Hierarchy For All Packages

Package Hierarchies:

• com.pacbio.secondary.vis.common.collection,
• com.pacbio.secondary.vis.common.utils,
• com.pacbio.secondary.vis.common.utils.constants,
• com.pacbio.secondary.vis.common.utils.exception,
• com.pacbio.secondary.vis.common.utils.filefilter,
• com.pacbio.secondary.vis.data.base,
• com.pacbio.secondary.vis.data.chromosomeband,
• com.pacbio.secondary.vis.data.contig,
• com.pacbio.secondary.vis.data.db,
• com.pacbio.secondary.vis.data.filesystem,
• com.pacbio.secondary.vis.data.gene,
• com.pacbio.secondary.vis.data.graph,
• com.pacbio.secondary.vis.data.interval,
• com.pacbio.secondary.vis.data.locus,
• com.pacbio.secondary.vis.data.marker,
• com.pacbio.secondary.vis.data.queue,
• com.pacbio.secondary.vis.data.read,
• com.pacbio.secondary.vis.data.session,
• com.pacbio.secondary.vis.data.session.options,
• com.pacbio.secondary.vis.data.session.timer,
• com.pacbio.secondary.vis.data.session.tracks,
• com.pacbio.secondary.vis.data.table.model,
• com.pacbio.secondary.vis.data.variableresolution.model,
• com.pacbio.secondary.vis.data.variableresolution.model.gff,
• com.pacbio.secondary.vis.data.variableresolution.record,
• com.pacbio.secondary.vis.data.xmlinfo,
• com.pacbio.secondary.vis.gui.app,
• com.pacbio.secondary.vis.gui.control,
• com.pacbio.secondary.vis.gui.control.treetable,
• com.pacbio.secondary.vis.gui.desktop,
• com.pacbio.secondary.vis.gui.dialogs,
• com.pacbio.secondary.vis.gui.draw.print,
• com.pacbio.secondary.vis.gui.draw.track,
• com.pacbio.secondary.vis.gui.draw.utils,
• com.pacbio.secondary.vis.gui.draw.views,
• com.pacbio.secondary.vis.gui.evt,
• com.pacbio.secondary.vis.gui.frame,
• com.pacbio.secondary.vis.gui.panels,
• com.pacbio.secondary.vis.gui.panels.base,
• com.pacbio.secondary.vis.gui.table,
• com.pacbio.secondary.vis.gui.table.renderer,
• com.pacbio.secondary.vis.io.epipro,
• com.pacbio.secondary.vis.io.export,
• com.pacbio.secondary.vis.io.fasta,
• com.pacbio.secondary.vis.io.gff,
• com.pacbio.secondary.vis.io.gff.modifications,
• com.pacbio.secondary.vis.io.gff.summary,
• com.pacbio.secondary.vis.io.gff.variants,
• com.pacbio.secondary.vis.io.hdf.constants,
• com.pacbio.secondary.vis.io.hdf.data,
• com.pacbio.secondary.vis.io.hdf.exception,
• com.pacbio.secondary.vis.io.hdf.file.bash5,
• com.pacbio.secondary.vis.io.hdf.file.cmph5,
• com.pacbio.secondary.vis.io.hdf.file.hdf5,
• com.pacbio.secondary.vis.io.hdf.hyperslabinfo,
• com.pacbio.secondary.vis.io.hdf.referenceinfo,
• com.pacbio.secondary.vis.io.hdf.streaming,
• com.pacbio.secondary.vis.io.hdf.test,
• com.pacbio.secondary.vis.io.importer,
• com.pacbio.secondary.vis.io.indexer.fasta,
• com.pacbio.secondary.vis.io.indexer.gff,
• com.pacbio.secondary.vis.io.indexer.gff.metadata,
• com.pacbio.secondary.vis.io.indexer.indexinfo,
• com.pacbio.secondary.vis.io.indexer.text,
• com.pacbio.secondary.vis.io.motifs,
• com.pacbio.secondary.vis.io.ucsc.gtf.reader,
• com.pacbio.secondary.vis.io.update,
• com.pacbio.secondary.vis.io.vcf,
• com.pacbio.secondary.vis.smrtcloud,
• com.pacbio.secondary.vis.svc.hdf.client,
• com.pacbio.secondary.vis.svc.hdf.client.auto,
• com.pacbio.secondary.vis.svc.server,
• com.pacbio.secondary.vis.svc.server.data,
• com.pacbio.secondary.vis.svc.server.data.parser,
• com.pacbio.secondary.vis.svc.server.hdf,
• com.pacbio.secondary.vis.svc.server.jnlp,
• com.pacbio.secondary.vis.svc.server.test,
• com.pacbio.secondary.vis.svc.server.threads,
• com.pacbio.secondary.vis.svc.server.utils,
• com.pacbio.secondary.vis.svc.vis.client,
• com.pacbio.secondary.vis.svc.vis.client.auto,
• com.pacbio.secondary.vis.update,
• pub.vlsolutions.swing.docking,
• pub.vlsolutions.swing.docking.animation,
• pub.vlsolutions.swing.docking.event,
• pub.vlsolutions.swing.docking.ui,
• pub.vlsolutions.swing.docking.ws,
• pub.vlsolutions.swing.tabbedpane,
• pub.vlsolutions.swing.toolbars

Class Hierarchy

• java.lang.Object
  • com.pacbio.secondary.vis.gui.control.treetable.AbstractCellEditor (implements javax.swing.CellEditor)
  • javax.swing.AbstractCellEditor (implements javax.swing.CellEditor, java.io.Serializable)
    • com.pacbio.secondary.vis.gui.table.renderer.ColorEditor (implements java.awt.event.ActionListener, javax.swing.table.TableCellEditor)
