins, org.intermine.api.search, org.intermine.api.tag, org.intermine.api.template, org.intermine.api.util, org.intermine.api.xml, org.intermine.bio.chado, org.intermine.bio.chado.config, org.intermine.bio.dataconversion, org.intermine.bio.gbrowse, org.intermine.bio.io.gff3, org.intermine.bio.logic, org.intermine.bio.ontology, org.intermine.bio.postprocess, org.intermine.bio.task, org.intermine.bio.util, org.intermine.codegen, org.intermine.dataconversion, org.intermine.dataloader, org.intermine.dwr, org.intermine.metadata, org.intermine.model, org.intermine.modelproduction, org.intermine.modelproduction.xml, org.intermine.objectstore, org.intermine.objectstore.fastcollections, org.intermine.objectstore.intermine, org.intermine.objectstore.proxy, org.intermine.objectstore.query, org.intermine.objectstore.query.iql, org.intermine.objectstore.querygen, org.intermine.objectstore.safe, org.intermine.objectstore.translating, org.intermine.pathquery, org.intermine.postprocess, org.intermine.sql, org.intermine.sql.logging, org.intermine.sql.precompute, org.intermine.sql.query, org.intermine.sql.writebatch, org.intermine.task, org.intermine.util, org.intermine.web, org.intermine.web.autocompletion, org.intermine.web.bag, org.intermine.web.commandline, org.intermine.web.filters, org.intermine.web.logic, org.intermine.web.logic.aspects, org.intermine.web.logic.bag, org.intermine.web.logic.config, org.intermine.web.logic.export, org.intermine.web.logic.export.http, org.intermine.web.logic.export.rowformatters, org.intermine.web.logic.export.string, org.intermine.web.logic.help, org.intermine.web.logic.pathqueryresult, org.intermine.web.logic.profile, org.intermine.web.logic.query, org.intermine.web.logic.querybuilder, org.intermine.web.logic.results, org.intermine.web.logic.session, org.intermine.web.logic.template, org.intermine.web.logic.widget, org.intermine.web.logic.widget.config, org.intermine.web.search, org.intermine.web.struts, org.intermine.web.tags.disclosure, org.intermine.web.tags.table, org.intermine.web.tags.util, org.intermine.web.task, org.intermine.web.util, org.intermine.webservice.client.core, org.intermine.webservice.client.exceptions, org.intermine.webservice.client.services, org.intermine.webservice.client.template, org.intermine.webservice.client.util, org.intermine.webservice.exceptions, org.intermine.webservice.server, org.intermine.webservice.server.core, org.intermine.webservice.server.exceptions, org.intermine.webservice.server.lists, org.intermine.webservice.server.model, org.intermine.webservice.server.output, org.intermine.webservice.server.query.result, org.intermine.webservice.server.template, org.intermine.webservice.server.template.result, org.intermine.webservice.server.widget, org.intermine.xml, org.intermine.xml.full

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.intermine.util.CacheHoldingArrayList<E>
        • org.intermine.api.results.flatouterjoins.MultiRow<E>
        • org.intermine.objectstore.query.ResultsRow<E>
      • org.intermine.objectstore.query.Results (implements org.intermine.objectstore.proxy.LazyCollection<E>)
        • org.intermine.objectstore.query.SingletonResults (implements java.util.Set<E>)
      • org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
      • org.intermine.api.results.WebResults (implements org.intermine.api.results.WebTable)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • org.intermine.util.ConsistentSet<E>
      • org.intermine.objectstore.proxy.ProxyCollection<E> (implements org.intermine.objectstore.proxy.LazyCollection<E>)
  • org.intermine.sql.query.AbstractConstraint (implements org.intermine.sql.query.SQLStringable)
    • org.intermine.sql.query.Constraint
    • org.intermine.sql.query.ConstraintSet
    • org.intermine.sql.query.InListConstraint
    • org.intermine.sql.query.NotConstraint
    • org.intermine.sql.query.SubQueryConstraint
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.LinkedHashMap<K,V> (implements java.util.Map<K,V>)
        • org.intermine.web.logic.SortableMap
  • org.intermine.sql.query.AbstractTable (implements org.intermine.sql.query.SQLStringable)
    • org.intermine.sql.query.SubQuery
    • org.intermine.sql.query.Table
  • org.intermine.sql.query.AbstractValue (implements org.intermine.sql.query.SQLStringable)
    • org.intermine.sql.query.Constant
    • org.intermine.sql.query.Field
    • org.intermine.sql.query.Function
    • org.intermine.sql.query.OrderDescending
  • org.apache.struts.action.Action
    • org.intermine.web.struts.BagDetailsAction
    • org.intermine.web.struts.CollectionDetailsAction
    • org.apache.struts.actions.DispatchAction
      • org.intermine.web.struts.InterMineDispatchAction
        • org.intermine.web.struts.ChangeTableAction
        • org.intermine.web.struts.ModifyQueryChangeAction
        • org.intermine.web.struts.UserTemplateAction
      • org.intermine.web.struts.LoadQueryAction
      • org.apache.struts.actions.LookupDispatchAction
        • org.intermine.web.struts.InterMineLookupDispatchAction
      • org.intermine.web.struts.ModifyDetails
      • org.intermine.web.struts.QueryBuilderChange
      • org.intermine.web.struts.QueryBuilderViewChange
      • org.intermine.web.struts.TreeAction
    • org.intermine.web.struts.GetAttributeAsFileAction
    • org.intermine.web.struts.InterMineAction
      • org.intermine.web.struts.AddColumnAction
      • org.intermine.web.struts.AddToBagAction
      • org.intermine.web.struts.AvailableColumnsController
      • org.intermine.web.struts.BagUploadConfirmAction
      • org.intermine.web.struts.BeginAction
      • org.intermine.web.struts.BuildBagAction
      • org.intermine.web.struts.ChangePasswordAction
      • org.intermine.web.struts.ChangeTableSizeAction
      • org.intermine.web.struts.ContactAction
      • org.intermine.web.struts.CreateTemplateAction
      • org.intermine.web.struts.CurrentQueryAction
      • org.intermine.web.struts.EditTemplateAction
      • org.intermine.web.struts.ExportQueryAction
      • org.intermine.web.struts.ExportTagsAction
      • org.intermine.web.struts.FindInListAction
      • org.intermine.web.struts.GotoWebSearchableAction
      • org.intermine.web.struts.HeartbeatAction
      • org.intermine.web.struts.ImportQueriesAction
      • org.intermine.web.struts.ImportTagsAction
      • org.intermine.web.logic.profile.LoginHandler
        • org.intermine.web.struts.CreateAccountAction
        • org.intermine.web.struts.LoginAction
        • org.intermine.web.struts.PasswordResetAction
      • org.intermine.web.struts.LogoutAction
      • org.intermine.web.struts.ModifyBagAction
      • org.intermine.web.struts.ModifyBagDetailsAction
      • org.intermine.web.struts.ModifyQueryAction
