Hierarchy For All Packages

Package Hierarchies:

apollo.analysis, apollo.analysis.filter, apollo.bop, apollo.config, apollo.dataadapter, apollo.dataadapter.analysis, apollo.dataadapter.chado, apollo.dataadapter.chado.jdbc, apollo.dataadapter.chadoxml, apollo.dataadapter.das, apollo.dataadapter.das.simple, apollo.dataadapter.das2, apollo.dataadapter.debug, apollo.dataadapter.ensj, apollo.dataadapter.ensj.controller, apollo.dataadapter.ensj.model, apollo.dataadapter.ensj.view, apollo.dataadapter.ensj19, apollo.dataadapter.exception, apollo.dataadapter.flychadoxml, apollo.dataadapter.flygamexml, apollo.dataadapter.gamexml, apollo.dataadapter.gbrowse, apollo.dataadapter.genbank, apollo.dataadapter.gff3, apollo.dataadapter.graph, apollo.dataadapter.mysql, apollo.dataadapter.otter, apollo.dataadapter.otter.parser, apollo.dataadapter.sample, apollo.dataadapter.synteny, apollo.dataadapter.synteny.builder, apollo.datamodel, apollo.datamodel.seq, apollo.editor, apollo.external, apollo.gui, apollo.gui.annotinfo, apollo.gui.detailviewers, apollo.gui.detailviewers.blixem, apollo.gui.detailviewers.exonviewer, apollo.gui.detailviewers.seqexport, apollo.gui.detailviewers.sequencealigner, apollo.gui.detailviewers.sequencealigner.AAPanel, apollo.gui.detailviewers.sequencealigner.actions, apollo.gui.detailviewers.sequencealigner.comparators, apollo.gui.detailviewers.sequencealigner.DNAPanel, apollo.gui.detailviewers.sequencealigner.filters, apollo.gui.detailviewers.sequencealigner.listeners, apollo.gui.detailviewers.sequencealigner.menus, apollo.gui.detailviewers.sequencealigner.overview, apollo.gui.detailviewers.sequencealigner.renderers, apollo.gui.drawable, apollo.gui.event, apollo.gui.evidencepanel, apollo.gui.featuretree, apollo.gui.genomemap, apollo.gui.menus, apollo.gui.synteny, apollo.gui.tweeker, apollo.io, apollo.main, apollo.seq, apollo.seq.io, apollo.test, apollo.util, apollo.util.interval

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • apollo.gui.detailviewers.sequencealigner.actions.AddFilterAction
    • apollo.gui.detailviewers.sequencealigner.actions.AddResultFilterAction
    • apollo.gui.detailviewers.sequencealigner.actions.CreateExonAction
    • apollo.gui.detailviewers.sequencealigner.actions.CreateIntronAction
    • apollo.gui.detailviewers.sequencealigner.actions.DeleteExonAction
    • apollo.gui.detailviewers.sequencealigner.actions.DisplaySequenceAction
    • apollo.gui.detailviewers.sequencealigner.actions.FrameShiftAction
    • apollo.gui.detailviewers.sequencealigner.actions.MergeExonAction
    • apollo.gui.detailviewers.sequencealigner.actions.SequenceEditAction
    • apollo.gui.detailviewers.sequencealigner.actions.SetEndAction
    • apollo.gui.detailviewers.sequencealigner.actions.SetTranslationStartAction
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.AbstractSequentialList<E>
        • java.util.LinkedList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.Queue<E>, java.io.Serializable)
          • apollo.gui.detailviewers.sequencealigner.comparators.MultiComparatorArrayList<T> (implements apollo.gui.detailviewers.sequencealigner.comparators.MultiComparator<T>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • apollo.util.FeatureList
          • apollo.gui.Selection
        • apollo.gui.detailviewers.sequencealigner.filters.MultiFilterAnd<T> (implements apollo.gui.detailviewers.sequencealigner.filters.MultiFilter<T>)
        • apollo.gui.detailviewers.sequencealigner.filters.MultiFilterOr<T> (implements apollo.gui.detailviewers.sequencealigner.filters.MultiFilter<T>)
  • org.bdgp.io.AbstractDataAdapter (implements org.bdgp.io.VisualDataAdapter)
    • apollo.dataadapter.AbstractApolloAdapter (implements apollo.dataadapter.ApolloDataAdapterI)
      • apollo.dataadapter.analysis.AnalysisAdapter
      • apollo.dataadapter.BaseGFFAdapter
        • apollo.dataadapter.GFFAdapter
          • apollo.dataadapter.SyntenyGFFAdapter (implements apollo.dataadapter.ApolloDataAdapterI)
      • apollo.dataadapter.synteny.builder.BuilderAdapter
      • apollo.dataadapter.chado.ChadoAdapter
      • apollo.dataadapter.chadoxml.ChadoXmlAdapter
        • apollo.dataadapter.flychadoxml.FlyChadoXmlAdapter
      • apollo.dataadapter.das2.DAS2Adapter
      • apollo.dataadapter.DummySequenceAdapter
      • apollo.dataadapter.EfetchSequenceAdapter
      • apollo.dataadapter.EnsCGIAdapter
      • apollo.dataadapter.ensj.EnsJAdapter
      • apollo.dataadapter.ensj19.EnsJAdapter
        • apollo.dataadapter.ensj19.AnnotationEnsJAdapter
      • apollo.dataadapter.gamexml.GAMEAdapter
        • apollo.dataadapter.flygamexml.FlyGAMEAdapter
      • apollo.dataadapter.GbrowseAdapter
      • apollo.dataadapter.genbank.GenbankAdapter
      • apollo.dataadapter.gff3.GFF3Adapter
      • apollo.dataadapter.graph.GraphAdapter
      • apollo.dataadapter.otter.OtterAdapter
      • apollo.dataadapter.otter.OtterXMLAdapter
      • apollo.dataadapter.sample.SampleAdapter
      • apollo.dataadapter.SerialDiskAdapter
      • apollo.dataadapter.das.simple.SimpleDASAdapter
      • apollo.dataadapter.synteny.SyntenyAdapter
      • apollo.dataadapter.synteny.SyntenyComparaAdapter
    • apollo.analysis.SeqAnalysisBase (implements apollo.analysis.AnalysisDataAdapterI, apollo.analysis.SeqAnalysisI)
      • apollo.analysis.SeqAnalysisLocal
      • apollo.analysis.SeqAnalysisRemote
        • apollo.analysis.SeqAnalysisBDGP
        • apollo.analysis.SeqAnalysisNCBI
  • apollo.datamodel.seq.AbstractLazySequence.LazyLoadControlledObject
  • apollo.dataadapter.analysis.AbstractParser (implements apollo.dataadapter.analysis.AnalysisParserI)
    • apollo.dataadapter.analysis.AlignmentParser
      • apollo.dataadapter.analysis.BlastParser
      • apollo.dataadapter.analysis.BlatParser
      • apollo.dataadapter.analysis.Sim4Parser
    • apollo.dataadapter.analysis.GeneFinderParser
      • apollo.dataadapter.analysis.FgeneshGFFParser
      • apollo.dataadapter.analysis.FgeneshParser
      • apollo.dataadapter.analysis.GenieParser
      • apollo.dataadapter.analysis.GenscanParser
    • apollo.dataadapter.analysis.RpMaskerParser
    • apollo.dataadapter.analysis.tRNA_Parser
  • apollo.datamodel.AbstractSequence (implements apollo.datamodel.SequenceI)
    • apollo.datamodel.seq.AbstractLazySequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.dataadapter.ensj.AlternateEnsJSequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.dataadapter.ensj19.AlternateEnsJSequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.dataadapter.das.DASLazySequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.datamodel.seq.DebugLazySequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.datamodel.seq.EnsCGISequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.dataadapter.ensj19.EnsJSequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.datamodel.seq.GAMESequence
      • apollo.datamodel.seq.PFetchSequence (implements apollo.datamodel.seq.LazySequenceI)
      • apollo.datamodel.seq.SRSSequence (implements apollo.datamodel.seq.LazySequenceI)
    • apollo.datamodel.Sequence (implements apollo.datamodel.SequenceI)
      • apollo.datamodel.seq.GenbankSequence
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel (implements java.util.List<E>)
    • apollo.gui.SeqSelectorTable.SequenceMatchModel
    • apollo.gui.evidencepanel.TablePanel.FilteredFeatureModel
  • apollo.dataadapter.synteny.builder.AdapterModel
  • apollo.dataadapter.synteny.AlignBlockChooser.OKButtonListener (implements java.awt.event.ActionListener)
  • apollo.analysis.filter.AnalysisFilter (implements apollo.analysis.filter.AnalysisFilterI)
  • apollo.analysis.filter.AnalysisInput
  • apollo.dataadapter.analysis.AnalysisPanel.displayTierItemListener (implements java.awt.event.ItemListener)
  • apollo.dataadapter.analysis.AnalysisPanel.fileItemListener (implements java.awt.event.ItemListener)
  • apollo.editor.AnnotationChangeLog (implements apollo.editor.AnnotationChangeListener, java.io.Serializable)
  • apollo.editor.AnnotationEditor (implements apollo.gui.ControlledObjectI, apollo.gui.drawable.DrawableAnnotationConstants)
  • apollo.editor.AnnotationEditor.FeatChangeData
  • apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI.ShowTypesActionListener (implements java.awt.event.ActionListener)
  • apollo.gui.detailviewers.sequencealigner.AnnotationFeatureComparator (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.listeners.AnnotationHeaderMouseListener (implements java.awt.event.MouseListener)
  • apollo.dataadapter.ensj.model.AnnotationsModel