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • com.pacbio.secondary.vis.common.collection.LinkedSortedMultiSet<T> (implements java.util.SortedSet<E>)
      • com.pacbio.secondary.vis.common.collection.TreeSortedMultiSet<T> (implements java.util.SortedSet<E>)
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • com.pacbio.secondary.vis.data.table.model.TableModelBase
      • com.pacbio.secondary.vis.data.table.model.TableModelAnnotations
      • com.pacbio.secondary.vis.data.table.model.TableModelDeNovo
      • com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval
      • com.pacbio.secondary.vis.data.table.model.TableModelTrack
  • com.pacbio.secondary.vis.gui.control.treetable.AbstractTreeTableModel (implements com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel)
    • com.pacbio.secondary.vis.data.filesystem.LocalFileSystemModel (implements com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel)
    • com.pacbio.secondary.vis.data.filesystem.RemoteFileSystemModel (implements com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel)
  • com.pacbio.secondary.vis.io.hdf.constants.AlignmentConstants
  • pub.vlsolutions.swing.docking.AnchorConstraints
  • pub.vlsolutions.swing.docking.AnchorManager
  • pub.vlsolutions.swing.docking.animation.AnimationEvent
  • com.pacbio.secondary.vis.common.utils.constants.ArrayConstants
  • com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo (implements java.io.Serializable)
    • com.pacbio.secondary.vis.io.indexer.indexinfo.FASTAFileIndexInfo (implements java.io.Serializable)
    • com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo (implements java.io.Serializable)
  • pub.vlsolutions.swing.docking.AutoHideBorderLayout (implements java.awt.LayoutManager2)
  • pub.vlsolutions.swing.docking.AutoHidePolicy
  • com.pacbio.secondary.vis.gui.draw.utils.AxisUtils
  • com.pacbio.secondary.vis.common.utils.Base64Utils
  • com.pacbio.secondary.vis.data.base.BaseDataModel
    • com.pacbio.secondary.vis.io.epipro.EpiProReadsReader
    • com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel (implements com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer)
      • com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel
        • com.pacbio.secondary.vis.io.gff.GFF3Reader
        • com.pacbio.secondary.vis.io.gff.modifications.GFFModificationsReader
        • com.pacbio.secondary.vis.io.gff.summary.GFFSummaryReader
        • com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader
          • com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader
          • com.pacbio.secondary.vis.io.vcf.VCFReader
        • com.pacbio.secondary.vis.io.ucsc.gtf.reader.UCSCGTFReader
      • com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModelsMerger (implements javax.swing.event.ChangeListener)
      • com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataSet (implements javax.swing.event.ChangeListener)
      • com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionMemoryDataModel
  • com.pacbio.secondary.vis.data.base.BaseDataRecord
    • com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesDataRecord (implements com.pacbio.secondary.vis.data.interval.IntervalScale<T>)
  • pub.vlsolutions.swing.docking.BorderSplitter
  • com.pacbio.secondary.vis.common.collection.ByteArrayList
  • com.pacbio.secondary.vis.common.collection.ChangeNotifier (implements com.pacbio.secondary.vis.gui.evt.IChangeNotifier)
  • com.pacbio.secondary.vis.data.chromosomeband.ChromosomeBand
  • com.pacbio.secondary.vis.smrtcloud.CloudTimer
  • com.pacbio.secondary.vis.smrtcloud.CloudUtils
  • com.pacbio.secondary.vis.io.hdf.constants.CMPH5Constants
  • com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo
  • com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo
  • com.pacbio.secondary.vis.common.utils.constants.ColorConstants
  • com.pacbio.secondary.vis.common.utils.constants.ColorPalette
  • com.pacbio.secondary.vis.data.session.options.CommandLineOptions
  • 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)
            • pub.vlsolutions.swing.docking.DockableStoreButton (implements pub.vlsolutions.swing.docking.DockableDragSource, pub.vlsolutions.swing.docking.DockDropReceiver)