      • org.intermine.web.struts.ModifyTemplateAction
      • org.intermine.web.struts.ObjectDetailsController
      • org.intermine.web.struts.PollQueryAction
      • org.intermine.web.struts.PortalQueryAction
      • org.intermine.web.struts.QueryBuilderConstraintAction
      • org.intermine.web.struts.QueryBuilderViewAction
      • org.intermine.web.struts.QueryClassSelectAction
      • org.intermine.web.struts.QueryForGraphAction
      • org.intermine.web.struts.RequestPasswordAction
      • org.intermine.web.struts.ResultsAction
      • org.intermine.web.struts.SaveBagAction
      • org.intermine.web.struts.SaveFromIdsToBagAction
      • org.intermine.web.struts.SaveQueryAction
      • org.intermine.web.struts.SummariseTemplatesAction
      • org.intermine.web.struts.TableExportAction
      • org.intermine.web.struts.TabLinkPreviewAction
      • org.intermine.web.struts.TempImageLoader
      • org.intermine.web.struts.TemplateAction
        • org.intermine.web.struts.TemplatesExportAction
      • org.intermine.web.struts.TemplateSettingsAction
      • org.intermine.web.struts.TemplatesImportAction
      • org.intermine.web.struts.TipAction
      • org.intermine.web.struts.WidgetAction
    • org.apache.struts.tiles.actions.TilesAction
      • org.intermine.web.struts.AspectController
      • org.intermine.web.struts.BagBuildController
      • org.intermine.web.struts.BagDetailsController
      • org.intermine.web.struts.BagUploadConfirmController
      • org.intermine.web.struts.BagUploadConfirmIssueController
      • org.intermine.web.struts.ClassChooserController
      • org.intermine.web.struts.ConvertBagController
      • org.intermine.web.struts.CountTableController
      • org.intermine.web.struts.ErrorMessagesController
      • org.intermine.web.struts.ExportController
      • org.intermine.web.struts.ExportOptionsController
      • org.intermine.web.struts.FavouritesController
      • org.intermine.web.struts.HintsController
      • org.intermine.web.struts.HtmlHeadController
      • org.intermine.web.struts.InlineTagEditorController
      • org.intermine.web.struts.KeywordSearchResultsController
      • org.intermine.web.struts.LoginController
      • org.intermine.web.struts.MyMineController
      • org.intermine.web.struts.ObjectDetailsAspectController
      • org.intermine.web.struts.ObjectDetailsInListController
      • org.intermine.web.struts.ObjectDetailsTemplateController
      • org.intermine.web.struts.ObjectTrailController
      • org.intermine.web.struts.ObjectViewController
      • org.intermine.web.struts.PasswordResetController
      • org.intermine.web.struts.QueryBuilderConstraintController
      • org.intermine.web.struts.QueryBuilderController
      • org.intermine.web.struts.QueryBuilderSummaryController
      • org.intermine.web.struts.SubMenuController
      • org.intermine.web.struts.TableController
      • org.intermine.web.struts.TemplateController
      • org.intermine.web.struts.TemplateListController
      • org.intermine.web.struts.TemplatesController
      • org.intermine.web.struts.TipController
      • org.intermine.web.struts.TreeController
      • org.intermine.web.struts.WebSearchableListController
  • org.apache.struts.action.ActionForm (implements java.io.Serializable)
    • org.intermine.web.struts.BagUploadConfirmForm
    • org.intermine.web.struts.BuildBagForm
    • org.intermine.web.struts.ChangePasswordForm
    • org.intermine.web.struts.ChangeTableSizeForm
    • org.intermine.web.struts.CreateAccountForm
    • org.intermine.web.struts.EnrichmentWidgetForm
    • org.intermine.web.struts.FindInListForm
    • org.intermine.web.struts.ImportTagsForm
    • org.intermine.web.struts.LoginForm
    • org.intermine.web.struts.ModifyBagDetailsForm
    • org.intermine.web.struts.ModifyBagForm
    • org.intermine.web.struts.ModifyQueryForm
    • org.intermine.web.struts.ModifyTemplateForm
    • org.intermine.web.struts.PasswordResetForm
    • org.intermine.web.struts.QueryBuilderConstraintForm
    • org.intermine.web.struts.QueryClassSelectForm
    • org.intermine.web.struts.RequestPasswordForm
    • org.intermine.web.struts.SaveBagForm
    • org.intermine.web.struts.SaveQueryForm
    • org.intermine.web.struts.TableExportForm
      • org.intermine.web.struts.CSVExportForm
    • org.intermine.web.struts.TemplateForm
    • org.intermine.web.struts.TemplateSettingsForm
    • org.apache.struts.validator.ValidatorForm (implements java.io.Serializable)
      • org.intermine.web.struts.ContactForm
      • org.intermine.web.struts.ImportQueriesForm
      • org.intermine.web.struts.TemplatesImportForm
    • org.intermine.web.struts.WidgetForm
  • org.intermine.dwr.AjaxServices
  • org.intermine.util.AlwaysMap<K,V> (implements java.util.Map<K,V>)
  • org.intermine.web.logic.aspects.Aspect
  • org.intermine.web.logic.aspects.AspectBinding
  • org.intermine.web.logic.aspects.AspectSource
  • org.intermine.api.tag.AspectTagUtil
  • org.intermine.xml.full.Attribute
  • org.intermine.web.util.AttributeLinkURL
  • org.intermine.web.autocompletion.AutoCompleter
  • org.intermine.web.logic.bag.BagConversionHelper
  • org.intermine.web.logic.bag.BagConverter
  • org.intermine.web.logic.bag.BagHelper
  • org.intermine.api.bag.BagManager
  • org.intermine.api.bag.BagOperations
  • org.intermine.api.bag.BagQuery
  • org.intermine.api.bag.BagQueryConfig
  • org.intermine.api.bag.BagQueryHelper
  • org.intermine.api.bag.BagQueryResult
  • org.intermine.api.bag.BagQueryRunner
  • org.intermine.dataloader.BaseEquivalentObjectFetcher (implements org.intermine.dataloader.EquivalentObjectFetcher)
    • org.intermine.dataloader.HintingFetcher
      • org.intermine.dataloader.BatchingFetcher
        • org.intermine.dataloader.ParallelBatchingFetcher
  • org.intermine.sql.writebatch.Batch
  • org.intermine.sql.writebatch.BatchWriterSimpleImpl (implements org.intermine.sql.writebatch.BatchWriter)
    • org.intermine.sql.writebatch.BatchWriterPreparedStatementImpl
      • org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
  • org.intermine.web.logic.widget.BenjaminiHochberg (implements org.intermine.web.logic.widget.ErrorCorrection)
  • org.intermine.sql.precompute.BestQuery
    • org.intermine.sql.precompute.BestQueryExplainer
      • org.intermine.sql.precompute.BestQueryExplainerVerbose
    • org.intermine.sql.precompute.BestQueryFallback
    • org.intermine.sql.precompute.BestQueryLogger
    • org.intermine.sql.precompute.BestQueryStorer
    • org.intermine.sql.precompute.EncloseSubqueryBestQuery
  • org.intermine.sql.precompute.BestQueryExplainer.Candidate
  • org.intermine.bio.util.BioConverterUtil
  • org.intermine.bio.util.BioQueries
  • org.intermine.bio.postprocess.BiosegIndexTask
