Hierarchy For All Packages

Package Hierarchies:

phenote.charactertemplate, phenote.config, phenote.dataadapter, phenote.dataadapter.annotation, phenote.dataadapter.birn, phenote.dataadapter.delimited, phenote.dataadapter.fly, phenote.dataadapter.importer, phenote.dataadapter.ncbi, phenote.dataadapter.nexus, phenote.dataadapter.phenosyntax, phenote.dataadapter.phenoxml, phenote.dataadapter.worm, phenote.datamodel, phenote.edit, phenote.error, phenote.gui, phenote.gui.actions, phenote.gui.factories, phenote.gui.field, phenote.gui.menu, phenote.gui.selection, phenote.jobs, phenote.main, phenote.matrix.model, phenote.matrix.view, phenote.presentation.tags, phenote.servlet, phenote.util

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • phenote.gui.actions.AboutAction
    • phenote.gui.actions.ActionManager.SaveAction
    • phenote.gui.actions.BackAction
    • phenote.gui.actions.CopyAction
    • phenote.gui.actions.DbCommitAction
    • phenote.gui.actions.DuplicateAnnotationAction
    • phenote.gui.actions.ForwardAction
    • phenote.gui.actions.MakeOntolAction
    • phenote.gui.actions.NCBIQueryAction
    • phenote.gui.actions.NewFileAction
    • phenote.gui.actions.OpenFileAction
    • phenote.gui.actions.RedoAction
    • phenote.gui.actions.ResponderChainAction
    • phenote.gui.actions.SaveAsFileAction
    • phenote.gui.actions.SaveFileAction
    • phenote.gui.actions.TermRequestAction
    • phenote.gui.actions.UndoAction
  • javax.swing.AbstractCellEditor (implements javax.swing.CellEditor, java.io.Serializable)
    • javax.swing.DefaultCellEditor (implements javax.swing.table.TableCellEditor, javax.swing.tree.TreeCellEditor)
      • phenote.gui.CorrectLineBorderCellEditor
  • phenote.datamodel.AbstractCharacter (implements phenote.datamodel.CharacterI)
    • phenote.datamodel.AnnotationCharacter
    • phenote.datamodel.Character (implements phenote.datamodel.CharacterI)
  • phenote.dataadapter.AbstractCommitConstraint (implements phenote.dataadapter.Constraint)
    • phenote.dataadapter.RequiredFieldConstraint
    • phenote.dataadapter.worm.WormConstraint
    • phenote.dataadapter.worm.WormInteractionConstraint
  • org.bbop.framework.AbstractComponentFactory<T> (implements org.bbop.framework.GUIComponentFactory<T>)
    • phenote.gui.factories.CharacterTableFactory
      • phenote.gui.factories.ScratchGroupTableFactory
    • phenote.charactertemplate.CharacterTemplateTableFactory
    • org.oboedit.gui.factory.GraphViewFactory
      • phenote.gui.factories.PhenoteGraphViewFactory
    • phenote.matrix.view.MatrixComponentFactory
    • phenote.gui.factories.NCBIInfoFactory
    • phenote.gui.factories.PhenoteEditorFactory
    • phenote.gui.factories.ProtocolEditorFactory
    • phenote.gui.factories.ScratchGroupsViewFactory
    • phenote.charactertemplate.TemplateChooserFactory
    • phenote.gui.factories.TermInfoFactory
    • org.oboedit.gui.factory.TermPanelFactory
      • phenote.gui.factories.PhenoteOntologyTreeEditorFactory
    • org.oboedit.gui.factory.TreeViewFactory
      • phenote.gui.factories.PhenoteTreeViewFactory
  • phenote.dataadapter.AbstractFileAdapter (implements phenote.dataadapter.DataAdapterI)
    • phenote.dataadapter.annotation.AnnotationOBOFileAdapter
    • phenote.dataadapter.annotation.AnnotationOWLFileAdapter
    • phenote.dataadapter.delimited.DelimitedFileAdapter
    • phenote.dataadapter.annotation.GOAssociationFileAdapter
    • phenote.dataadapter.nexus.NEXUSAdapter
    • phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter
    • phenote.dataadapter.phenoxml.PhenoXmlAdapter
  • ca.odell.glazedlists.matchers.AbstractMatcherEditor<E> (implements ca.odell.glazedlists.matchers.MatcherEditor<E>)
    • phenote.gui.field.CharFieldMatcherEditor
  • org.bbop.framework.AbstractSingleActionTask (implements org.bbop.framework.GUITask, java.lang.Runnable)
    • org.bbop.framework.AbstractApplicationStartupTask