  • apollo.dataadapter.ensj19.AnnotationSourceChooser.FindDataSetsListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.AnnotationSourceChooser.RemoveDatasetsListenerForServer (implements java.awt.event.ItemListener)
  • apollo.main.Apollo
  • apollo.external.ApolloControlServer
  • apollo.gui.ApolloJalviewEventBridge (implements jalview.gui.event.AlignViewportListener, apollo.editor.AnnotationChangeListener, apollo.gui.event.BaseFocusListener, jalview.gui.event.ColumnSelectionListener, apollo.dataadapter.DataLoadListener, apollo.gui.event.FeatureSelectionListener, apollo.gui.event.NamedFeatureSelectionListener, apollo.editor.ResultChangeListener, jalview.gui.event.SequenceSelectionListener)
  • apollo.test.ApolloLaundry (implements apollo.gui.ApolloLoaderI)
  • apollo.gui.ApolloRunner
  • apollo.gui.ArrayListTransferHandler.ArrayListTransferable (implements java.awt.datatransfer.Transferable)
  • junit.framework.Assert
    • junit.framework.TestCase (implements junit.framework.Test)
      • apollo.dataadapter.gff3.AllTests
      • apollo.util.AllTests
      • apollo.test.ApolloTest
        • apollo.test.TestJDBCTransactions
        • apollo.test.TestTransactions
      • apollo.analysis.BlastXMLParserTest
      • apollo.util.FileUtilTest
      • apollo.gui.GenericFileFilterTest
      • apollo.dataadapter.gff3.GFF3AdapterTest
      • apollo.dataadapter.gff3.GFF3EntryTest
      • apollo.util.OBOParserTest
      • apollo.util.PairTest
      • apollo.analysis.PrimerBlastHtmlParserTest
      • apollo.analysis.RemoteBlastNCBITest
      • apollo.analysis.RemotePrimerBlastNCBITest
      • apollo.analysis.SeqAnalysisTest
      • apollo.test.TestApollo
  • apollo.dataadapter.mysql.BaseAdaptor
    • apollo.dataadapter.gbrowse.AnalysisAdaptor
    • apollo.dataadapter.gbrowse.DBAdaptor
    • apollo.dataadapter.gbrowse.FeatureAdaptor
  • apollo.gui.detailviewers.sequencealigner.filters.BaseFilter<T> (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.gui.detailviewers.sequencealigner.BaseRendererFactory
  • apollo.analysis.BlastXMLParser
  • apollo.gui.detailviewers.blixem.BlixemRunner
  • apollo.bop.bop
  • java.awt.BorderLayout (implements java.awt.LayoutManager2, java.io.Serializable)
    • apollo.gui.genomemap.ApolloLayoutManager
      • apollo.gui.genomemap.ColumnApolloLayout
  • apollo.dataadapter.synteny.builder.BuilderAdapterGUI.ModelChangeListener (implements java.awt.event.ActionListener)
  • apollo.datamodel.seq.CacheSequenceLoader
    • apollo.datamodel.seq.CacheSeqIdLoader
  • apollo.datamodel.seq.CacheSequenceLoader.SequenceRange (implements org.bdgp.util.Range)
  • apollo.util.CaseInsensitiveStringHash (implements java.io.Serializable)
  • apollo.dataadapter.CGI (implements java.lang.Runnable)
  • apollo.dataadapter.chado.ChadoAdHocFlatFileWriter
  • apollo.dataadapter.chado.ChadoDatabase
  • apollo.config.ChadoJdbcNameAdapter (implements apollo.config.ApolloNameAdapterI)
  • apollo.dataadapter.chado.jdbc.ChadoProgram
  • apollo.dataadapter.chado.ChadoTransaction
    • apollo.dataadapter.chado.ChadoUpdateTransaction
  • apollo.dataadapter.chado.ChadoTransaction.Operation
  • apollo.dataadapter.chado.ChadoTransactionTransformer (implements apollo.dataadapter.TransactionTransformer)
  • apollo.dataadapter.chadoxml.ChadoTransactionXMLTemplate
  • apollo.dataadapter.chadoxml.ChadoXmlUtils
  • apollo.dataadapter.chadoxml.ChadoXmlWrite
  • apollo.editor.ChangeList (implements apollo.gui.ControlledObjectI)
  • apollo.datamodel.Chromosome
  • apollo.dataadapter.ChromosomeAdapter
  • apollo.datamodel.ChromosomeBand
  • apollo.dataadapter.synteny.ChromosomeDrawer
  • apollo.gui.ChromosomeField
  • apollo.util.CigarUtil
  • apollo.util.ClipboardUtil
  • apollo.util.CollectionUtil
  • apollo.config.ColumnProperty (implements java.lang.Cloneable, java.io.Serializable)
  • apollo.main.CommandLine
  • apollo.datamodel.Comment (implements java.lang.Cloneable, java.io.Serializable)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorBase<T> (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorFactory
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorReverse<T> (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureDisplayType (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureFrame (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureLength (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureName (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorSeqFeatureScore (implements java.util.Comparator<T>)
  • 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.JButton (implements javax.accessibility.Accessible)
            • apollo.gui.genomemap.StrandedZoomableApolloPanel.ShiftAwareButton
            • apollo.gui.evidencepanel.TablePanel.TypeCellRenderer (implements javax.swing.table.TableCellRenderer)
          • javax.swing.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
            • javax.swing.JMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
              • apollo.gui.menus.AnalysisMenu (implements java.awt.event.ActionListener, apollo.gui.drawable.DrawableAnnotationConstants)
              • apollo.gui.menus.BookmarkMenu
              • apollo.gui.menus.EditMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.FileMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.HelpMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.LinksMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.PeptideMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.ShowMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.SyntenyChoiceMenu
              • apollo.gui.menus.SyntenyViewMenu (implements java.awt.event.ActionListener, apollo.gui.drawable.DrawableAnnotationConstants)
              • apollo.gui.menus.TiersMenu (implements java.awt.event.ActionListener, apollo.gui.drawable.DrawableAnnotationConstants)
              • apollo.gui.menus.TranscriptMenu
              • apollo.gui.menus.TypesMenu (implements java.awt.event.ActionListener)
              • apollo.gui.menus.ViewMenu (implements java.awt.event.ActionListener, apollo.gui.drawable.DrawableAnnotationConstants)
              • apollo.gui.menus.WindowMenu
          • javax.swing.JToggleButton (implements javax.accessibility.Accessible)
            • javax.swing.JCheckBox (implements javax.accessibility.Accessible)
              • apollo.dataadapter.ensj19.EnsJAdapterGUI.DataTypeButton
        • apollo.gui.detailviewers.sequencealigner.BaseFineEditorHorizontalColHeader
        • apollo.gui.detailviewers.exonviewer.BaseFineEditorRowHeader
        • apollo.gui.detailviewers.sequencealigner.BaseFineEditorRowHeader
        • apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer (implements apollo.gui.detailviewers.exonviewer.BaseRenderer)
          • apollo.gui.detailviewers.exonviewer.AminoAcidRenderer
          • apollo.gui.detailviewers.exonviewer.SelectableDNARenderer
        • apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer (implements apollo.gui.detailviewers.sequencealigner.renderers.BaseRenderer)
          • apollo.gui.detailviewers.sequencealigner.AminoAcidRendererOLD
          • apollo.gui.detailviewers.sequencealigner.ResultRenderer
          • apollo.gui.detailviewers.sequencealigner.SelectableDNARenderer
        • apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent
        • javax.swing.JComboBox (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
          • apollo.dataadapter.ensj.view.UpdateWorkRoundComboBox
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • apollo.gui.evidencepanel.TablePanel.CellRenderer
        • javax.swing.JOptionPane (implements javax.accessibility.Accessible)
          • apollo.gui.detailviewers.sequencealigner.menus.AddFilterPanel
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.bdgp.swing.AbstractDataAdapterUI (implements org.bdgp.io.DataAdapterUI)
            • org.bdgp.swing.AbstractIntDataAdapUI (implements org.bdgp.io.InteractiveDataAdapterUI)
              • apollo.dataadapter.analysis.AnalysisAdapterGUI
            • apollo.dataadapter.synteny.builder.BuilderAdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
            • apollo.dataadapter.chado.ChadoAdapterGUI (implements java.awt.event.ActionListener, java.awt.event.ItemListener)
            • apollo.dataadapter.EnsCGIAdapterGUI
            • apollo.dataadapter.ensj.EnsJAdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
            • apollo.dataadapter.ensj19.EnsJAdapterGUI
              • apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