  • org.intermine.bio.dataconversion.BioStoreHook (implements org.intermine.dataconversion.DataConverterStoreHook)
  • org.intermine.web.logic.widget.Bonferroni (implements org.intermine.web.logic.widget.ErrorCorrection)
  • org.intermine.bio.postprocess.CalculateLocations
  • org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
  • org.intermine.bio.chado.ChadoCV
  • org.intermine.bio.chado.ChadoCVFactory
  • org.intermine.bio.chado.ChadoCVTerm
  • org.intermine.bio.dataconversion.ChadoProcessor
    • org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
    • org.intermine.bio.dataconversion.SequenceProcessor
      • org.intermine.bio.dataconversion.FlyBaseProcessor
      • org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
      • org.intermine.bio.dataconversion.WormBaseProcessor
    • org.intermine.bio.dataconversion.StockProcessor
  • org.intermine.objectstore.intermine.CheckForIsNotNullConstraint (implements org.intermine.objectstore.query.ConstraintTraverseAction)
  • org.intermine.metadata.ClassDescriptor (implements java.lang.Comparable<T>)
  • org.intermine.api.config.ClassKeyHelper
  • org.intermine.objectstore.query.Clob (implements org.intermine.objectstore.query.QuerySelectable)
  • org.intermine.objectstore.query.ClobAccess (implements java.lang.CharSequence, org.intermine.objectstore.proxy.Lazy)
    • org.intermine.bio.util.ClobAccessReverseComplement
    • org.intermine.objectstore.query.PendingClob
  • org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory
  • org.intermine.webservice.server.CodeTranslator
  • org.intermine.util.CollectionUtil
  • org.intermine.api.results.Column
  • org.intermine.util.CombinedIterator<E> (implements java.util.Iterator<E>)
  • org.intermine.bio.chado.config.ConfigAction
    • org.intermine.bio.chado.config.DoNothingAction
    • org.intermine.bio.chado.config.MatchingFieldConfigAction
      • org.intermine.bio.chado.config.CreateCollectionAction
      • org.intermine.bio.chado.config.CreateSynonymAction
      • org.intermine.bio.chado.config.SetFieldConfigAction
  • org.intermine.api.config.Constants
  • org.intermine.objectstore.query.Constraint
    • org.intermine.objectstore.query.BagConstraint (implements org.intermine.objectstore.query.ConstraintWithBag)
    • org.intermine.objectstore.query.ClassConstraint
    • org.intermine.objectstore.query.ConstraintSet
    • org.intermine.objectstore.query.ContainsConstraint
    • org.intermine.objectstore.query.MultipleInBagConstraint (implements org.intermine.objectstore.query.ConstraintWithBag)
    • org.intermine.objectstore.query.OverlapConstraint
    • org.intermine.objectstore.query.SimpleConstraint
    • org.intermine.objectstore.query.SubqueryConstraint
    • org.intermine.objectstore.query.SubqueryExistsConstraint
  • org.intermine.objectstore.query.ConstraintHelper
  • org.intermine.webservice.server.template.result.ConstraintInput
  • org.intermine.objectstore.query.ConstraintOp
  • org.intermine.pathquery.Constraints
  • org.intermine.pathquery.ConstraintValueParser
  • org.intermine.webservice.client.core.ContentType
  • org.intermine.api.bag.ConvertedObjectPair
  • org.intermine.bio.postprocess.CreateFlankingRegions
  • org.intermine.bio.postprocess.CreateFlyBaseLinkIns
  • org.intermine.bio.postprocess.CreateReferences
  • org.intermine.bio.util.CreateSiteMaps
  • org.intermine.sql.Database (implements org.intermine.util.Shutdownable)
  • org.intermine.sql.DatabaseFactory
  • org.intermine.objectstore.intermine.DatabaseSchema
  • org.intermine.objectstore.intermine.DatabaseSchema.Fields
  • org.intermine.sql.DatabaseUtil
  • org.intermine.dataconversion.DataConverter
    • org.intermine.dataconversion.DBConverter
      • org.intermine.bio.dataconversion.BioDBConverter
        • org.intermine.bio.dataconversion.ChadoDBConverter
          • org.intermine.bio.dataconversion.GenomeDBConverter
    • org.intermine.dataconversion.DirectoryConverter
      • org.intermine.bio.dataconversion.BioDirectoryConverter
        • org.intermine.bio.dataconversion.PdbConverter
        • org.intermine.bio.dataconversion.UniprotConverter
    • org.intermine.dataconversion.FileConverter
      • org.intermine.bio.dataconversion.BioFileConverter
        • org.intermine.bio.dataconversion.BioGridConverter
        • org.intermine.bio.dataconversion.GoConverter
        • org.intermine.bio.dataconversion.InparanoidConverter
        • org.intermine.bio.dataconversion.InterProConverter
        • org.intermine.bio.dataconversion.KeggPathwayConverter
        • org.intermine.bio.dataconversion.PsiConverter
        • org.intermine.bio.dataconversion.UniprotKeywordConverter
        • org.intermine.bio.dataconversion.WormBaseIdentifiersConverter
      • org.intermine.bio.dataconversion.PubMedGeneConverter
    • org.intermine.dataconversion.FullXmlConverter
    • org.intermine.bio.dataconversion.GFF3Converter
    • org.intermine.bio.dataconversion.OboConverter
  • org.intermine.dataloader.DataLoader
    • org.intermine.dataloader.DirectDataLoader
    • org.intermine.dataloader.ObjectStoreDataLoader
    • org.intermine.dataloader.XmlDataLoader
  • org.intermine.dataloader.DataLoaderHelper
  • org.intermine.dataloader.DataTracker
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.intermine.api.bag.BagQueryHandler
    • org.intermine.xml.full.FullHandler
    • org.intermine.api.xml.InterMineBagHandler
    • org.intermine.pathquery.PathQueryHandler
      • org.intermine.api.xml.SavedQueryHandler
      • org.intermine.api.xml.TemplateQueryHandler
    • org.intermine.api.xml.TagHandler
  • org.intermine.task.DelimitedFileConfiguration
  • java.util.Dictionary<K,V>
    • java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.Properties
        • org.intermine.util.NonOverrideableProperties
  • org.intermine.web.logic.query.DisplayConstraint
  • org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
  • org.intermine.web.logic.query.DisplayConstraintFactory
  • org.intermine.web.logic.query.DisplayConstraintHelpMessages
  • org.intermine.web.logic.config.Displayer
  • org.intermine.web.logic.results.DisplayField
    • org.intermine.web.logic.results.DisplayCollection
    • org.intermine.web.logic.results.DisplayReference
  • org.intermine.web.struts.DisplayLookupMessageHandler
  • org.intermine.web.logic.results.DisplayObject
  • org.intermine.web.logic.querybuilder.DisplayPath
    • org.intermine.web.logic.querybuilder.SummaryPath (implements java.lang.Comparable<T>)
  • org.intermine.util.DynamicBean (implements net.sf.cglib.proxy.MethodInterceptor)
  • org.intermine.util.DynamicUtil
  • org.intermine.web.logic.widget.EnrichmentWidgetLdr
  • org.intermine.bio.dataconversion.EntrezPublicationsRetriever
  • org.intermine.dataloader.EquivalentObjectHints