            • pub.vlsolutions.swing.docking.ws.WorkspaceButton
          • javax.swing.JMenuItem (implements javax.accessibility.Accessible, javax.swing.MenuElement)
            • javax.swing.JCheckBoxMenuItem (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
              • com.pacbio.secondary.vis.gui.control.JCheckBoxMenuItemEx
            • javax.swing.JRadioButtonMenuItem (implements javax.accessibility.Accessible)
              • com.pacbio.secondary.vis.gui.control.JRadioButtonMenuItemEx
            • pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem
          • javax.swing.JToggleButton (implements javax.accessibility.Accessible)
            • com.pacbio.secondary.vis.gui.control.JToolbarToggleButton
        • pub.vlsolutions.swing.docking.DragControlerGlassPane
        • pub.vlsolutions.swing.docking.FloatingDialog.Resizer
        • pub.vlsolutions.swing.docking.FloatingDialog.TitlePanel
        • com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase
          • com.pacbio.secondary.vis.gui.draw.views.GenomicViewData
            • com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw (implements java.awt.print.Printable)
              • com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents
                • com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular
                • com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal
                  • com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData (implements java.awt.event.ActionListener)
                    • com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw
                      • com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails
                        • com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect
                  • com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion (implements java.io.Serializable)
                • com.pacbio.secondary.vis.gui.draw.views.GenomicViewVertical
                  • com.pacbio.secondary.vis.gui.draw.views.GenomicViewSingleContig (implements java.io.Serializable)
        • javax.swing.JComboBox<E> (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
          • com.pacbio.secondary.vis.gui.control.JComboBoxCtrl
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • pub.vlsolutions.swing.docking.AutoHideButton
          • com.pacbio.secondary.vis.gui.table.renderer.ColorRenderer (implements javax.swing.table.TableCellRenderer)
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer
            • com.pacbio.secondary.vis.gui.table.renderer.IntegerRenderer
            • com.pacbio.secondary.vis.gui.table.renderer.IntervalRenderer
            • com.pacbio.secondary.vis.gui.table.renderer.LongRenderer
          • com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer.EpiProPaletteDisplay
          • com.pacbio.secondary.vis.gui.control.JLabelCtrl
        • javax.swing.JLayeredPane (implements javax.accessibility.Accessible)
          • pub.vlsolutions.swing.docking.DockingDesktop
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • pub.vlsolutions.swing.docking.AutoHideButtonPanel
          • pub.vlsolutions.swing.docking.AutoHideExpandPanel (implements pub.vlsolutions.swing.docking.SingleDockableContainer)
          • pub.vlsolutions.swing.docking.CompoundDockingPanel (implements pub.vlsolutions.swing.docking.DockDropReceiver)
          • com.pacbio.secondary.vis.gui.dialogs.DNAColorsOptionsPane
          • com.pacbio.secondary.vis.gui.panels.base.DockablePaneBase (implements pub.vlsolutions.swing.docking.Dockable)
            • com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel (implements java.awt.event.ActionListener)
            • com.pacbio.secondary.vis.gui.panels.base.TablePanelBase (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.panels.GenomicTablePanel (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
            • com.pacbio.secondary.vis.gui.panels.WebBrowserPanel (implements java.beans.PropertyChangeListener)
          • pub.vlsolutions.swing.docking.DockablePanel (implements pub.vlsolutions.swing.docking.Dockable)
          • pub.vlsolutions.swing.docking.DockingPanel (implements pub.vlsolutions.swing.docking.DockDropReceiver)