            • apollo.dataadapter.flychadoxml.FlyChadoXmlAdapterGUI
            • apollo.dataadapter.flygamexml.FlyGAMEAdapterGUI
            • apollo.dataadapter.GbrowseAdapterGUI
            • apollo.gui.GenericFileAdapterGUI
              • apollo.dataadapter.chadoxml.ChadoXmlAdapterGUI
              • apollo.dataadapter.das2.DAS2AdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
              • apollo.dataadapter.gamexml.GAMEAdapterGUI
              • apollo.dataadapter.genbank.GenbankAdapterGUI
              • apollo.dataadapter.gff3.GFF3AdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
              • apollo.dataadapter.GFFAdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
              • apollo.dataadapter.graph.GraphAdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
              • apollo.dataadapter.otter.OtterXMLAdapterGUI
              • apollo.dataadapter.SerialAdapterGUI
            • apollo.dataadapter.otter.OtterAdapterGUI
            • apollo.dataadapter.sample.SampleAdapterGUI
            • apollo.dataadapter.das.simple.SimpleDASAdapterGUI (implements apollo.dataadapter.ApolloDataAdapterGUI)
            • apollo.dataadapter.synteny.SyntenyAdapterGUI
            • apollo.dataadapter.synteny.SyntenyComparaAdapterGUI
          • apollo.gui.detailviewers.sequencealigner.AbstractScrollablePanel (implements apollo.gui.BaseScrollable, javax.swing.Scrollable)
            • apollo.gui.detailviewers.sequencealigner.TierPanelAddressHeader
          • apollo.gui.detailviewers.sequencealigner.AbstractTierPanel (implements apollo.gui.detailviewers.sequencealigner.TierPanelI)
            • apollo.gui.detailviewers.sequencealigner.TierPanel
          • apollo.dataadapter.analysis.AnalysisPanel
          • apollo.dataadapter.ensj19.AnnotationSourceChooser
            • apollo.dataadapter.ensj19.OtterAnnotationSourceChooser
          • apollo.dataadapter.ensj.view.AnnotationsPanel (implements java.awt.event.ActionListener)
          • apollo.gui.genomemap.ApolloPanel (implements apollo.gui.genomemap.ApolloPanelI, apollo.gui.event.BaseFocusListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener, apollo.gui.event.FeatureSelectionListener, java.awt.event.KeyListener, javax.swing.event.MouseInputListener, java.awt.event.MouseWheelListener, apollo.gui.event.RubberbandListener, apollo.gui.event.ViewListener)
          • apollo.dataadapter.synteny.ChromosomePanel (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
          • apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel
          • apollo.gui.ControlledPanel
            • apollo.gui.FindPanel (implements java.awt.event.ActionListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener)
            • apollo.gui.genomemap.NavigationBar (implements java.awt.event.ActionListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener)
            • apollo.gui.SeqMatchPanel (implements apollo.gui.ControlledObjectI)
            • apollo.gui.genomemap.StrandedZoomableApolloPanel (implements java.awt.event.ActionListener, java.awt.event.AdjustmentListener, apollo.gui.genomemap.ApolloPanelHolderI, apollo.gui.event.BaseFocusListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener, apollo.gui.drawable.DrawableAnnotationConstants, apollo.gui.event.NamedFeatureSelectionListener, apollo.gui.event.OrientationListener, apollo.gui.event.ReverseComplementListener, apollo.gui.event.RubberbandListener, apollo.gui.event.ScrollListener, apollo.gui.event.SetActiveCurStateListener, apollo.gui.event.ZoomListener)
            • apollo.gui.evidencepanel.TablePanel
              • apollo.gui.evidencepanel.EvidencePanel
              • apollo.gui.evidencepanel.SetDetailPanel
            • apollo.gui.TypePanel (implements java.awt.event.ActionListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener, apollo.gui.event.FeatureSelectionListener, apollo.config.PropSchemeChangeListener)
          • apollo.dataadapter.ensj.view.DatabasePanel
          • apollo.dataadapter.ensj19.DataSourceConfigurationPanel
          • apollo.gui.evidencepanel.EvidencePanelContainer
          • apollo.gui.annotinfo.FeatureEditPanel
            • apollo.gui.annotinfo.GeneEditPanel
          • apollo.gui.FeaturePropertyPanel
          • apollo.analysis.filter.FilterPanel (implements apollo.analysis.filter.FilterPanelI)
            • apollo.analysis.filter.BlastFilterPanel
            • apollo.analysis.filter.GenscanFilterPanel
            • apollo.analysis.filter.NoFilterPanel
            • apollo.analysis.filter.Sim4FilterPanel
          • apollo.dataadapter.synteny.FullEnsJDBCSyntenyPanel
          • apollo.gui.FullSyntenyPanel (implements java.awt.event.ActionListener)
          • apollo.gui.GlyphChooser (implements java.awt.event.ActionListener)
          • apollo.dataadapter.GuiTabPanel
            • apollo.dataadapter.FileTabPanel
            • apollo.dataadapter.flygamexml.GAMEPanel
              • apollo.dataadapter.flychadoxml.LoaderPanel
                • apollo.dataadapter.flychadoxml.LocationChadoPanel
              • apollo.dataadapter.flygamexml.LocationGAMEPanel
          • apollo.dataadapter.ensj.view.LocationPanel
          • apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerPanel (implements apollo.editor.AnnotationChangeListener, apollo.gui.BaseScrollable, apollo.gui.ControlledObjectI, apollo.gui.event.FeatureSelectionListener, java.beans.PropertyChangeListener)
            • apollo.gui.detailviewers.sequencealigner.AAPanel.AAMultiSequenceAlignerPanel
            • apollo.gui.detailviewers.sequencealigner.DNAPanel.DNAMultiSequenceAlignerPanel
          • apollo.gui.detailviewers.sequencealigner.MultiTierPanel (implements apollo.gui.BaseScrollable, javax.swing.Scrollable)
            • apollo.gui.detailviewers.sequencealigner.DNAPanel.HomogeneousPanel
            • apollo.gui.detailviewers.sequencealigner.AAPanel.ReferencePanel
            • apollo.gui.detailviewers.sequencealigner.DNAPanel.ReferencePanel
          • apollo.dataadapter.ensj.view.OptionsPanel
          • apollo.gui.PrefsPanel
          • apollo.gui.PropertyPanel (implements java.awt.event.ActionListener, javax.swing.event.MouseInputListener)
          • apollo.gui.detailviewers.exonviewer.SeqAlignPanel (implements apollo.gui.BaseScrollable, javax.swing.Scrollable)
            • apollo.gui.detailviewers.exonviewer.BaseEditorPanel
          • apollo.gui.detailviewers.sequencealigner.SeqAlignPanel (implements apollo.gui.BaseScrollable, javax.swing.Scrollable)
            • apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
          • apollo.gui.detailviewers.exonviewer.SeqAlignPanel.DefaultRowHeader
          • apollo.analysis.SeqAnalysisGUI (implements org.bdgp.io.DataAdapterUI)
          • apollo.gui.SliderWindow (implements javax.swing.event.ChangeListener)
          • apollo.dataadapter.ensj19.SourceChooserWithHistory
          • apollo.gui.StatusBar
          • apollo.gui.StatusPane
          • apollo.gui.StyleWizard
          • apollo.gui.synteny.SyntenyLinkPanel (implements apollo.gui.event.BaseFocusListener, apollo.gui.event.ChainedRepaintListener, apollo.gui.event.FeatureSelectionListener, java.awt.event.MouseMotionListener, apollo.config.PropSchemeChangeListener, apollo.gui.event.RubberbandListener, apollo.gui.event.ScrollListener, apollo.gui.event.ZoomListener)
          • apollo.gui.synteny.SyntenyPanel (implements apollo.gui.event.ReverseComplementListener)
          • apollo.gui.TableColumnChooser (implements java.awt.event.ActionListener)
          • apollo.dataadapter.ensj.view.TypesPanel
          • apollo.gui.TypesWizard
          • apollo.dataadapter.ensj.view.View
          • apollo.dataadapter.synteny.builder.View
        • javax.swing.JPopupMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • apollo.gui.menus.AnnotationMenu (implements java.awt.event.ActionListener, apollo.gui.drawable.DrawableAnnotationConstants)
          • apollo.gui.detailviewers.sequencealigner.AnnotationRighClickMenu
          • apollo.gui.menus.GraphMenu (implements java.awt.event.ActionListener)
          • apollo.gui.menus.PropertyMenu (implements java.awt.event.ActionListener)
          • apollo.gui.detailviewers.sequencealigner.ResultRightClickMenu
          • apollo.gui.menus.ScaleMenu
          • apollo.gui.menus.SyntenyLinkMenu (implements java.awt.event.ActionListener)
          • apollo.dataadapter.synteny.SyntenyMenu (implements java.awt.event.ActionListener)
          • apollo.gui.menus.ThresholdMenu (implements java.awt.event.ActionListener)