  • org.intermine.webservice.client.util.ErrorMessageParser
  • org.intermine.web.logic.export.ExcelExporter (implements org.intermine.web.logic.export.Exporter)
  • org.apache.struts.action.ExceptionHandler
    • org.intermine.web.struts.InterMineExceptionHandler
  • org.intermine.sql.query.ExplainResult
    • org.intermine.sql.query.DummyExplainResult
    • org.intermine.sql.query.PostgresExplainResult
  • org.intermine.web.logic.export.ExporterImpl (implements org.intermine.web.logic.export.Exporter)
  • org.intermine.web.logic.export.ExportHelper
  • org.intermine.api.results.ExportResultsIterator (implements java.util.Iterator<E>)
  • org.intermine.objectstore.intermine.ExtraQueryTime
  • org.intermine.web.logic.config.FieldConfig
  • org.intermine.web.logic.config.FieldConfigHelper
  • org.intermine.metadata.FieldDescriptor
    • org.intermine.metadata.AttributeDescriptor
    • org.intermine.metadata.ReferenceDescriptor
      • org.intermine.metadata.CollectionDescriptor
  • org.intermine.sql.writebatch.FlushJobBatchCommit (implements org.intermine.sql.writebatch.FlushJob)
  • org.intermine.sql.writebatch.FlushJobPostgresCopyImpl (implements org.intermine.sql.writebatch.FlushJob)
  • org.intermine.sql.writebatch.FlushJobStatementBatchImpl (implements org.intermine.sql.writebatch.FlushJob)
  • org.intermine.sql.writebatch.FlushJobUpdateStatistics (implements org.intermine.sql.writebatch.FlushJob)
  • java.text.Format (implements java.lang.Cloneable, java.io.Serializable)
    • java.text.NumberFormat
      • java.text.DecimalFormat
        • org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
  • org.intermine.util.FormattedTextParser
  • org.intermine.webservice.server.output.Formatter
    • org.intermine.webservice.server.output.CSVFormatter
    • org.intermine.webservice.server.output.TabFormatter
    • org.intermine.webservice.server.output.XMLFormatter
  • org.intermine.web.struts.ForwardParameters
  • org.intermine.xml.full.FullParser
  • org.intermine.xml.full.FullRenderer
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • org.intermine.webservice.server.template.AvailableTemplatesServlet
      • org.intermine.webservice.server.lists.ListsServlet
      • org.intermine.webservice.server.model.ModelServlet
      • org.intermine.webservice.server.query.result.QueryResultServlet
      • org.intermine.webservice.server.template.result.TemplateResultServlet
      • org.intermine.webservice.server.VersionServlet
      • org.intermine.webservice.server.widget.WidgetsServlet
  • org.intermine.bio.dataconversion.GenesFileProcessor
  • org.intermine.bio.io.gff3.GFF3Parser
  • org.intermine.bio.io.gff3.GFF3Record
  • org.intermine.bio.dataconversion.GFF3RecordHandler
    • org.intermine.bio.dataconversion.MalariaGFF3RecordHandler
    • org.intermine.bio.dataconversion.MirandaGFF3RecordHandler
  • org.intermine.bio.dataconversion.GFF3SeqHandler
  • org.intermine.web.logic.widget.GridDataSet
  • org.intermine.web.filters.HeaderFilter (implements javax.servlet.Filter)
  • org.intermine.web.logic.help.HintManager
  • org.intermine.bio.logic.HomologueMapping
  • org.intermine.web.util.HttpClient
  • org.intermine.webservice.client.util.HttpConnection
  • org.intermine.web.logic.export.http.HttpExporterBase
    • org.intermine.web.logic.export.http.StandardHttpExporter (implements org.intermine.web.logic.export.http.TableHttpExporter)
      • org.intermine.web.logic.export.http.CSVHttpExporter
      • org.intermine.web.logic.export.http.ExcelHttpExporter
      • org.intermine.web.logic.export.http.TabHttpExporter
  • org.intermine.web.logic.export.http.HttpExportUtil
  • org.intermine.web.logic.widget.Hypergeometric
  • org.intermine.util.IdentityMap<E> (implements java.util.Map<K,V>)
  • org.intermine.bio.dataconversion.IdResolver
  • org.intermine.bio.dataconversion.IdResolverFactory
    • org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
    • org.intermine.bio.dataconversion.HgncIdResolverFactory
    • org.intermine.bio.dataconversion.MockIdResolverFactory
    • org.intermine.bio.dataconversion.WormBaseChadoIdResolverFactory
  • org.intermine.sql.writebatch.IndirectionTableBatch (implements org.intermine.sql.writebatch.Table)
  • org.intermine.web.struts.InitialiserPlugin (implements org.apache.struts.action.PlugIn)
  • org.intermine.web.logic.results.InlineResultsTable
  • java.io.InputStream (implements java.io.Closeable)
    • org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
  • org.intermine.dataloader.IntegrationWriterAbstractImpl (implements org.intermine.dataloader.IntegrationWriter)
    • org.intermine.dataloader.IntegrationWriterDataTrackingImpl
  • org.intermine.dataloader.IntegrationWriterFactory
  • org.intermine.bio.postprocess.IntergenicRegionUtil
  • org.intermine.api.InterMineAPI
  • org.intermine.api.profile.InterMineBag (implements java.lang.Cloneable, org.intermine.api.search.WebSearchable)
  • org.intermine.api.xml.InterMineBagBinding
  • org.intermine.modelproduction.xml.InterMineModelParser (implements org.intermine.modelproduction.ModelParser)
  • org.intermine.util.IntPresentSet
  • org.intermine.bio.postprocess.IntronUtil
  • org.intermine.util.IntToIntMap
  • org.intermine.objectstore.query.iql.IqlQuery
  • org.intermine.objectstore.query.iql.IqlQueryParser
  • org.intermine.xml.full.Item (implements java.lang.Comparable<T>)
  • org.intermine.xml.full.ItemFactory
  • org.intermine.xml.full.ItemHelper
  • org.intermine.util.IteratorIterable<T> (implements java.lang.Iterable<T>)
  • org.intermine.codegen.JavaModelOutput
  • org.intermine.web.search.KeywordSearch
  • org.intermine.web.struts.KeywordSearchFacet
  • org.intermine.web.search.KeywordSearchFacetData
  • org.intermine.web.search.KeywordSearchHit
  • org.intermine.web.struts.KeywordSearchResult
  • org.intermine.sql.precompute.LimitOffsetQuery
  • org.intermine.webservice.server.LinkGeneratorBase
    • org.intermine.webservice.server.query.result.QueryResultLinkGenerator
    • org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
  • org.intermine.webservice.server.core.ListManager
  • org.intermine.webservice.server.lists.ListsRequestParser
  • org.intermine.pathquery.LogicExpression
  • org.intermine.pathquery.LogicExpression.Node
    • org.intermine.pathquery.LogicExpression.Operator
      • org.intermine.pathquery.LogicExpression.And
      • org.intermine.pathquery.LogicExpression.Or
    • org.intermine.pathquery.LogicExpression.Variable
  • org.intermine.web.autocompletion.LuceneIndex
  • org.intermine.web.autocompletion.LuceneObjectClass
  • org.intermine.web.autocompletion.LuceneSearchEngine
  • org.intermine.util.MailUtils
  • org.intermine.api.query.MainHelper
  • org.intermine.api.query.MainHelper.SummaryConfig