      • org.oboedit.gui.tasks.DefaultGUIStartupTask
        • phenote.main.PhenoteStartupTask
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • phenote.gui.OntologyUpdate.OntologyUpdateTableModel
  • phenote.gui.actions.ActionManager
  • phenote.edit.AddTransaction (implements phenote.edit.TransactionI)
  • phenote.servlet.AdminBean
  • phenote.servlet.AdminController (implements org.springframework.web.servlet.mvc.Controller)
  • phenote.main.AnnotationImporterCLI
  • phenote.dataadapter.importer.AnnotationImporterGeneric
  • org.springframework.context.support.ApplicationObjectSupport (implements org.springframework.context.ApplicationContextAware)
    • org.springframework.web.context.support.WebApplicationObjectSupport (implements org.springframework.web.context.ServletContextAware)
      • org.springframework.web.servlet.support.WebContentGenerator
        • org.springframework.web.servlet.mvc.AbstractController (implements org.springframework.web.servlet.mvc.Controller)
          • org.springframework.web.servlet.mvc.BaseCommandController
            • org.springframework.web.servlet.mvc.AbstractCommandController
              • phenote.servlet.PhenoteController
  • phenote.edit.AutoAnnotIdGenerator
  • phenote.datamodel.BasicAnnotationMappingDriver (implements phenote.datamodel.AnnotationMappingDriver)
    • phenote.datamodel.DefaultMappingDriver
      • phenote.datamodel.EnvironmentalSampleAssociationMappingDriver
    • phenote.datamodel.PhenotypeAssociationMappingDriver
  • phenote.gui.field.BigTextPopup
  • phenote.matrix.model.CharacterComparator (implements java.util.Comparator<T>)
  • phenote.datamodel.CharacterIFactory
  • phenote.datamodel.CharacterList (implements phenote.datamodel.CharacterListI)
  • phenote.dataadapter.CharacterListManager
  • phenote.dataadapter.fly.CharacterListTransferable (implements java.awt.datatransfer.Transferable)
  • phenote.gui.CharacterTableController
  • phenote.gui.CharacterTableFormat (implements ca.odell.glazedlists.gui.AdvancedTableFormat<E>, ca.odell.glazedlists.gui.WritableTableFormat<E>)
    • phenote.charactertemplate.CharacterTemplateTableFormat (implements ca.odell.glazedlists.gui.WritableTableFormat<E>)
  • phenote.datamodel.CharField
  • phenote.gui.field.CharFieldGui (implements ca.odell.glazedlists.event.ListEventListener<E>)
    • phenote.gui.field.AbstractAutoCompList
      • phenote.gui.field.RelationCompList
      • phenote.gui.field.TermCompList
    • phenote.gui.field.CharacterListFieldGui
    • phenote.gui.field.FreeTextField
      • phenote.gui.field.IdFieldGui (implements phenote.gui.selection.IDSelectionListener)
      • phenote.gui.field.ReadOnlyFieldGui
    • phenote.gui.field.PickListFieldGui
  • phenote.datamodel.CharFieldManager
  • phenote.gui.field.CharFieldMatcher (implements ca.odell.glazedlists.matchers.Matcher<E>)
  • phenote.datamodel.CharFieldValue (implements java.lang.Cloneable)
  • phenote.util.Collections
  • phenote.main.CommandLine
  • phenote.datamodel.Comparison
  • phenote.gui.ComparisonCharacterGui
  • phenote.gui.ComparisonGui
  • phenote.gui.field.CompletionObject
  • phenote.gui.field.CompletionRelation
  • phenote.gui.field.CompletionTerm
  • phenote.gui.field.CompListSearcher
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.AbstractButton (implements java.awt.ItemSelectable, javax.swing.SwingConstants)
          • javax.swing.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
            • javax.swing.JMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
              • org.bbop.swing.AbstractDynamicMenuItem (implements org.bbop.swing.DynamicMenuItem)
                • org.bbop.swing.DynamicMenu
                  • phenote.gui.menu.EditMenu
                  • phenote.gui.menu.FileMenu
                  • phenote.gui.menu.PhenoteHelpMenu
                  • phenote.gui.menu.SettingsMenu
              • phenote.gui.EditMenu
              • phenote.gui.OldHelpMenu