          • apollo.gui.menus.TierPopupMenu (implements java.awt.event.ActionListener)
          • apollo.gui.menus.TreeMenu (implements java.awt.event.ActionListener)
        • javax.swing.JScrollBar (implements javax.accessibility.Accessible, java.awt.Adjustable)
          • apollo.gui.ApolloScrollBar
        • javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          • apollo.gui.featuretree.FeatureTreePanel (implements java.awt.event.MouseListener)
        • javax.swing.JSplitPane (implements javax.accessibility.Accessible)
          • apollo.gui.UnBorderedSplitPane
        • 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)
          • apollo.gui.detailviewers.sequencealigner.MultiTierPanelHeaderTable
        • apollo.gui.detailviewers.sequencealigner.overview.Overview
        • apollo.gui.detailviewers.sequencealigner.ReferenceTierPanelHeader
        • apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer (implements apollo.gui.detailviewers.sequencealigner.renderers.BaseRendererI)
          • apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidBaseRenderer
          • apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRenderer
          • apollo.gui.detailviewers.sequencealigner.renderers.AminoAcidRendererSpaced
          • apollo.gui.detailviewers.sequencealigner.renderers.AnnotationRenderer (implements apollo.gui.detailviewers.sequencealigner.RegionSelectableI)
          • apollo.gui.detailviewers.sequencealigner.renderers.DNAResultRenderer
        • apollo.gui.detailviewers.sequencealigner.overview.TranscriptOverview
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • apollo.dataadapter.synteny.AlignBlockChooser
            • apollo.dataadapter.ensj19.DriverDialog (implements java.awt.event.ActionListener)
            • apollo.gui.detailviewers.sequencealigner.FindDialog
            • apollo.gui.detailviewers.sequencealigner.GoToDialog
            • apollo.gui.detailviewers.sequencealigner.menus.InsertionDialog
            • apollo.gui.ProxyDialog (implements java.awt.event.ActionListener)
            • apollo.dataadapter.URLDiagnosticTool
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • apollo.analysis.AnalysisGUI
            • apollo.gui.ApolloFrame (implements apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener, apollo.gui.event.LazyLoadListener)
              • apollo.gui.synteny.CompositeApolloFrame
            • apollo.gui.detailviewers.exonviewer.BaseFineEditor (implements apollo.editor.AnnotationChangeListener, apollo.gui.ControlledObjectI, apollo.gui.event.FeatureSelectionListener)
            • apollo.gui.detailviewers.sequencealigner.BaseFineEditor (implements apollo.editor.AnnotationChangeListener, apollo.gui.ControlledObjectI, apollo.gui.event.FeatureSelectionListener)
            • apollo.gui.annotinfo.FeatureEditorDialog (implements apollo.editor.AnnotationChangeListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener, apollo.gui.FeatureNavigationI, apollo.gui.event.FeatureSelectionListener)
            • apollo.gui.featuretree.FeatureTreeFrame (implements apollo.editor.AnnotationChangeListener, apollo.gui.event.BaseFocusListener, apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener, apollo.gui.FeatureNavigationI, apollo.gui.event.FeatureSelectionListener)
            • apollo.gui.detailviewers.sequencealigner.MultiSequenceAlignerFrame
            • apollo.gui.PreferencesDialog (implements apollo.gui.ControlledObjectI, apollo.dataadapter.DataLoadListener)
            • apollo.gui.PreferenceWindow
            • apollo.gui.ProgressFrame
            • apollo.gui.detailviewers.seqexport.SeqExport (implements apollo.dataadapter.DataLoadListener)
            • apollo.gui.tweeker.Tweeker (implements java.awt.event.ActionListener)
  • javax.swing.plaf.ComponentUI
    • javax.swing.plaf.ScrollBarUI
      • javax.swing.plaf.basic.BasicScrollBarUI (implements java.awt.LayoutManager, javax.swing.SwingConstants)
        • javax.swing.plaf.metal.MetalScrollBarUI
          • apollo.gui.ApolloMetalScrollBarUI
  • apollo.gui.synteny.CompositeApolloFrame.MacApplicationSupport (implements org.simplericity.macify.eawt.ApplicationListener)
  • apollo.datamodel.CompositeDataHolder (implements apollo.datamodel.ApolloDataI)
  • apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.ChooserActionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.CompositeDataSourceConfigurationPanel.DatabaseFindListener (implements java.awt.event.ActionListener)
  • apollo.analysis.filter.Compress
  • apollo.config.Config
  • apollo.dataadapter.ensj.controller.Controller
  • apollo.dataadapter.synteny.builder.Controller
  • apollo.gui.Controller (implements apollo.editor.AnnotationChangeListener, apollo.gui.event.BaseFocusListener, apollo.dataadapter.DataLoadListener, apollo.gui.event.FeatureSelectionListener, apollo.gui.event.LazyLoadListener, apollo.gui.event.NamedFeatureSelectionListener, apollo.gui.event.OrientationListener, apollo.config.PropSchemeChangeListener, apollo.editor.ResultChangeListener, apollo.gui.event.ReverseComplementListener, apollo.gui.event.ScrollListener, apollo.gui.event.SetActiveCurStateListener, java.awt.event.WindowListener, apollo.gui.event.ZoomListener)
    • apollo.gui.MultiController
  • apollo.analysis.filter.Coverage
  • apollo.gui.synteny.CurationManager
  • apollo.dataadapter.CurationState
  • apollo.dataadapter.das2.DAS2AdapterGUI.DSNListener (implements java.awt.event.ItemListener)
  • apollo.dataadapter.das2.DAS2AdapterGUI.HistoryListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.das2.DAS2AdapterGUI.ProxyListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.das2.DAS2AdapterGUI.ServerListener (implements java.awt.event.ItemListener)
  • apollo.dataadapter.das2.DAS2Request (implements apollo.dataadapter.das.DASServerI)
  • apollo.dataadapter.das2.DAS2Writer
  • apollo.dataadapter.mysql.Database
    • apollo.dataadapter.mysql.MySQLDatabase
  • apollo.dataadapter.ensj.model.DatabaseModel
  • apollo.dataadapter.ensj.DataFetcher
  • apollo.dataadapter.DataInput
  • apollo.dataadapter.DataInputType
  • apollo.main.DataLoader
  • apollo.dataadapter.ensj.DataModelConversionUtil
  • apollo.dataadapter.ensj19.DataSourceConfigurationPanel.EnsemblDBSelectionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.DataSourceConfigurationPanel.HostListener (implements java.awt.event.ActionListener)
  • apollo.datamodel.seq.DataUtil
  • apollo.util.DateUtil
  • apollo.datamodel.DbXref (implements java.io.Serializable)
  • apollo.config.DefaultDisplayPrefs (implements apollo.config.DisplayPrefsI)
    • apollo.config.EnsjDisplayPrefs
    • apollo.config.FlyDisplayPrefs
    • apollo.config.ParameciumDisplayPrefs
    • apollo.config.TigrAnnotDisplayPrefs
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • apollo.dataadapter.das2.DAS2FeatureSaxParser
    • apollo.dataadapter.das.simple.DASDsnContentHandler
    • apollo.dataadapter.das.simple.DASEntryPointContentHandler
    • apollo.dataadapter.das.simple.DASFeatureContentHandler
    • apollo.dataadapter.das.simple.DASSequenceContentHandler
    • apollo.dataadapter.otter.parser.OtterContentHandler
    • apollo.dataadapter.das2.SegmentParser
    • apollo.dataadapter.das2.SourceParser
  • apollo.config.DefaultNameAdapter (implements apollo.config.ApolloNameAdapterI)
    • apollo.config.GmodNameAdapter
      • apollo.config.FlyNameAdapter
      • apollo.config.RiceNameAdapter
    • apollo.config.SimpleNameAdapter
    • apollo.config.TigrSybilNameAdapter
  • apollo.gui.DetailInfo
  • 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
        • apollo.dataadapter.StateInformation
  • apollo.gui.DisabledEditor (implements javax.swing.table.TableCellEditor)
  • apollo.dataadapter.debug.DisplayTool
  • apollo.gui.drawable.DrawableDisplayTool
  • apollo.gui.drawable.DrawableSeqFeature (implements apollo.gui.drawable.Drawable, apollo.gui.SelectableI)
    • apollo.gui.drawable.DoubleHeadedArrow
    • apollo.gui.drawable.DrawableFeatureSet (implements apollo.gui.drawable.DrawableSetI)
      • apollo.gui.drawable.DrawableEnsemblFeatureSet (implements apollo.gui.drawable.DrawableSetI)
      • apollo.gui.drawable.DrawableGeneFeatureSet (implements apollo.gui.drawable.DrawableSetI)
        • apollo.gui.drawable.DrawablePhaseHighlightGeneFeatureSet (implements apollo.gui.drawable.DrawableSetI)
          • apollo.gui.drawable.DrawablePhaseHighlightNoHatGeneFeatureSet (implements apollo.gui.drawable.DrawableSetI)
      • apollo.gui.drawable.DrawablePrimerSet