  • org.intermine.util.MappingUtil
  • org.intermine.modelproduction.MetadataManager
  • org.intermine.bio.logic.Mine
  • org.intermine.dataconversion.MockItemWriter (implements org.intermine.dataconversion.ItemWriter)
  • org.intermine.metadata.Model
  • org.intermine.web.logic.querybuilder.ModelBrowserHelper
  • org.intermine.modelproduction.ModelMerger
  • org.intermine.api.results.flatouterjoins.MultiRowValue<E>
    • org.intermine.api.results.flatouterjoins.MultiRowFirstValue<E>
    • org.intermine.api.results.flatouterjoins.MultiRowLaterValue<E>
  • org.intermine.api.util.NameUtil
  • org.intermine.pathquery.Node
    • org.intermine.web.logic.query.MetadataNode
  • org.intermine.objectstore.intermine.NotXmlParser
  • org.intermine.objectstore.intermine.NotXmlRenderer
  • org.intermine.util.NullFirstComparator (implements java.util.Comparator<T>)
  • org.intermine.dataloader.ObjectDescription
  • org.intermine.util.ObjectPipe<E> (implements java.util.Iterator<E>)
  • org.intermine.objectstore.ObjectStoreAbstractImpl (implements org.intermine.objectstore.ObjectStore)
    • org.intermine.objectstore.intermine.ObjectStoreInterMineImpl (implements org.intermine.util.Shutdownable)
      • org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl (implements org.intermine.objectstore.ObjectStoreWriter, org.intermine.util.Shutdownable)
    • org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
  • org.intermine.objectstore.query.ObjectStoreBag (implements org.intermine.objectstore.query.QuerySelectable)
  • org.intermine.objectstore.query.ObjectStoreBagCombination (implements org.intermine.objectstore.query.QuerySelectable)
  • org.intermine.objectstore.query.ObjectStoreBagsForObject (implements org.intermine.objectstore.query.QuerySelectable)
  • org.intermine.objectstore.ObjectStoreFactory
  • org.intermine.dataconversion.ObjectStoreItemWriter (implements org.intermine.dataconversion.ItemWriter)
  • org.intermine.objectstore.ObjectStorePassthruImpl (implements org.intermine.objectstore.ObjectStore)
    • org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
    • org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
    • org.intermine.objectstore.safe.ObjectStoreSafeImpl
  • org.intermine.objectstore.ObjectStoreSummary
  • org.intermine.objectstore.ObjectStoreWriterFactory
  • org.intermine.web.struts.ObjectTrailController.TrailElement
  • org.intermine.bio.ontology.OboParser
  • org.intermine.bio.ontology.OboRelation
  • org.intermine.bio.ontology.OboTerm
  • org.intermine.bio.ontology.OboTermSynonym
  • org.intermine.bio.ontology.OboToModel
  • org.intermine.bio.ontology.OboToModelProcessor
  • org.intermine.bio.ontology.OboTypeDefinition
  • org.intermine.sql.precompute.OptimiserCache
  • org.intermine.sql.precompute.OptimiserCacheLine
  • org.intermine.sql.precompute.OptimiserMappingChecker (implements org.intermine.util.MappingUtilChecker<T>)
  • org.intermine.objectstore.query.OrderDescending (implements org.intermine.objectstore.query.QueryOrderable)
  • org.intermine.pathquery.OrderElement
  • org.intermine.bio.util.OrganismData
  • org.intermine.bio.util.OrganismRepository
  • org.intermine.bio.logic.OrthologueLinkManager
  • org.intermine.webservice.server.output.Output
    • org.intermine.webservice.server.output.MemoryOutput
      • org.intermine.webservice.server.output.HTMLOutput
    • org.intermine.webservice.server.output.StreamedOutput
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.ByteArrayOutputStream
      • org.intermine.util.SensibleByteArrayOutputStream
        • org.intermine.sql.writebatch.PostgresByteArrayOutputStream
    • java.io.FilterOutputStream
      • java.io.DataOutputStream (implements java.io.DataOutput)
        • org.intermine.sql.writebatch.PostgresDataOutputStream
    • org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
  • org.intermine.objectstore.query.OverlapRange
  • org.intermine.bio.postprocess.OverlapUtil
  • org.intermine.bio.postprocess.OverlapViewTask
  • org.intermine.web.logic.results.PagedTable
  • org.intermine.objectstore.intermine.ParallelPrecomputer
  • org.intermine.objectstore.intermine.ParallelPrecomputer.Job (implements java.lang.Comparable<T>)
  • org.intermine.util.PasswordHasher
  • org.intermine.pathquery.Path
  • org.intermine.pathquery.PathConstraint
    • org.intermine.pathquery.PathConstraintAttribute
    • org.intermine.pathquery.PathConstraintBag
    • org.intermine.pathquery.PathConstraintIds
    • org.intermine.pathquery.PathConstraintLookup
    • org.intermine.pathquery.PathConstraintLoop
    • org.intermine.pathquery.PathConstraintMultiValue
    • org.intermine.pathquery.PathConstraintNull
    • org.intermine.pathquery.PathConstraintSubclass
  • org.intermine.objectstore.query.PathExpressionField (implements org.intermine.objectstore.query.QueryPathExpression)
  • org.intermine.pathquery.PathQuery (implements java.lang.Cloneable)
    • org.intermine.api.template.TemplateQuery (implements org.intermine.api.search.WebSearchable)
  • org.intermine.api.query.PathQueryAPI
  • org.intermine.pathquery.PathQueryBinding
    • org.intermine.api.xml.TemplateQueryBinding
  • org.intermine.webservice.server.query.result.PathQueryBuilder
  • org.intermine.api.query.PathQueryExecutor
  • org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
  • org.intermine.api.util.PathUtil
  • org.intermine.web.commandline.PerformanceTester
  • org.intermine.web.bag.PkQueryIdUpgrader (implements org.intermine.api.bag.IdUpgrader)
  • org.intermine.web.logic.PortalHelper
  • org.intermine.postprocess.PostProcessor
    • org.intermine.bio.postprocess.GoPostprocess
    • org.intermine.bio.postprocess.UpdateOrthologues
  • org.intermine.bio.postprocess.PostProcessUtil
  • org.intermine.sql.precompute.PrecomputedTable (implements java.lang.Comparable<T>, org.intermine.sql.query.SQLStringable)
  • org.intermine.sql.precompute.PrecomputedTableManager
  • org.intermine.objectstore.query.PrefetchManager
  • org.intermine.metadata.PrimaryKey
  • org.intermine.metadata.PrimaryKeyUtil
  • org.intermine.dataloader.PriorityConfig
  • org.intermine.api.profile.Profile
  • org.intermine.web.ProfileBinding
  • org.intermine.api.profile.ProfileManager
  • org.intermine.web.ProfileManagerBinding
  • org.apache.tools.ant.ProjectComponent
    • org.apache.tools.ant.Task
      • org.intermine.task.AcceptanceTestTask
      • org.intermine.task.AnalyseDbTask
      • org.intermine.task.BuildDbTask
      • org.intermine.task.CreateIndexesTask
      • org.intermine.task.DirectDataLoaderTask
        • org.intermine.task.FileDirectDataLoaderTask
          • org.intermine.bio.dataconversion.FastaLoaderTask
            • org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