          • pub.vlsolutions.swing.docking.DockView (implements pub.vlsolutions.swing.docking.DockDropReceiver, pub.vlsolutions.swing.docking.SingleDockableContainer)
            • pub.vlsolutions.swing.docking.DetachedDockView
            • pub.vlsolutions.swing.docking.DockViewAsTab (implements pub.vlsolutions.swing.docking.SingleDockableContainer)
              • pub.vlsolutions.swing.docking.MaximizedDockViewAsTab
            • pub.vlsolutions.swing.docking.MaximizedDockView
            • pub.vlsolutions.swing.docking.TabbedDockView
          • pub.vlsolutions.swing.docking.DockViewTitleBar (implements pub.vlsolutions.swing.docking.DockableDragSource)
          • com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane
          • com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel (implements java.awt.event.ActionListener, java.beans.PropertyChangeListener)
          • com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane
          • pub.vlsolutions.swing.toolbars.ToolBarContainer
          • pub.vlsolutions.swing.toolbars.ToolBarPanel
          • com.pacbio.secondary.vis.gui.control.VioletStatusBar
          • com.pacbio.secondary.vis.gui.control.VioletToolBarTest (implements java.awt.event.ActionListener)
          • pub.vlsolutions.swing.toolbars.VLToolBar
          • com.pacbio.secondary.vis.gui.panels.WholeGenomePanel
        • javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          • com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase (implements pub.vlsolutions.swing.docking.Dockable)
        • javax.swing.JSlider (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase.JDoubleSlider
        • javax.swing.JSplitPane (implements javax.accessibility.Accessible)
          • pub.vlsolutions.swing.docking.SplitContainer (implements pub.vlsolutions.swing.docking.DockDropReceiver)
        • javax.swing.JTabbedPane (implements javax.accessibility.Accessible, java.io.Serializable, javax.swing.SwingConstants)
          • pub.vlsolutions.swing.docking.DockTabbedPane (implements pub.vlsolutions.swing.docking.DockableDragSource, pub.vlsolutions.swing.docking.DockDropReceiver, pub.vlsolutions.swing.docking.TabbedDockableContainer)
          • pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader (implements pub.vlsolutions.swing.docking.DockableDragSource)
            • pub.vlsolutions.swing.docking.MaximizedDockViewAsTab.MaximizedTabHeader
        • javax.swing.JTable (implements javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.Scrollable, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener)
          • com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane.EpiProOptionsTable
          • com.pacbio.secondary.vis.gui.table.GenomicTableBase
            • com.pacbio.secondary.vis.gui.table.GenomicTableDeNovo
            • com.pacbio.secondary.vis.gui.table.GenomicTableInterval
            • com.pacbio.secondary.vis.gui.table.GenomicTableTrack
          • com.pacbio.secondary.vis.gui.control.treetable.JTreeTable
        • javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • javax.swing.JEditorPane
            • com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.BookmarksEditorPane
            • com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane
        • javax.swing.JToolBar (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • com.pacbio.secondary.vis.gui.control.VioletToolBar
          • com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserToolBar
        • javax.swing.JToolTip (implements javax.accessibility.Accessible)
          • com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip
          • com.pacbio.secondary.vis.gui.control.JMultiLineHtmlToolTip
          • com.pacbio.secondary.vis.gui.control.JMultiLineToolTip
        • javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer (implements javax.swing.table.TableCellRenderer)
        • com.pacbio.secondary.vis.gui.control.PaletteCtrl
        • pub.vlsolutions.swing.toolbars.ToolBarGripper
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • pub.vlsolutions.swing.docking.DockingSelectorDialog
            • pub.vlsolutions.swing.docking.FloatingDialog (implements pub.vlsolutions.swing.docking.FloatingDockableContainer)
            • com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog
              • com.pacbio.secondary.vis.gui.dialogs.AboutDialog (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.dialogs.GoToDialog (implements java.awt.event.ActionListener, java.beans.PropertyChangeListener)
              • com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog
              • com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog (implements java.awt.event.ActionListener)
              • com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase
              • com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener, java.beans.PropertyChangeListener, javax.swing.event.TableModelListener)
            • com.pacbio.secondary.vis.gui.dialogs.ProgressDialog (implements java.awt.event.ActionListener, com.pacbio.secondary.vis.gui.evt.IProgressNotifier)
            • com.pacbio.secondary.vis.gui.frame.VioletFrameBase
              • com.pacbio.secondary.vis.gui.frame.VioletFrameChanges (implements javax.swing.event.ChangeListener, java.awt.event.ComponentListener, pub.vlsolutions.swing.docking.event.DockableSelectionListener, pub.vlsolutions.swing.docking.event.DockableStateChangeListener, javax.swing.event.TableModelListener)
                • com.pacbio.secondary.vis.gui.frame.VioletFrameIO
                  • com.pacbio.secondary.vis.gui.frame.VioletFrameActions (implements java.awt.event.ActionListener)
                    • com.pacbio.secondary.vis.gui.frame.VioletFrameCreate
                      • com.pacbio.secondary.vis.gui.frame.VioletFrame
                        • com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop
                        • com.pacbio.secondary.vis.gui.frame.VioletFrameSummary
  • pub.vlsolutions.swing.docking.animation.ComponentAnimator
  • javax.swing.plaf.ComponentUI
    • javax.swing.plaf.ButtonUI
      • javax.swing.plaf.basic.BasicButtonUI
        • javax.swing.plaf.basic.BasicToggleButtonUI
          • pub.vlsolutions.swing.toolbars.VLButtonUI
    • javax.swing.plaf.LabelUI
      • javax.swing.plaf.basic.BasicLabelUI (implements java.beans.PropertyChangeListener)
        • pub.vlsolutions.swing.docking.ui.AutoHideButtonUI (implements java.beans.PropertyChangeListener)
    • javax.swing.plaf.PanelUI
      • javax.swing.plaf.basic.BasicPanelUI
        • pub.vlsolutions.swing.docking.ui.AutoHideButtonPanelUI (implements java.beans.PropertyChangeListener)
        • pub.vlsolutions.swing.docking.ui.AutoHideExpandPanelUI
        • pub.vlsolutions.swing.docking.ui.DetachedDockViewUI
      • pub.vlsolutions.swing.docking.ui.DockViewTitleBarUI (implements java.beans.PropertyChangeListener)
      • pub.vlsolutions.swing.docking.ui.DockViewUI
    • javax.swing.plaf.SplitPaneUI
      • javax.swing.plaf.basic.BasicSplitPaneUI
        • pub.vlsolutions.swing.docking.ui.DockingSplitPaneUI
    • javax.swing.plaf.TabbedPaneUI
      • javax.swing.plaf.basic.BasicTabbedPaneUI (implements javax.swing.SwingConstants)
        • com.pacificbiosciences.swing.laf.gem.GTabbedPaneUI
          • com.pacbio.secondary.vis.gui.dialogs.AlignedTabbedPaneUI
    • pub.vlsolutions.swing.toolbars.ToolBarGripperUI
  • pub.vlsolutions.swing.docking.CompoundDockable (implements pub.vlsolutions.swing.docking.Dockable)
  • com.pacbio.secondary.vis.common.utils.ContextHelpUtils
  • com.pacbio.secondary.vis.data.contig.ContigInfo
    • com.pacbio.secondary.vis.data.contig.DeNovoContigInfo (implements java.lang.Comparable<T>)
  • com.pacbio.secondary.vis.io.importer.DataFileInfo
  • com.pacbio.secondary.vis.data.session.DataStorageBase
    • com.pacbio.secondary.vis.data.session.DataStorage
  • com.pacbio.secondary.vis.svc.server.data.parser.DeNovoSummaryParser
  • com.pacbio.secondary.vis.data.session.DeNovoSummaryStorage
  • com.pacbio.secondary.vis.data.queue.DetailsDataRequest
  • com.pacbio.secondary.vis.data.queue.DetailsDataRequestsQueue
  • com.pacbio.secondary.vis.data.session.options.DetailsOptions (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.session.DetailsStorage
  • pub.vlsolutions.swing.docking.DockableActionCustomizer
  • pub.vlsolutions.swing.docking.DockableContainerFactory
    • pub.vlsolutions.swing.docking.DefaultDockableContainerFactory
      • pub.vlsolutions.swing.docking.TabFactory