      • apollo.gui.drawable.DrawableResultFeatureSet
    • apollo.gui.drawable.DrawableGeneSeqFeature (implements apollo.gui.drawable.Drawable, apollo.gui.SelectableI)
      • apollo.gui.drawable.DrawablePhaseHighlightGeneSeqFeature (implements apollo.gui.drawable.Drawable, apollo.gui.SelectableI)
    • apollo.gui.drawable.DrawableHalfArrow (implements apollo.gui.drawable.Drawable)
    • apollo.gui.drawable.DrawableResultSeqFeature (implements apollo.gui.drawable.Drawable, apollo.gui.SelectableI)
    • apollo.gui.drawable.PromoterGlyph
    • apollo.gui.drawable.SiteCodon
    • apollo.gui.drawable.ThinRectangle
    • apollo.gui.drawable.Triangle
    • apollo.gui.drawable.Zigzag
  • apollo.gui.drawable.DrawableUtil
  • apollo.dataadapter.EnsCGIAdapterGUI.ChrStartEndListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj19.EnsJAdapterGUI.ChromosomeDropdownPopupListener (implements javax.swing.event.PopupMenuListener)
  • apollo.dataadapter.ensj19.EnsJAdapterGUI.DataSourceChangeListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj.EnsJAdapterUtil
  • apollo.dataadapter.ensj.EnsJConnectionUtil
  • apollo.dataadapter.ensj.controller.EventHandler
    • apollo.dataadapter.ensj.controller.ChangeDatabaseHandler
    • apollo.dataadapter.ensj.controller.ClearSeqRegionsHandler
    • apollo.dataadapter.ensj.controller.FindCoordSystemsHandler
    • apollo.dataadapter.ensj.controller.FindEnsemblDatabaseNamesHandler
    • apollo.dataadapter.ensj.controller.FindSeqRegionsHandler
    • apollo.dataadapter.ensj.controller.HideShowAnnotationsHandler
    • apollo.dataadapter.ensj.controller.HideShowDatabasesHandler
    • apollo.dataadapter.ensj.controller.HideShowLocationsHandler
    • apollo.dataadapter.ensj.controller.HideShowOptionsHandler
    • apollo.dataadapter.ensj.controller.HideShowTypesHandler
    • apollo.dataadapter.ensj.controller.LoadSeqRegionByHistoryHandler
    • apollo.dataadapter.ensj.controller.ReadHandler
    • apollo.dataadapter.ensj.controller.SelectNewEnsemblDatabaseHandler
    • apollo.dataadapter.ensj.controller.SelectSeqRegionHandler
    • apollo.dataadapter.ensj.controller.ShowAbInitioCountsByTypeHandler
    • apollo.dataadapter.ensj.controller.ShowDitagFeatureCountsByTypeHandler
    • apollo.dataadapter.ensj.controller.ShowDnaDnaAlignCountsByTypeHandler
    • apollo.dataadapter.ensj.controller.ShowDnaProteinAlignCountsByTypeHandler
    • apollo.dataadapter.ensj.controller.ShowGeneCountsByTypeHandler
    • apollo.dataadapter.ensj.controller.ShowSimpleFeatureCountsByTypeHandler
    • apollo.dataadapter.ensj.controller.UpdateHandler
    • apollo.dataadapter.ensj.controller.UseSeqRegionLocationHandler
    • apollo.dataadapter.ensj.controller.UseStableIDLocationHandler
  • java.util.EventObject (implements java.io.Serializable)
    • apollo.gui.event.BaseFocusEvent
    • apollo.gui.event.ChainedRepaintEvent
    • apollo.dataadapter.DataLoadEvent
    • apollo.editor.FeatureChangeEvent
      • apollo.editor.AnnotationChangeEvent
        • apollo.editor.AnnotationAddEvent
        • apollo.editor.AnnotationCompoundEvent
        • apollo.editor.AnnotationDeleteEvent
        • apollo.editor.AnnotationReplaceEvent
        • apollo.editor.AnnotationUpdateEvent (implements apollo.editor.UpdateDetailsI)
        • apollo.editor.AnnotSessionDoneEvent
      • apollo.editor.ResultChangeEvent
    • apollo.gui.event.FeatureSelectionEvent
    • apollo.gui.event.LazyLoadEvent
    • apollo.gui.event.NamedFeatureSelectionEvent
    • apollo.gui.event.OrientationEvent
    • apollo.config.PropSchemeChangeEvent
    • apollo.gui.event.ReverseComplementEvent
    • apollo.gui.event.RubberbandEvent
    • apollo.gui.event.ScrollEvent
    • apollo.gui.event.SetActiveCurStateEvent
    • apollo.gui.event.TierManagerEvent
    • apollo.gui.event.ViewEvent
    • apollo.gui.event.VisibilityEvent
    • apollo.gui.event.ZoomEvent
  • apollo.dataadapter.ensj.controller.EventRouter
    • apollo.dataadapter.ensj.controller.ActionEventRouter (implements java.awt.event.ActionListener)
    • apollo.dataadapter.ensj.controller.KeyEventRouter (implements java.awt.event.KeyListener)
    • apollo.dataadapter.ensj.controller.PopupRouter (implements javax.swing.event.PopupMenuListener)
  • apollo.datamodel.Evidence (implements apollo.datamodel.EvidenceConstants, java.io.Serializable)
  • apollo.datamodel.EvidenceFinder (implements java.io.Serializable)
  • apollo.gui.evidencepanel.EvidencePanelOrientationManager
  • apollo.datamodel.EvidenceSet (implements java.io.Serializable)
  • apollo.util.FastaHeader
  • apollo.util.FeatureAlphabeticalComparator (implements apollo.util.Comparator)
  • apollo.util.FeatureComparator (implements org.bdgp.util.Comparator)
  • apollo.util.FeatureIterator (implements java.util.ListIterator<E>)
  • apollo.gui.detailviewers.sequencealigner.FeaturePlaceFinder
    • apollo.gui.detailviewers.sequencealigner.CompactFeaturePlaceFinder
    • apollo.gui.detailviewers.sequencealigner.SemiCompactFeaturePlaceFinder
  • apollo.config.FeatureProperty (implements java.lang.Cloneable, java.io.Serializable)
  • apollo.dataadapter.FeatureSetBuilder
    • apollo.dataadapter.ensj.EnsJFeatureSetBuilder
  • javax.swing.filechooser.FileFilter
    • apollo.util.ExampleFileFilter
    • apollo.gui.GenericFileFilter
  • apollo.io.FileParse
    • apollo.seq.io.FastaFile
    • apollo.seq.io.GFFFile
  • apollo.util.FileUtil
  • apollo.gui.detailviewers.sequencealigner.filters.FilterDisplayType (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.gui.detailviewers.sequencealigner.filters.FilterFactory
  • apollo.gui.detailviewers.sequencealigner.filters.FilterInverse<T> (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.gui.detailviewers.sequencealigner.filters.FilterName (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.gui.detailviewers.sequencealigner.filters.FilterReadingFrame (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.gui.detailviewers.sequencealigner.filters.FilterSequenceType (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.gui.detailviewers.sequencealigner.filters.FilterStrand (implements apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
  • apollo.dataadapter.chado.jdbc.FlybaseChadoInstance
    • apollo.dataadapter.chado.jdbc.RiceChadoInstance
  • apollo.dataadapter.chado.jdbc.FlybaseWrite
  • apollo.dataadapter.genbank.FlyIdValidator (implements apollo.dataadapter.genbank.FeatureValidatorI)
  • apollo.util.Format
  • apollo.dataadapter.gamexml.GAMESave
  • apollo.dataadapter.GbrowseAdapterGUI.ChrStartEndListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.genbank.GenbankFormatter
  • apollo.dataadapter.genbank.GenbankRead
  • apollo.dataadapter.genbank.GenbankReport
  • apollo.dataadapter.genbank.GenbankValidator
  • apollo.analysis.GenericProgramHandler (implements apollo.analysis.ProgramHandlerI)
    • apollo.analysis.BlastHandler
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • apollo.external.ApolloControlServlet
  • apollo.dataadapter.gff3.GFF3Entry
  • apollo.dataadapter.GFFSyntenyAdapter (implements apollo.dataadapter.SyntenyAdapterI)
  • apollo.dataadapter.graph.GraphAdapterGUI.ColorActionListener (implements java.awt.event.ActionListener)
  • java.awt.Graphics
    • apollo.gui.genomemap.FastClippingGraphics
  • java.awt.GridBagConstraints (implements java.lang.Cloneable, java.io.Serializable)
    • apollo.dataadapter.GuiTabPanel.ApolloGridBagConstraints
  • apollo.gui.synteny.GuiCurationState
  • apollo.gui.genomemap.GuideLine (implements apollo.gui.BaseScrollable)
  • apollo.util.GuiUtil
  • apollo.analysis.HashDB
  • apollo.analysis.HashMatch
  • apollo.gui.detailviewers.sequencealigner.HorizontalScrollBarAdjustmentListener (implements java.awt.event.AdjustmentListener)
  • apollo.util.HTMLUtil
  • apollo.analysis.filter.HuffNode
  • apollo.datamodel.Identifier (implements java.lang.Cloneable, java.io.Serializable)
  • apollo.external.IgbBridge (implements apollo.gui.event.FeatureSelectionListener)
  • apollo.util.interval.Interval (implements java.lang.Comparable<T>)
  • apollo.util.interval.IntervalTree
  • apollo.util.IOUtil
  • apollo.dataadapter.chado.jdbc.JdbcChadoAdapter
    • apollo.dataadapter.chado.jdbc.PostgresChadoAdapter
    • apollo.dataadapter.chado.jdbc.SybaseChadoAdapter
  • apollo.bop.JDBCPipelineAdapter
  • apollo.test.JDBCTransactionLoader
  • apollo.bop.JobOutput
  • apollo.datamodel.Karyotype
  • apollo.dataadapter.KaryotypeAdapter (implements apollo.dataadapter.KaryotypeAdapterI)
  • apollo.dataadapter.KaryotypeUtil