              • org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask
              • org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask
            • org.intermine.bio.dataconversion.NCBIFastaLoaderTask
            • org.intermine.bio.dataconversion.UniProtFastaLoaderTask
          • org.intermine.task.TSVFileReaderTask
      • org.intermine.task.DropPrecomputedTablesTask
      • org.intermine.web.task.DumpDefaultTemplatesTask
      • org.intermine.task.DynamicAttributeTask
        • org.intermine.task.ConverterTask
          • org.intermine.task.DBConverterTask
          • org.intermine.task.DirectoryConverterTask
          • org.intermine.task.FileConverterTask
          • org.intermine.task.FullXmlConverterTask
          • org.intermine.bio.task.OboConverterTask
        • org.intermine.bio.postprocess.PostProcessOperationsTask
        • org.intermine.task.PostProcessorTask
      • org.intermine.bio.dataconversion.EntrezOrganismRetriever
      • org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
      • org.intermine.bio.task.GFF3ConverterTask
      • org.intermine.task.GrantTask
      • org.intermine.web.task.LoadDefaultTemplatesTask
      • org.intermine.task.ModelMergerTask
      • org.intermine.task.ModelOutputTask
      • org.intermine.dataloader.ObjectStoreDataLoaderTask
      • org.intermine.task.PrecomputeTask
      • org.intermine.web.task.PrecomputeTemplatesTask
      • org.intermine.web.task.ProfileReadTask
      • org.intermine.web.task.ProfileWriteTask
      • org.intermine.task.RetrieveMetadataTask
      • org.intermine.bio.util.SiteMapTask
      • org.intermine.bio.task.SOClassNameMapMakerTask
      • org.intermine.bio.task.SOToModelTask
      • org.intermine.task.StaticMethodTask
      • org.intermine.task.StoreMetadataTask
      • org.intermine.task.SummariseObjectStoreTask
      • org.intermine.objectstore.intermine.TorqueModelOutputTask
      • org.intermine.bio.dataconversion.UniprotFilterTask
      • org.intermine.bio.gbrowse.WriteGFFTask
      • org.intermine.dataloader.XmlDataLoaderTask
  • org.intermine.util.PropertiesUtil
  • org.intermine.objectstore.proxy.ProxyReference (implements org.intermine.model.InterMineObject, org.intermine.objectstore.proxy.Lazy)
  • org.intermine.util.PseudoSet<E> (implements java.util.Set<E>)
    • org.intermine.util.AlwaysSet<E>
  • org.intermine.bio.dataconversion.PubMedReference
  • org.intermine.objectstore.query.Query (implements org.intermine.objectstore.query.FromElement, org.intermine.objectstore.query.Queryable)
  • org.intermine.sql.query.Query (implements org.intermine.sql.query.SQLStringable)
  • org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
  • org.intermine.objectstore.query.QueryCast (implements org.intermine.objectstore.query.QueryEvaluable)
  • org.intermine.objectstore.query.QueryClass (implements org.intermine.objectstore.query.FromElement, org.intermine.objectstore.query.QueryNode)
  • org.intermine.objectstore.query.QueryClassBag (implements org.intermine.objectstore.query.FromElement)
  • org.intermine.objectstore.query.QueryCloner
  • org.intermine.objectstore.query.QueryCollectionPathExpression (implements org.intermine.objectstore.query.Queryable, org.intermine.objectstore.query.QueryPathExpressionWithSelect)
  • org.intermine.objectstore.query.QueryCreator
  • org.intermine.objectstore.query.QueryExpression (implements org.intermine.objectstore.query.QueryEvaluable)
  • org.intermine.objectstore.query.QueryField (implements org.intermine.objectstore.query.QueryEvaluable)
  • org.intermine.objectstore.query.QueryForeignKey (implements org.intermine.objectstore.query.QueryEvaluable)
  • org.intermine.objectstore.query.QueryFunction (implements org.intermine.objectstore.query.QueryEvaluable)
  • org.intermine.objectstore.querygen.QueryGenUtil
  • org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
  • org.intermine.objectstore.query.QueryHelper
  • org.intermine.sql.logging.QueryLogger
  • org.intermine.web.logic.query.QueryMonitorTimeout (implements org.intermine.web.logic.query.QueryMonitor)
    • org.intermine.web.logic.query.PageTableQueryMonitor
    • org.intermine.web.logic.session.QueryCountQueryMonitor
  • org.intermine.objectstore.query.QueryObjectPathExpression (implements org.intermine.objectstore.query.Queryable, org.intermine.objectstore.query.QueryPathExpressionWithSelect)
  • org.intermine.sql.precompute.QueryOptimiser
  • org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator (implements java.util.Comparator<T>)
  • org.intermine.sql.precompute.QueryOptimiserContext
  • org.intermine.objectstore.query.QueryReference
    • org.intermine.objectstore.query.QueryCollectionReference
    • org.intermine.objectstore.query.QueryObjectReference (implements org.intermine.objectstore.query.QueryOrderable)
  • org.intermine.objectstore.query.QueryValue (implements org.intermine.objectstore.query.QueryEvaluable)
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.BufferedReader
      • org.intermine.bio.dataconversion.PdbConverter.PdbBufferedReader
  • org.intermine.api.results.flatouterjoins.ReallyFlatIterator (implements java.util.Iterator<E>)
  • java.lang.ref.Reference<T>
    • java.lang.ref.WeakReference<T>
      • org.intermine.objectstore.intermine.ObjectStoreInterMineImpl.BagTableToRemove
  • org.intermine.xml.full.Reference
  • org.intermine.xml.full.ReferenceList
  • org.intermine.util.ReferenceMap<K,V> (implements java.util.Map<K,V>)
    • org.intermine.util.SoftReferenceMap<K,V>
      • org.intermine.util.CacheMap<K,V>
        • org.intermine.web.logic.results.DisplayObjectFactory
    • org.intermine.util.WeakReferenceMap<K,V>
      • org.intermine.util.WeakReferenceHashMap<K,V>
  • org.intermine.bio.dataconversion.ReferencesFileProcessor
  • org.intermine.xml.full.RendererComparator (implements java.util.Comparator<T>)
  • org.intermine.webservice.client.core.RequestImpl (implements org.intermine.webservice.client.core.Request)
    • org.intermine.webservice.client.services.QueryService.QueryRequest
    • org.intermine.webservice.client.services.TemplateService.TemplateRequest
  • org.apache.struts.action.RequestProcessor
    • org.apache.struts.tiles.TilesRequestProcessor
      • org.intermine.web.struts.InterMineRequestProcessor
  • org.intermine.web.logic.RequestUtil
  • org.intermine.web.logic.export.ResponseUtil
  • org.intermine.api.results.ResultElement (implements java.io.Serializable)
  • org.intermine.web.logic.export.ResultElementConverter
  • org.intermine.webservice.server.core.ResultProcessor
  • org.intermine.objectstore.query.ResultsBatches
  • org.intermine.objectstore.intermine.ResultsConverter
  • org.intermine.objectstore.query.ResultsInfo