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • phenote.matrix.view.MatrixTableRenderer
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.bbop.framework.AbstractGUIComponent (implements org.bbop.framework.GUIComponent)
            • phenote.charactertemplate.AbstractTemplateChooser (implements phenote.charactertemplate.TemplateChooser)
              • phenote.charactertemplate.TreeChooser
            • phenote.gui.CharacterTable (implements phenote.gui.CharacterTableSource)
            • phenote.charactertemplate.CharacterTemplateTable (implements phenote.gui.CharacterTableSource, phenote.charactertemplate.TemplateChoiceListener)
            • phenote.gui.field.FieldPanel
            • phenote.gui.field.FieldPanelContainer
            • phenote.matrix.view.MatrixComponent
            • phenote.gui.NcbiInfo
            • phenote.gui.ScratchGroupsView
            • phenote.gui.StandardToolbar
            • phenote.gui.TermInfo2
          • phenote.gui.StackedBox (implements javax.swing.Scrollable)
          • phenote.gui.VerticalScrollingOnlyPanel (implements javax.swing.Scrollable)
        • javax.swing.JPopupMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • phenote.gui.FieldRightClickMenu
          • phenote.gui.TableRightClickMenu
        • javax.swing.JTable (implements javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.Scrollable, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener)
          • phenote.gui.BugWorkaroundTable
        • javax.swing.JToolBar (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • phenote.gui.TermInfoToolbar
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • phenote.gui.GetInfo
            • phenote.config.ProxyDialog (implements java.awt.event.ActionListener)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • phenote.gui.LoadingScreen
            • org.bbop.framework.MainFrame
              • phenote.gui.PhenoteMainFrame
            • phenote.gui.TermRequestGUI
        • javax.swing.JWindow (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer)
          • phenote.gui.SplashScreen
  • phenote.edit.CompoundTransaction (implements phenote.edit.TransactionI)
  • phenote.config.Config
  • phenote.config.ConfigFileQueryGui
  • phenote.gui.ConfigGui
  • phenote.config.ConfigWriter
  • phenote.dataadapter.ConstraintManager
  • phenote.dataadapter.ConstraintStatus
  • phenote.config.DataAdapterConfig
    • phenote.config.QueryableAdapConfig
  • phenote.servlet.DataInputServer
  • phenote.edit.DeleteTransaction (implements phenote.edit.TransactionI)
  • phenote.dataadapter.delimited.DelimFieldParser
  • phenote.dataadapter.delimited.DelimitedChar
  • phenote.edit.DirtyDocumentIndicator (implements phenote.edit.CharChangeListener, phenote.dataadapter.CharListChangeListener, phenote.dataadapter.LoadSaveListener, org.bbop.framework.VetoableShutdownListener)
  • net.infonode.docking.theme.DockingWindowsTheme
    • phenote.gui.PhenoteDockingTheme
  • phenote.edit.EditManager
  • javax.swing.text.EditorKit (implements java.lang.Cloneable, java.io.Serializable)
    • javax.swing.text.DefaultEditorKit
      • javax.swing.text.StyledEditorKit
        • javax.swing.text.html.HTMLEditorKit (implements javax.accessibility.Accessible)
          • phenote.gui.TermInfo2.HTMLEditorKit2
  • phenote.util.Enumerator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  • phenote.error.ErrorManager
  • java.util.EventObject (implements java.io.Serializable)
    • phenote.edit.CharChangeEvent
    • phenote.dataadapter.CharListChangeEvent
    • phenote.gui.selection.CharSelectionEvent
    • phenote.error.ErrorEvent
    • phenote.gui.selection.IDSelectionEvent
    • phenote.gui.selection.TermSelectionEvent
    • phenote.gui.selection.UseTermEvent
  • phenote.util.EverythingEqualComparator<T> (implements java.util.Comparator<T>)
  • phenote.config.FieldConfig
  • phenote.util.FileUtil