  • java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • apollo.dataadapter.ensj19.AnnotationSourceChooser.RemoveDatasetsListenerForPort
    • apollo.dataadapter.ensj19.DataSourceConfigurationPanel.DataChangeListener
    • apollo.util.NumericKeyFilter
  • apollo.gui.genomemap.LinearView (implements apollo.gui.genomemap.ViewI)
    • apollo.gui.genomemap.ContainerView (implements apollo.gui.genomemap.ContainerViewI, apollo.gui.genomemap.PickViewI)
      • apollo.gui.genomemap.LaidoutViewContainer (implements apollo.gui.genomemap.PickViewI)
      • apollo.gui.genomemap.SplitterView (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
    • apollo.gui.genomemap.ManagedView (implements apollo.gui.genomemap.ManagedViewI)
      • apollo.gui.genomemap.DragView (implements apollo.gui.genomemap.DragViewI)
      • apollo.gui.genomemap.TierView (implements java.awt.event.AdjustmentListener, apollo.gui.ControlledObjectI, apollo.gui.genomemap.DropTargetViewI, apollo.gui.genomemap.PickViewI, apollo.gui.event.TierManagerListener, apollo.gui.genomemap.TierViewI)
        • apollo.gui.genomemap.FeatureView (implements apollo.gui.genomemap.PopupViewI, apollo.gui.genomemap.SelectViewI)
          • apollo.gui.genomemap.AnnotationView (implements apollo.editor.AnnotationChangeListener, apollo.gui.ControlledObjectI, apollo.gui.genomemap.DropTargetViewI)
          • apollo.gui.genomemap.ResultView (implements apollo.gui.genomemap.KeyViewI, apollo.editor.ResultChangeListener)
        • apollo.gui.genomemap.SiteView
    • apollo.gui.genomemap.ScrollAdjustedView
      • apollo.gui.genomemap.GraphView (implements javax.swing.event.ChangeListener)
        • apollo.gui.genomemap.DiscreteGraphView
      • apollo.gui.genomemap.ScaleView (implements apollo.gui.genomemap.PickViewI, apollo.gui.genomemap.PopupViewI)
      • apollo.gui.genomemap.TranslationView
  • apollo.datamodel.Link
  • apollo.datamodel.LinkSet
  • apollo.config.LinkType (implements java.lang.Cloneable)
  • apollo.main.LoadUtil
  • apollo.dataadapter.ensj.model.LocationModel
  • apollo.gui.menus.MenuManager
  • apollo.gui.event.MethodRunnerActionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.ensj.model.Model
  • apollo.dataadapter.synteny.builder.Model
  • java.awt.event.MouseAdapter (implements java.awt.event.MouseListener)
    • apollo.gui.evidencepanel.TablePanel.CopyMouseListener
  • apollo.gui.event.MouseButtonEvent
  • javax.swing.event.MouseInputAdapter (implements javax.swing.event.MouseInputListener)
    • apollo.gui.detailviewers.sequencealigner.AnnotationEditorMouseListener
    • apollo.gui.detailviewers.sequencealigner.ResultMouseListener
    • apollo.gui.detailviewers.exonviewer.SeqAlignPanel.ScrollMouseListener
    • apollo.gui.detailviewers.sequencealigner.SeqAlignPanel.ScrollMouseListener
    • apollo.gui.evidencepanel.TablePanel.SortMouseListener
  • apollo.seq.io.MSPFile
  • apollo.dataadapter.mysql.MySQLInstance
  • apollo.gui.NonWindowControlledObject (implements apollo.gui.ControlledObjectI, java.util.EventListener)
    • apollo.gui.ControllerDebugListener (implements apollo.editor.AnnotationChangeListener, apollo.gui.event.BaseFocusListener, apollo.dataadapter.DataLoadListener, apollo.gui.event.FeatureSelectionListener, apollo.gui.event.LazyLoadListener, apollo.config.PropSchemeChangeListener, apollo.editor.ResultChangeListener)
  • apollo.config.NoOverlap (implements apollo.config.OverlapI)
  • apollo.util.OBOParser
  • apollo.dataadapter.ensj.model.OptionsModel
  • apollo.config.ORF_Overlap (implements apollo.config.OverlapI)
  • apollo.dataadapter.otter.parser.OtterXMLRenderingVisitor (implements apollo.util.Visitor)
  • apollo.util.Pair<T,U>
  • apollo.gui.detailviewers.sequencealigner.PanelFactory
  • apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance
  • apollo.config.ParameciumNameAdapter (implements apollo.config.ApolloNameAdapterI)
  • apollo.dataadapter.genbank.PeptideNote
  • apollo.config.PeptideStatus
  • apollo.dataadapter.genbank.PeptideValidator (implements apollo.dataadapter.genbank.FeatureValidatorI)
  • apollo.gui.genomemap.PixelMask (implements apollo.gui.genomemap.PixelMaskI)
  • apollo.gui.genomemap.PlotUtil
  • apollo.gui.PopupPropertyListener (implements java.beans.PropertyChangeListener)
  • apollo.analysis.PrimerBlastHtmlParser
  • apollo.analysis.ProgramHandlerFactory
  • apollo.gui.detailviewers.PropertyDisplay
  • apollo.config.PropertyScheme (implements java.io.Serializable)
  • apollo.dataadapter.genbank.PublicDbFeature
  • apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
    • apollo.dataadapter.chado.jdbc.JdbcChadoWriter
  • apollo.util.QuickSort
  • apollo.datamodel.Range (implements apollo.datamodel.RangeI, java.io.Serializable)
    • apollo.gui.tweeker.CutSite
    • apollo.datamodel.GenomicRange
      • apollo.datamodel.CurationSet (implements apollo.datamodel.ApolloDataI, java.io.Serializable)
    • apollo.datamodel.SeqFeature (implements apollo.datamodel.Comparable, apollo.datamodel.SeqFeatureI)
      • apollo.datamodel.FeaturePair (implements apollo.datamodel.FeaturePairI)
      • apollo.datamodel.FeatureSet (implements apollo.datamodel.FeatureSetI)
        • apollo.datamodel.AnnotatedFeature (implements apollo.datamodel.AnnotatedFeatureI)
          • apollo.datamodel.AssemblyFeature (implements apollo.datamodel.AssemblyFeatureI)
          • apollo.datamodel.Exon (implements apollo.datamodel.ExonI)
          • apollo.datamodel.Protein
          • apollo.datamodel.SequenceEdit (implements java.io.Serializable)
          • apollo.datamodel.Transcript
        • apollo.datamodel.StrandedFeatureSet (implements apollo.datamodel.StrandedFeatureSetI)
  • apollo.util.interval.RbNode
  • apollo.util.interval.RbTree
  • apollo.gui.detailviewers.sequencealigner.ReferenceFactory (implements apollo.gui.detailviewers.sequencealigner.ReferenceFactoryI)
  • apollo.dataadapter.Region
  • apollo.analysis.RemoteBlastNCBI
  • apollo.analysis.RemoteBlastNCBI.BlastOptions
  • apollo.analysis.RemotePrimerBlastNCBI
  • apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions
  • apollo.seq.ResidueProperties
  • apollo.gui.tweeker.RestrictionEnzyme
  • apollo.gui.detailviewers.sequencealigner.ResultFeatureComparator (implements java.util.Comparator<T>)
  • apollo.gui.detailviewers.sequencealigner.listeners.ResultHeaderMouseListener (implements java.awt.event.MouseListener)
  • apollo.gui.detailviewers.sequencealigner.renderers.ResultRendererFactory
  • apollo.test.Robby
  • apollo.gui.genomemap.Rubberband (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
    • apollo.gui.genomemap.RubberbandRectangle
  • apollo.dataadapter.chado.jdbc.SchemaVersion
  • apollo.datamodel.Score (implements java.io.Serializable)
  • apollo.gui.ScoreCalculator
    • apollo.gui.WindowScoreCalculator
      • apollo.gui.GCScoreCalculator
      • apollo.gui.StoredScoreCalculator
        • apollo.gui.SgrScoreCalculator
        • apollo.gui.WiggleScoreCalculator
  • apollo.gui.SelectionItem
  • apollo.gui.SelectionManager (implements apollo.gui.ControlledObjectI)
  • apollo.gui.SelectionType
  • apollo.analysis.SeqAnalysisFactory
  • apollo.analysis.SeqAnalysisGUI.LaunchRunnable (implements java.lang.Runnable)
  • apollo.util.SeqFeatureUtil
  • apollo.gui.SeqSelectorTable
  • apollo.dataadapter.chado.SeqType
  • apollo.gui.SequenceSelector
  • apollo.util.SequenceUtil
  • apollo.dataadapter.das.simple.SimpleDASAdapterGUI.DSNListener (implements java.awt.event.ItemListener)
  • apollo.dataadapter.das.simple.SimpleDASAdapterGUI.HistoryListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.das.simple.SimpleDASAdapterGUI.ProxyListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.das.simple.SimpleDASAdapterGUI.ServerListener (implements java.awt.event.ItemListener)
  • apollo.dataadapter.das.simple.SimpleDASDsn (implements apollo.dataadapter.das.DASDsn)
  • apollo.dataadapter.das.simple.SimpleDASFeature (implements apollo.dataadapter.das.DASFeature)
  • apollo.dataadapter.das.simple.SimpleDASSegment (implements apollo.dataadapter.das.DASSegment)
  • apollo.dataadapter.das.simple.SimpleDASSequence (implements apollo.dataadapter.das.DASSequence)
  • apollo.dataadapter.das.simple.SimpleDASServer (implements apollo.dataadapter.das.DASServerI)
  • apollo.config.SimpleOverlap (implements apollo.config.OverlapI)
  • apollo.gui.genomemap.Sites
  • apollo.datamodel.SpeciesComparison
  • apollo.analysis.StreamMatch
  • apollo.config.Style
  • apollo.util.SwingMissingUtil
  • apollo.gui.SwingWorker