  • org.intermine.sql.writebatch.Row (implements java.lang.Comparable<T>)
  • org.intermine.web.logic.export.RowFormatterImpl (implements org.intermine.web.logic.export.RowFormatter)
    • org.intermine.web.logic.export.rowformatters.CSVRowFormatter
    • org.intermine.web.logic.export.rowformatters.TabRowFormatter
  • org.intermine.api.profile.SavedQuery
  • org.intermine.api.xml.SavedQueryBinding
  • org.intermine.util.SAXParser
  • org.intermine.api.search.SearchFilterEngine
  • org.intermine.api.search.SearchRepository
  • org.intermine.sql.query.SelectValue (implements org.intermine.sql.query.SQLStringable)
  • org.intermine.webservice.client.core.Service
    • org.intermine.webservice.client.services.FindTemplatesService
    • org.intermine.webservice.client.services.ListService
    • org.intermine.webservice.client.services.ModelService
    • org.intermine.webservice.client.services.QueryService
    • org.intermine.webservice.client.services.TemplateService
  • org.intermine.webservice.client.core.ServiceFactory
  • org.intermine.web.logic.session.SessionActivationListener (implements javax.servlet.http.HttpSessionActivationListener, java.io.Serializable)
  • org.intermine.web.logic.session.SessionListener (implements javax.servlet.http.HttpSessionListener)
  • org.intermine.web.logic.session.SessionMethods
  • org.intermine.bio.postprocess.SetCollectionCounts
  • javax.servlet.jsp.tagext.SimpleTagSupport (implements javax.servlet.jsp.tagext.SimpleTag)
    • org.intermine.web.tags.disclosure.BaseDisclosureTag
      • org.intermine.web.tags.disclosure.DisclosureBodyTag
      • org.intermine.web.tags.disclosure.DisclosureDetailsTag
      • org.intermine.web.tags.disclosure.DisclosureHeadTag
      • org.intermine.web.tags.disclosure.DisclosureTag
      • org.intermine.web.tags.disclosure.DisclosureTitleTag
    • org.intermine.web.tags.table.NavigationBarTag
    • org.intermine.web.tags.table.TableTag
    • org.intermine.web.tags.util.TreatStringTag
  • org.intermine.dataloader.Source
  • org.intermine.dataloader.SourcePriorityComparator (implements java.util.Comparator<T>)
  • org.intermine.objectstore.intermine.SqlGenerator
  • org.intermine.webservice.server.StatusDictionary
  • org.intermine.util.StringConstructor (implements java.lang.CharSequence)
  • org.intermine.web.logic.export.string.StringTableExporter
  • org.intermine.util.StringUtil
  • org.intermine.util.StringUtil.LineWrappedString
  • org.intermine.web.logic.querybuilder.SummaryConstraint
  • org.intermine.util.SynchronisedIterator<E> (implements java.util.Iterator<E>)
  • org.intermine.sql.writebatch.TableBatch (implements org.intermine.sql.writebatch.Table)
  • org.intermine.web.logic.config.TableExportConfig
  • org.intermine.web.logic.export.http.TableExporterFactory
  • org.intermine.web.logic.results.TableHelper
  • org.intermine.web.logic.widget.TableWidgetLdr
  • org.intermine.webservice.client.core.TabTableResult
  • org.intermine.api.xml.TagBinding
  • org.intermine.api.profile.TagManager
  • org.intermine.api.profile.TagManagerFactory
  • org.intermine.api.template.TemplateComparator (implements java.util.Comparator<T>)
  • org.intermine.web.logic.template.TemplateHelper
  • org.intermine.api.template.TemplateManager
  • org.intermine.webservice.client.template.TemplateParameter
  • org.intermine.api.template.TemplatePopulator
  • org.intermine.api.template.TemplatePrecomputeHelper
  • org.intermine.api.template.TemplateSummariser
  • org.intermine.api.template.TemplateValue
  • org.intermine.util.TextTable
  • java.lang.Thread (implements java.lang.Runnable)
    • org.intermine.util.ShutdownHook
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.intermine.sql.precompute.BestQueryException
      • org.intermine.InterMineException
        • org.intermine.pathquery.ParseValueException
      • org.intermine.metadata.MetaDataException
      • org.intermine.modelproduction.ModelMergerException
      • org.intermine.objectstore.ObjectStoreException
        • org.intermine.objectstore.intermine.CompletelyFalseException
        • org.intermine.objectstore.DataChangedException
        • org.intermine.objectstore.ObjectStoreLimitReachedException
        • org.intermine.objectstore.ObjectStoreQueryDurationException
      • org.intermine.pathquery.PathException
      • org.intermine.sql.precompute.QueryOptimiserException
      • java.lang.RuntimeException
        • org.intermine.web.logic.export.ExportException
        • org.intermine.bio.dataconversion.GenesProcessorException
        • org.intermine.api.bag.IncompatibleTypesException
        • org.intermine.web.logic.results.PageOutOfRangeException
        • org.intermine.api.profile.ProfileAlreadyExistsException
        • org.intermine.bio.dataconversion.ReferencesProcessorException
        • org.intermine.webservice.client.exceptions.ServiceException
          • org.intermine.webservice.client.exceptions.BadRequestException
          • org.intermine.webservice.client.exceptions.InternalErrorException
          • org.intermine.webservice.client.exceptions.NotConnectedException
          • org.intermine.webservice.client.exceptions.NotImplementedException
          • org.intermine.webservice.client.exceptions.ResourceNotFoundException
          • org.intermine.webservice.client.exceptions.ServiceForbiddenException
          • org.intermine.webservice.client.exceptions.ServiceUnavailableException
        • org.intermine.webservice.exceptions.ServiceException
          • org.intermine.webservice.exceptions.BadRequestException
          • org.intermine.webservice.exceptions.InternalErrorException
          • org.intermine.webservice.exceptions.NoContentException
          • org.intermine.webservice.exceptions.ResourceNotFoundException
          • org.intermine.webservice.exceptions.ServiceForbiddenException
        • org.intermine.webservice.server.exceptions.ServiceException
          • org.intermine.webservice.server.exceptions.BadRequestException
          • org.intermine.webservice.server.exceptions.InternalErrorException
          • org.intermine.webservice.server.exceptions.NoContentException
          • org.intermine.webservice.server.exceptions.ResourceNotFoundException
          • org.intermine.webservice.server.exceptions.ServiceForbiddenException
        • org.intermine.api.template.TemplatePopulatorException
        • org.intermine.api.bag.UnknownBagTypeException
        • org.intermine.api.profile.UserNotFoundException
  • org.intermine.web.logic.widget.ToolTipGenerator (implements org.jfree.chart.labels.CategoryToolTipGenerator)
  • org.intermine.objectstore.intermine.TorqueModelOutput
  • org.intermine.bio.postprocess.TransferSequences
  • org.intermine.objectstore.translating.Translator