  • phenote.dataadapter.fly.FlybaseDataAdapter (implements phenote.dataadapter.DataAdapterI)
  • phenote.dataadapter.fly.FlyCharacter (implements phenote.dataadapter.fly.FlyCharacterI)
  • phenote.dataadapter.fly.FlyCharList
  • phenote.dataadapter.fly.FlyCharListTransferable (implements java.awt.datatransfer.Transferable)
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • phenote.servlet.DataInputServlet
      • org.springframework.web.servlet.HttpServletBean
        • org.springframework.web.servlet.FrameworkServlet
          • org.springframework.web.servlet.DispatcherServlet
            • phenote.servlet.PhenoteServlet
  • phenote.gui.GridBagUtil
  • phenote.gui.GuiUtil
  • phenote.util.HtmlUtil
  • phenote.util.LinkCollection
  • phenote.dataadapter.LoadSaveManager
  • phenote.matrix.model.MatrixController
  • phenote.gui.MenuManager
  • java.awt.event.MouseAdapter (implements java.awt.event.MouseListener)
    • phenote.gui.PopupListener
  • phenote.datamodel.OboUtil
  • java.util.Observable
    • phenote.dataadapter.ScratchGroup
  • phenote.main.OldHelpManager
  • phenote.dataadapter.ncbi.OMIMAdapter (implements phenote.dataadapter.ncbi.NCBIDataAdapterI)
  • phenote.datamodel.Ontology
  • phenote.config.OntologyConfig
  • phenote.dataadapter.OntologyDataAdapter
  • phenote.dataadapter.OntologyDataAdapter2
  • phenote.dataadapter.OntologyMaker (implements phenote.dataadapter.OntologyMakerI)
    • phenote.dataadapter.AbstractGroupAdapter (implements phenote.dataadapter.GroupAdapterI)
      • phenote.dataadapter.AllFieldsGroupAdapter
      • phenote.dataadapter.fly.FlyGenotypeGroupAdapter
      • phenote.dataadapter.worm.WormReferenceGroupAdapter
    • phenote.dataadapter.fly.ProformaAlleleParser
  • phenote.gui.OntologyUpdate
  • phenote.gui.OntologyUpdate.JTableButtonMouseListener (implements java.awt.event.MouseListener)
  • phenote.gui.OntologyUpdate.JTableButtonRenderer (implements javax.swing.table.TableCellRenderer)
  • phenote.gui.OntologyUpdate.JTableProgressBarRenderer (implements javax.swing.table.TableCellRenderer)
  • phenote.dataadapter.phenosyntax.PhenoSyntaxChar
  • phenote.dataadapter.phenosyntax.PhenoSyntaxCharList
  • phenote.main.Phenote
  • phenote.servlet.PhenoteBean
  • phenote.main.PhenotePlus
  • phenote.main.PhenoteVersion
  • phenote.servlet.PhenoteWebConfiguration
  • phenote.datamodel.PhenotypeCharacterWrapper (implements phenote.datamodel.PhenotypeCharacterI)
  • phenote.matrix.model.PhenotypeMatrixCell (implements phenote.matrix.model.MatrixCell)
  • phenote.matrix.model.PhenotypeMatrixColumn (implements phenote.matrix.model.MatrixColumn)
  • phenote.matrix.model.PhenotypeMatrixRow (implements phenote.matrix.model.MatrixRow)
  • phenote.gui.field.PostCompGui
  • phenote.config.Preferences
  • phenote.dataadapter.ncbi.PubMedAdapter (implements phenote.dataadapter.ncbi.NCBIDataAdapterI)
  • org.springframework.scheduling.quartz.QuartzJobBean (implements org.quartz.Job)
    • phenote.jobs.OntologyUpdateJob
  • phenote.dataadapter.ScratchGroupsManager
  • phenote.gui.field.SearchParamPanel
  • phenote.gui.SearchParams (implements phenote.gui.SearchParamsI)
  • phenote.gui.selection.SelectionBridge (implements org.oboedit.gui.event.SelectionListener, phenote.gui.selection.TermSelectionListener)
  • phenote.gui.SelectionHistory
  • phenote.gui.selection.SelectionManager
  • phenote.gui.ShrimpDag
  • phenote.dataadapter.birn.SoapAdapter (implements phenote.dataadapter.QueryableDataAdapterI)
  • phenote.gui.SortDisabler (implements java.awt.event.ActionListener)
  • phenote.gui.SpringUtilities
  • phenote.gui.StackedBox.SeparatorBorder (implements javax.swing.border.Border)
  • phenote.gui.SynchOntologyDialog
  • phenote.gui.TableColumnPrefsSaver (implements java.beans.PropertyChangeListener, javax.swing.event.TableColumnModelListener)
  • javax.servlet.jsp.tagext.TagSupport (implements javax.servlet.jsp.tagext.IterationTag, java.io.Serializable)