  • apollo.datamodel.Synonym (implements java.io.Serializable)
  • apollo.dataadapter.SyntenyAdapter (implements apollo.dataadapter.SyntenyAdapterI)
  • apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.DnaAlignTypesButtonActionListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.FullPanelListener (implements java.awt.event.ActionListener)
  • apollo.dataadapter.synteny.SyntenyComparaAdapterGUI.ShowDataSourceConfigurationActionListener (implements java.awt.event.ActionListener)
  • apollo.gui.synteny.SyntenyLayout (implements java.awt.LayoutManager)
  • apollo.gui.menus.SyntenyMenuManager
  • apollo.datamodel.SyntenyRegion
  • apollo.dataadapter.mysql.Table
  • apollo.dataadapter.chado.jdbc.TableColumn
  • apollo.gui.evidencepanel.TablePanel.MegaComparator (implements org.bdgp.util.Comparator)
  • apollo.gui.evidencepanel.TablePanel.RowSelectionListener (implements javax.swing.event.ListSelectionListener)
  • apollo.dataadapter.otter.parser.TagHandler
    • apollo.dataadapter.otter.parser.EvidenceNameTagHandler
    • apollo.dataadapter.otter.parser.EvidenceTagHandler
    • apollo.dataadapter.otter.parser.EvidenceTypeTagHandler
    • apollo.dataadapter.otter.parser.ExonEndTagHandler
    • apollo.dataadapter.otter.parser.ExonFrameTagHandler
    • apollo.dataadapter.otter.parser.ExonStableIdTagHandler
    • apollo.dataadapter.otter.parser.ExonStartTagHandler
    • apollo.dataadapter.otter.parser.ExonStrandTagHandler
    • apollo.dataadapter.otter.parser.ExonTagHandler
    • apollo.dataadapter.otter.parser.GenericTagHandler
    • apollo.dataadapter.otter.parser.LocusAuthorEmailTagHandler
    • apollo.dataadapter.otter.parser.LocusAuthorTagHandler
    • apollo.dataadapter.otter.parser.LocusKnownTagHandler
    • apollo.dataadapter.otter.parser.LocusNameTagHandler
    • apollo.dataadapter.otter.parser.LocusRemarkTagHandler
    • apollo.dataadapter.otter.parser.LocusStableIdTagHandler
    • apollo.dataadapter.otter.parser.LocusSynonymTagHandler
    • apollo.dataadapter.otter.parser.LocusTagHandler
    • apollo.dataadapter.otter.parser.LocusTypeTagHandler
    • apollo.dataadapter.otter.parser.OtterTagHandler
    • apollo.dataadapter.otter.parser.ResponseTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentAccessionTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentAssemblyEndTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentAssemblyStartTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentAuthorEmailTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentAuthorTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentChromosomeTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentFragmentOffsetTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentFragmentOrientationTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentIdTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentKeywordTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentRemarkTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentTagHandler
    • apollo.dataadapter.otter.parser.SequenceFragmentVersionTagHandler
    • apollo.dataadapter.otter.parser.SequenceSetAssemblyTypeTagHandler
    • apollo.dataadapter.otter.parser.SequenceSetAuthorTagHandler
    • apollo.dataadapter.otter.parser.SequenceSetTagHandler
    • apollo.dataadapter.otter.parser.TranscriptAuthorEmailTagHandler
    • apollo.dataadapter.otter.parser.TranscriptAuthorTagHandler
    • apollo.dataadapter.otter.parser.TranscriptCdsEndNotFoundTagHandler
    • apollo.dataadapter.otter.parser.TranscriptCdsStartNotFoundTagHandler
    • apollo.dataadapter.otter.parser.TranscriptClassTagHandler
    • apollo.dataadapter.otter.parser.TranscriptMRNAEndNotFoundTagHandler
    • apollo.dataadapter.otter.parser.TranscriptMRNAStartNotFoundTagHandler
    • apollo.dataadapter.otter.parser.TranscriptNameTagHandler
    • apollo.dataadapter.otter.parser.TranscriptRemarkTagHandler
    • apollo.dataadapter.otter.parser.TranscriptStableIdTagHandler
    • apollo.dataadapter.otter.parser.TranscriptTagHandler
    • apollo.dataadapter.otter.parser.TranscriptTranslationEndTagHandler
    • apollo.dataadapter.otter.parser.TranscriptTranslationStableIdTagHandler
    • apollo.dataadapter.otter.parser.TranscriptTranslationStartTagHandler
  • java.lang.Thread (implements java.lang.Runnable)
    • apollo.gui.AutoSaveThread
    • apollo.gui.CheckMemoryThread
    • apollo.gui.detailviewers.exonviewer.SeqAlignPanel.AutoscrollThread (implements apollo.gui.detailviewers.exonviewer.Directions)
    • apollo.gui.detailviewers.sequencealigner.SeqAlignPanel.AutoscrollThread (implements apollo.gui.detailviewers.sequencealigner.Directions)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • apollo.analysis.BlastXMLParser.BlastXMLParserException
      • apollo.dataadapter.exception.BopException
        • apollo.dataadapter.exception.NoOutputException
      • apollo.dataadapter.DataInputType.UnknownTypeException
      • org.bdgp.util.NestedException
        • org.bdgp.io.DataAdapterException
          • apollo.dataadapter.ApolloAdapterException
      • apollo.analysis.PrimerBlastHtmlParser.PrimerBlastHtmlParserException
      • java.lang.RuntimeException
        • apollo.dataadapter.ensj.FatalException
        • apollo.dataadapter.NonFatalDataAdapterException
        • apollo.dataadapter.ensj.NonFatalException
        • apollo.dataadapter.NotImplementedException
      • apollo.dataadapter.TransactionTransformException
  • apollo.gui.Tier
    • apollo.gui.genomemap.FeatureTier
    • apollo.gui.genomemap.SiteTier
  • apollo.gui.detailviewers.sequencealigner.Tier (implements apollo.gui.detailviewers.sequencealigner.TierI)
  • apollo.gui.detailviewers.sequencealigner.TierFactory (implements apollo.gui.detailviewers.sequencealigner.TierFactoryI)
  • apollo.gui.TierManager (implements apollo.gui.TierManagerI)
    • apollo.gui.genomemap.DrawableTierManager (implements apollo.gui.genomemap.DrawableTierManagerI)
      • apollo.gui.genomemap.FeatureTierManager (implements apollo.gui.genomemap.FeatureTierManagerI, apollo.config.PropSchemeChangeListener)
    • apollo.gui.genomemap.SiteTierManager
  • apollo.config.TierProperty (implements java.lang.Cloneable, java.io.Serializable)
  • apollo.config.TiersIO
  • apollo.config.TigrAnnotDisplayPrefs.TigrFeatureName
  • apollo.config.TigrAnnotNameAdapter (implements apollo.config.ApolloNameAdapterI)
  • apollo.dataadapter.chado.jdbc.TigrChadoInstance
    • apollo.dataadapter.chado.jdbc.TigrSybilChadoInstance
  • apollo.editor.Transaction (implements java.io.Serializable)
    • apollo.editor.AddTransaction
    • apollo.editor.CompoundTransaction
      • apollo.editor.UpdateParentTransaction
    • apollo.editor.DeleteTransaction
    • apollo.editor.UpdateTransaction
  • apollo.editor.TransactionClass (implements java.io.Serializable)
  • apollo.editor.TransactionManager (implements apollo.editor.AnnotationChangeListener, java.io.Serializable)
  • apollo.editor.TransactionOperation (implements java.io.Serializable)
  • apollo.dataadapter.TransactionOutputAdapter
    • apollo.dataadapter.chadoxml.ChadoTransactionXMLWriter
    • apollo.dataadapter.chado.jdbc.JDBCTransactionWriter
  • apollo.editor.TransactionSubpart (implements java.io.Serializable)
  • apollo.editor.TransactionUtil
  • apollo.dataadapter.gamexml.TransactionXMLAdapter
  • javax.swing.TransferHandler (implements java.io.Serializable)
    • apollo.gui.ArrayListTransferHandler
  • apollo.gui.Transformer
  • apollo.gui.Transformer.PixelRange
  • apollo.dataadapter.genbank.tRNAValidator (implements apollo.dataadapter.genbank.FeatureValidatorI)
  • apollo.analysis.filter.TwilightFilter
  • apollo.dataadapter.ensj.model.TypesModel
  • apollo.gui.URLQueryGenerator
  • apollo.editor.UserName
  • apollo.gui.detailviewers.sequencealigner.Utils
  • apollo.main.Version
  • apollo.gui.detailviewers.sequencealigner.VerticalScrollBarAdjustmentListener (implements java.awt.event.AdjustmentListener)
  • apollo.gui.detailviewers.sequencealigner.ViewportChangeListener (implements javax.swing.event.ChangeListener)
  • apollo.test.WashingLine (implements apollo.gui.ApolloLoaderI)
  • java.awt.event.WindowAdapter (implements java.awt.event.WindowFocusListener, java.awt.event.WindowListener, java.awt.event.WindowStateListener)
    • apollo.gui.event.BasicWindowListener
    • apollo.gui.event.EditWindowListener
    • apollo.dataadapter.URLDiagnosticTool.MyWindowListener
  • apollo.dataadapter.gamexml.XMLParser (implements org.xml.sax.ContentHandler)
  • apollo.dataadapter.genbank.XrefUtil