    • org.intermine.dataconversion.ItemToObjectTranslator
  • org.intermine.web.logic.TreeNode
  • org.intermine.web.logic.config.Type
  • org.intermine.api.bag.TypeConverter
  • org.intermine.util.TypeUtil
  • org.intermine.util.TypeUtil.FieldInfo
  • org.intermine.bio.dataconversion.UniprotConfig
  • org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
  • org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig
  • org.intermine.bio.dataconversion.UniprotEntry
  • org.intermine.bio.dataconversion.UniprotEntry.Dbref
  • org.intermine.bio.dataconversion.UniprotEntry.UniprotGene
  • org.intermine.bio.dataconversion.UniprotXmlFilter
  • org.intermine.objectstore.query.UnknownTypeValue
  • org.intermine.web.util.URLGenerator
  • org.intermine.webservice.client.util.URLParser
  • org.intermine.web.util.URLUtil
  • org.intermine.util.Util
  • org.intermine.webservice.client.core.Version
  • org.intermine.web.logic.config.WebConfig
  • org.intermine.api.query.WebResultsExecutor
  • org.intermine.webservice.server.WebService
    • org.intermine.webservice.server.template.AvailableTemplatesService
    • org.intermine.webservice.server.lists.ListsService
    • org.intermine.webservice.server.model.ModelService
    • org.intermine.webservice.server.query.result.QueryResultService
      • org.intermine.webservice.server.template.result.TemplateResultService
    • org.intermine.webservice.server.widget.WidgetsService
  • org.intermine.webservice.server.WebServiceConstants
  • org.intermine.webservice.server.WebServiceInput
    • org.intermine.webservice.server.lists.ListsServiceInput
    • org.intermine.webservice.server.query.result.QueryResultInput
    • org.intermine.webservice.server.template.result.TemplateResultInput
    • org.intermine.webservice.server.widget.WidgetsServiceInput
  • org.intermine.webservice.server.query.result.WebServiceRequestParser
    • org.intermine.webservice.server.query.result.QueryResultRequestParser
    • org.intermine.webservice.server.template.result.TemplateResultRequestParser
  • org.intermine.web.logic.results.WebState
  • org.intermine.web.logic.WebUtil
  • org.intermine.web.logic.widget.Widget
    • org.intermine.web.logic.widget.EnrichmentWidget
    • org.intermine.web.logic.widget.GraphWidget
    • org.intermine.web.logic.widget.GridWidget
    • org.intermine.web.logic.widget.HTMLWidget
    • org.intermine.web.logic.widget.TableWidget
  • org.intermine.web.logic.widget.config.WidgetConfig
    • org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
    • org.intermine.web.logic.widget.config.GraphWidgetConfig
    • org.intermine.web.logic.widget.config.GridWidgetConfig
    • org.intermine.web.logic.widget.config.HTMLWidgetConfig
    • org.intermine.web.logic.widget.config.TableWidgetConfig
  • org.intermine.webservice.server.widget.WidgetsRequestParser
  • org.intermine.web.logic.widget.WidgetUtil
  • java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
    • org.intermine.sql.logging.DatabaseWriter
    • java.io.PrintWriter
      • org.intermine.web.logic.export.CustomPrintWriter
  • org.intermine.util.XmlBinding
  • org.intermine.xml.XmlHelper
  • org.intermine.util.XmlUtil
  • org.intermine.webservice.server.query.result.XMLValidator
  • org.intermine.webservice.server.query.result.XMLValidatorErrorHandler (implements org.xml.sax.ErrorHandler)

Interface Hierarchy

• org.intermine.sql.writebatch.BatchWriter
• org.jfree.chart.urls.CategoryURLGenerator
  • org.intermine.web.logic.widget.GraphCategoryURLGenerator
• org.intermine.web.logic.Constants
• org.intermine.bio.util.Constants
• org.intermine.objectstore.query.ConstraintTraverseAction
• org.intermine.objectstore.query.ConstraintWithBag
• org.intermine.dataconversion.DataConverterStoreHook
• org.intermine.web.logic.widget.DataSetLdr
• org.intermine.dataloader.EquivalentObjectFetcher
• org.intermine.web.logic.widget.ErrorCorrection
• org.intermine.web.logic.export.Exporter
• org.intermine.model.FastPathObject
  • org.intermine.model.InterMineObject
• org.intermine.web.logic.export.FieldExporter
• org.intermine.sql.writebatch.FlushJob
• org.intermine.objectstore.query.FromElement
• org.intermine.web.logic.widget.GridDataSetLdr
• org.intermine.api.bag.IdUpgrader
• org.intermine.dataconversion.ItemWriter
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • java.util.List<E>
      • org.intermine.api.results.WebTable
    • java.util.Set<E>
      • org.intermine.objectstore.proxy.LazyCollection<E> (also extends org.intermine.objectstore.proxy.Lazy)
• org.intermine.objectstore.proxy.Lazy
  • org.intermine.objectstore.proxy.LazyCollection<E> (also extends java.util.Set<E>)
• org.intermine.util.MappingUtilChecker<T>
• org.intermine.modelproduction.ModelParser
• org.intermine.objectstore.ObjectStore
  • org.intermine.dataloader.IntegrationWriter
  • org.intermine.objectstore.ObjectStoreWriter
    • org.intermine.dataloader.IntegrationWriter
• org.intermine.objectstore.query.Queryable
• org.intermine.web.logic.query.QueryMonitor
• org.intermine.objectstore.query.QueryOrderable
  • org.intermine.objectstore.query.QueryEvaluable
  • org.intermine.objectstore.query.QueryNode (also extends org.intermine.objectstore.query.QuerySelectable)
    • org.intermine.objectstore.query.QueryEvaluable
• org.intermine.objectstore.query.QuerySelectable
  • org.intermine.objectstore.query.QueryEvaluable
  • org.intermine.objectstore.query.QueryNode (also extends org.intermine.objectstore.query.QueryOrderable)
    • org.intermine.objectstore.query.QueryEvaluable
  • org.intermine.objectstore.query.QueryPathExpression
    • org.intermine.objectstore.query.QueryPathExpressionWithSelect
  • org.intermine.objectstore.query.QueryPathExpressionWithSelect
• org.intermine.util.ReferenceMap.ReferenceWithKey<K>
• org.intermine.webservice.client.core.Request
• org.intermine.webservice.server.core.ResultRowParser
• org.intermine.web.logic.export.RowFormatter
• org.intermine.api.search.Scope
• org.intermine.model.ShadowClass
• org.intermine.util.Shutdownable
• org.intermine.sql.query.SQLStringable
• org.intermine.sql.writebatch.Table
• org.intermine.web.logic.export.http.TableHttpExporter
• org.intermine.api.profile.TagChecker
• org.intermine.api.tag.TagNames
• org.intermine.api.tag.TagTypes
• org.intermine.api.search.WebSearchable
• org.intermine.web.logic.widget.WidgetHelper
• org.intermine.web.logic.widget.WidgetURLQuery

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.intermine.webservice.client.core.Request.RequestType
    • org.intermine.web.search.KeywordSearchFacetType
    • org.intermine.pathquery.OuterJoinStatus
    • org.intermine.pathquery.OrderDirection
    • org.intermine.api.template.TemplateValue.ValueType
    • org.intermine.api.template.SwitchOffAbility