    • phenote.presentation.tags.FileUtilTag
    • phenote.presentation.tags.RelationshipTag
  • phenote.gui.TermInfo
  • phenote.gui.TermInfo2.TermInfo2Config (implements org.bbop.framework.ComponentConfiguration)
  • phenote.util.TermLinkComparator (implements java.util.Comparator<T>)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • phenote.datamodel.CharacterEx
      • phenote.datamodel.CharFieldException
      • phenote.gui.field.CharFieldGuiEx
      • phenote.config.ConfigException
      • phenote.config.ConfigFileQueryGui.CancelEx
      • phenote.dataadapter.DataAdapterEx
      • phenote.dataadapter.delimited.DelimitedChar.BadCharException
      • phenote.dataadapter.delimited.DelimitedChar.SyntaxParseException
      • phenote.dataadapter.delimited.DelimitedEx
      • phenote.gui.field.OboException
      • phenote.datamodel.OntologyException
      • phenote.dataadapter.phenosyntax.PhenoSyntaxChar.BadCharException
      • phenote.dataadapter.phenosyntax.PhenoSyntaxChar.SyntaxParseException
      • phenote.gui.SynchOntologyDialog.CancelEx
      • phenote.datamodel.TermNotFoundException
  • phenote.datamodel.TransferableCharacterList (implements java.awt.datatransfer.Transferable)
  • javax.swing.TransferHandler (implements java.io.Serializable)
    • phenote.gui.DelegatingTransferHandler
  • phenote.edit.UpdateTransaction (implements phenote.edit.TransactionI)
  • phenote.datamodel.ValueCharacterList (implements phenote.datamodel.CharacterListI)
  • phenote.dataadapter.worm.WormAdapter (implements phenote.dataadapter.QueryableDataAdapterI)
  • phenote.dataadapter.worm.WormAdapterReference (implements phenote.dataadapter.QueryableDataAdapterI)
  • phenote.dataadapter.worm.WormGoAdapter (implements phenote.dataadapter.QueryableDataAdapterI)
  • phenote.dataadapter.worm.WormInteractionAdapter (implements phenote.dataadapter.QueryableDataAdapterI)
  • phenote.dataadapter.worm.WormTransgeneAdapter (implements phenote.dataadapter.QueryableDataAdapterI)

Interface Hierarchy

• phenote.datamodel.AnnotationMappingDriver
• phenote.datamodel.CharacterListI
• phenote.gui.CharacterTableSource
• phenote.edit.CharChangeListener
• phenote.dataadapter.CharListChangeListener
• phenote.gui.selection.CharSelectionListener
• phenote.dataadapter.Constraint
• phenote.dataadapter.DataAdapterI
• phenote.error.ErrorListener
• java.util.EventListener
  • java.awt.event.ActionListener
    • phenote.charactertemplate.TemplateChooser (also extends org.bbop.framework.GUIComponent)
  • phenote.charactertemplate.TemplateChooser (also extends java.awt.event.ActionListener, org.bbop.framework.GUIComponent)
• phenote.dataadapter.fly.FlyCharacterI
• org.bbop.framework.GUIComponent
  • phenote.charactertemplate.TemplateChooser (also extends java.awt.event.ActionListener)
• phenote.gui.selection.IDSelectionListener
• phenote.dataadapter.LoadSaveListener
• phenote.matrix.model.MatrixCell
• phenote.matrix.model.MatrixColumn
• phenote.matrix.model.MatrixRow
• phenote.dataadapter.ncbi.NCBIDataAdapterI
• phenote.dataadapter.OntologyMakerI
  • phenote.dataadapter.GroupAdapterI
• phenote.datamodel.PhenotypeCharacterI
• phenote.datamodel.PhenotypeCharacterI.PhenotypeCharacterFactory
• phenote.dataadapter.QueryableDataAdapterI
• phenote.gui.field.SearchListener
• phenote.gui.SearchParamsI
• phenote.charactertemplate.TemplateChoiceListener
• phenote.gui.selection.TermSelectionListener
• phenote.edit.TransactionI
• java.awt.datatransfer.Transferable
  • phenote.datamodel.CharacterI
• phenote.gui.selection.UseTermListener

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • phenote.dataadapter.Status
    • phenote.datamodel.RelationshipEnumeration
    • phenote.datamodel.CharFieldEnum
    • phenote.gui.SearchFilterType
    • phenote.gui.field.CharFieldMatcherEditor.Mode
    • phenote.servlet.PhenoteBean.View
    • phenote.util.TermLinkComparator.RelationshipEnum