Interface Hierarchy

• apollo.analysis.filter.AnalysisFilterI
• apollo.dataadapter.analysis.AnalysisParserI
• apollo.dataadapter.ApolloDataAdapterGUI
• apollo.datamodel.ApolloDataI
• apollo.gui.ApolloLoaderI
• apollo.config.ApolloNameAdapterI
• apollo.gui.genomemap.ApolloPanelHolderI
• apollo.gui.genomemap.ApolloPanelI
• apollo.datamodel.AssemblyFeatureI
• apollo.gui.detailviewers.exonviewer.BaseRenderer
• apollo.gui.detailviewers.sequencealigner.renderers.BaseRenderer
• apollo.gui.detailviewers.sequencealigner.renderers.BaseRendererI
• apollo.gui.BaseScrollable
  • apollo.gui.detailviewers.sequencealigner.TierPanelI (also extends apollo.editor.AnnotationChangeListener, javax.swing.Scrollable)
• java.lang.Cloneable
  • apollo.dataadapter.chado.jdbc.ChadoInstance
  • apollo.datamodel.RangeI (also extends java.io.Serializable)
    • apollo.datamodel.AnnotatedFeatureI
      • apollo.datamodel.ExonI
    • apollo.datamodel.ExonI
    • apollo.datamodel.FeaturePairI
    • apollo.datamodel.FeatureSetI (also extends apollo.datamodel.SeqFeatureI, apollo.datamodel.TranslationI)
      • apollo.datamodel.AnnotatedFeatureI
        • apollo.datamodel.ExonI
      • apollo.datamodel.ExonI
      • apollo.datamodel.StrandedFeatureSetI
    • apollo.datamodel.SeqFeatureI
      • apollo.datamodel.AnnotatedFeatureI
        • apollo.datamodel.ExonI
      • apollo.datamodel.ExonI
      • apollo.datamodel.FeaturePairI
      • apollo.datamodel.FeatureSetI (also extends apollo.datamodel.TranslationI)
        • apollo.datamodel.AnnotatedFeatureI
          • apollo.datamodel.ExonI
        • apollo.datamodel.ExonI
        • apollo.datamodel.StrandedFeatureSetI
      • apollo.datamodel.StrandedFeatureSetI
    • apollo.datamodel.StrandedFeatureSetI
• apollo.datamodel.CodingPropertiesI
• apollo.datamodel.Comparable
• java.util.Comparator<T>
  • apollo.gui.detailviewers.sequencealigner.comparators.MultiComparator<T> (also extends java.util.List<E>)
• apollo.util.Comparator
• apollo.dataadapter.das.DASDsn
• apollo.dataadapter.das.DASFeature
• apollo.dataadapter.das.DASSegment
• apollo.dataadapter.das.DASSequence
• apollo.dataadapter.das.DASServerI
• org.bdgp.io.DataAdapter
  • org.bdgp.io.VisualDataAdapter
    • apollo.analysis.AnalysisDataAdapterI
    • apollo.dataadapter.ApolloDataAdapterI
• apollo.dataadapter.DataListener
• apollo.gui.detailviewers.exonviewer.Directions
• apollo.gui.detailviewers.sequencealigner.Directions
• apollo.config.DisplayPrefsI
• apollo.gui.drawable.DrawableAnnotationConstants
• apollo.gui.genomemap.DropTargetViewI
• apollo.gui.EditWindowI
• java.util.EventListener
  • apollo.editor.AnnotationChangeListener
    • apollo.gui.detailviewers.sequencealigner.TierI (also extends org.bdgp.util.Range)
    • apollo.gui.detailviewers.sequencealigner.TierPanelI (also extends apollo.gui.BaseScrollable, javax.swing.Scrollable)
  • apollo.gui.event.BaseFocusListener
  • apollo.gui.event.ChainedRepaintListener
  • apollo.dataadapter.DataLoadListener
  • apollo.editor.FeatureChangeListener
  • apollo.gui.event.FeatureSelectionListener
  • apollo.gui.event.LazyLoadListener
  • apollo.gui.event.NamedFeatureSelectionListener
  • apollo.gui.event.OrientationListener
  • apollo.config.PropSchemeChangeListener
  • apollo.editor.ResultChangeListener
  • apollo.gui.event.ReverseComplementListener
  • apollo.gui.event.RubberbandListener
  • apollo.gui.event.ScrollListener
  • apollo.gui.event.SetActiveCurStateListener
  • apollo.gui.event.TierManagerListener
  • apollo.gui.event.ViewListener
  • apollo.gui.event.VisibilityListener
  • apollo.gui.event.ZoomListener
• apollo.datamodel.EvidenceConstants
• apollo.gui.FeatureNavigationI
• apollo.dataadapter.genbank.FeatureValidatorI
• apollo.gui.detailviewers.sequencealigner.filters.Filter<T>
  • apollo.gui.detailviewers.sequencealigner.filters.MultiFilter<T> (also extends java.util.List<E>)
• apollo.analysis.filter.FilterPanelI
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • java.util.List<E>
      • apollo.gui.detailviewers.sequencealigner.comparators.MultiComparator<T> (also extends java.util.Comparator<T>)
      • apollo.gui.detailviewers.sequencealigner.filters.MultiFilter<T> (also extends apollo.gui.detailviewers.sequencealigner.filters.Filter<T>)
• apollo.dataadapter.KaryotypeAdapterI
• apollo.gui.genomemap.KeyViewI
• apollo.dataadapter.synteny.LinkerI
• apollo.gui.Orientations
• apollo.config.OverlapI
• apollo.gui.genomemap.PixelMaskI
• apollo.gui.genomemap.PopupViewI
• apollo.analysis.ProgramHandlerI
• org.bdgp.util.Range
  • apollo.gui.detailviewers.sequencealigner.TierI (also extends apollo.editor.AnnotationChangeListener)
• apollo.gui.detailviewers.sequencealigner.ReferenceFactoryI
• apollo.gui.detailviewers.sequencealigner.RegionSelectableI
• apollo.gui.genomemap.RevCompListener
• javax.swing.Scrollable
  • apollo.gui.detailviewers.sequencealigner.TierPanelI (also extends apollo.editor.AnnotationChangeListener, apollo.gui.BaseScrollable)
• apollo.gui.SelectableI
  • apollo.gui.drawable.Drawable
    • apollo.gui.drawable.DrawableSetI
  • apollo.gui.drawable.DrawableSetI
• apollo.analysis.SeqAnalysisI
• java.io.Serializable
  • apollo.gui.ControlledObjectI
    • apollo.gui.genomemap.ContainerViewI
    • apollo.gui.genomemap.DrawableTierManagerI
    • apollo.gui.genomemap.FeatureTierManagerI
    • apollo.gui.TierManagerI
      • apollo.gui.genomemap.DrawableTierManagerI
      • apollo.gui.genomemap.FeatureTierManagerI
  • apollo.datamodel.RangeI (also extends java.lang.Cloneable)
    • apollo.datamodel.AnnotatedFeatureI
      • apollo.datamodel.ExonI
    • apollo.datamodel.ExonI
    • apollo.datamodel.FeaturePairI
    • apollo.datamodel.FeatureSetI (also extends apollo.datamodel.SeqFeatureI, apollo.datamodel.TranslationI)
      • apollo.datamodel.AnnotatedFeatureI
        • apollo.datamodel.ExonI
      • apollo.datamodel.ExonI
      • apollo.datamodel.StrandedFeatureSetI
    • apollo.datamodel.SeqFeatureI
      • apollo.datamodel.AnnotatedFeatureI
        • apollo.datamodel.ExonI
      • apollo.datamodel.ExonI
      • apollo.datamodel.FeaturePairI
      • apollo.datamodel.FeatureSetI (also extends apollo.datamodel.TranslationI)
        • apollo.datamodel.AnnotatedFeatureI
          • apollo.datamodel.ExonI
        • apollo.datamodel.ExonI
        • apollo.datamodel.StrandedFeatureSetI
      • apollo.datamodel.StrandedFeatureSetI
    • apollo.datamodel.StrandedFeatureSetI
  • apollo.datamodel.SequenceI
    • apollo.datamodel.seq.LazySequenceI
• apollo.util.interval.StatisticUpdate
• apollo.gui.genomemap.StrandVisibilityListener
• apollo.dataadapter.SyntenyAdapterI
• apollo.gui.detailviewers.sequencealigner.TierFactoryI
• apollo.dataadapter.TransactionTransformer
• apollo.datamodel.TranslationI
  • apollo.datamodel.AnnotatedFeatureI
    • apollo.datamodel.ExonI
  • apollo.datamodel.ExonI
  • apollo.datamodel.FeatureSetI (also extends apollo.datamodel.SeqFeatureI)
    • apollo.datamodel.AnnotatedFeatureI
      • apollo.datamodel.ExonI
    • apollo.datamodel.ExonI
    • apollo.datamodel.StrandedFeatureSetI
  • apollo.datamodel.StrandedFeatureSetI
• apollo.editor.UpdateDetailsI
• apollo.gui.genomemap.ViewI
  • apollo.gui.genomemap.DragViewI
  • apollo.gui.genomemap.ManagedViewI
    • apollo.gui.genomemap.SelectViewI
    • apollo.gui.genomemap.TierViewI
      • apollo.gui.genomemap.SelectViewI
  • apollo.gui.genomemap.PickViewI
  • apollo.gui.genomemap.SelectViewI
  • apollo.gui.genomemap.TierViewI
    • apollo.gui.genomemap.SelectViewI
• apollo.util.Visitor

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • apollo.analysis.RemotePrimerBlastNCBI.PrimerBlastOptions.Database
    • apollo.analysis.RemoteBlastNCBI.BlastType
    • apollo.gui.WiggleScoreCalculator.WiggleType
    • apollo.gui.detailviewers.sequencealigner.TierI.Level
    • apollo.gui.detailviewers.sequencealigner.SeqFeatureTableModel.ColumnTypes
    • apollo.gui.detailviewers.sequencealigner.Orientation
    • apollo.gui.detailviewers.sequencealigner.Strand
    • apollo.gui.detailviewers.sequencealigner.FeaturePlaceFinder.Type
    • apollo.gui.detailviewers.sequencealigner.ReadingFrame
    • apollo.gui.detailviewers.sequencealigner.SequenceType
    • apollo.gui.detailviewers.sequencealigner.actions.FrameShiftAction.FrameShiftType
    • apollo.gui.detailviewers.sequencealigner.comparators.ComparatorFactory.TYPE
    • apollo.gui.detailviewers.sequencealigner.menus.AddFilterPanel.TYPES
    • apollo.gui.detailviewers.sequencealigner.overview.IntervalComponent.Valignment