  • pub.vlsolutions.swing.docking.event.DockableSelectionEvent
  • pub.vlsolutions.swing.docking.DockableState (implements java.lang.Comparable<T>)
  • pub.vlsolutions.swing.docking.event.DockableStateChangeEvent
  • pub.vlsolutions.swing.docking.event.DockableStateWillChangeEvent
  • pub.vlsolutions.swing.docking.event.DockEvent
    • pub.vlsolutions.swing.docking.event.DockDragEvent
    • pub.vlsolutions.swing.docking.event.DockDropEvent
  • pub.vlsolutions.swing.docking.DockGroup
  • pub.vlsolutions.swing.docking.event.DockingActionEvent (implements java.lang.Cloneable)
    • pub.vlsolutions.swing.docking.event.DockingActionDockableEvent
      • pub.vlsolutions.swing.docking.event.DockingActionAddDockableEvent
      • pub.vlsolutions.swing.docking.event.DockingActionCloseEvent
      • pub.vlsolutions.swing.docking.event.DockingActionCreateTabEvent
      • pub.vlsolutions.swing.docking.event.DockingActionSimpleStateChangeEvent
      • pub.vlsolutions.swing.docking.event.DockingActionSplitComponentEvent
      • pub.vlsolutions.swing.docking.event.DockingActionSplitDockableEvent
    • pub.vlsolutions.swing.docking.event.DockingActionSplitDockableContainerEvent
  • pub.vlsolutions.swing.docking.DockingBorderLayout (implements java.awt.LayoutManager2)
  • pub.vlsolutions.swing.docking.DockingConstants
  • pub.vlsolutions.swing.docking.DockingConstants.Hide
  • pub.vlsolutions.swing.docking.DockingConstants.Split
  • pub.vlsolutions.swing.docking.DockingContext
  • pub.vlsolutions.swing.docking.DockingPreferences
  • pub.vlsolutions.swing.docking.ui.DockingUISettings
  • pub.vlsolutions.swing.docking.DockingUtilities
  • pub.vlsolutions.swing.docking.DockKey
  • pub.vlsolutions.swing.docking.DragControlerFactory
  • com.pacbio.secondary.vis.common.utils.constants.EpiProPalette (implements java.io.Serializable)
  • com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.read.EpiProReadInfo.EpiProInfo
  • java.util.EventObject (implements java.io.Serializable)
    • javax.swing.event.ChangeEvent
      • com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent
  • com.pacbio.secondary.vis.io.export.ExportDataUtils
  • com.pacbio.secondary.vis.io.export.ExportRegionAsGFF
  • com.pacbio.secondary.vis.io.fasta.FastaFileReader
  • com.pacbio.secondary.vis.gui.table.renderer.FeatureRenderer (implements javax.swing.table.TableCellRenderer)
  • javax.swing.filechooser.FileFilter
    • com.pacbio.secondary.vis.common.utils.filefilter.FileFilterGeneric
  • com.pacbio.secondary.vis.io.indexer.indexinfo.FileIndexInfo
  • com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterDirectory (implements java.io.FilenameFilter)
  • com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterGeneric (implements java.io.FilenameFilter)
  • com.pacbio.secondary.vis.common.utils.filefilter.FilenameFilterMultipleExtensions (implements java.io.FilenameFilter)
  • com.pacbio.secondary.vis.common.utils.FileUtils
  • com.pacbio.secondary.vis.common.utils.constants.FontConstants
  • com.pacbio.secondary.vis.data.db.GeneDB
  • com.pacbio.secondary.vis.data.gene.GeneInfo
  • com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures
    • com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler
      • com.pacbio.secondary.vis.svc.server.hdf.GenomicDataBuilder
        • com.pacbio.secondary.vis.svc.server.hdf.GenomicDataServer
  • com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures.WsReadStructure (implements java.lang.Comparable<T>)
  • com.pacbio.secondary.vis.common.utils.GenomicUtils
  • com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewKeyListener (implements java.awt.event.KeyListener)
  • com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfoCalculator
  • com.pacbio.secondary.vis.io.gff.summary.GFFSummaryConstants
  • com.pacbio.secondary.vis.common.utils.constants.GraphConstants
  • com.pacbio.secondary.vis.data.graph.GraphPrimitive (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.graph.GraphStructure (implements java.io.Serializable)
  • com.pacbio.secondary.vis.gui.draw.utils.GraphUtil
  • com.pacbio.secondary.vis.common.utils.GUIUtils
  • com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5ChunkInfo
  • com.pacbio.secondary.vis.io.hdf.file.hdf5.HDF5File
    • com.pacbio.secondary.vis.io.hdf.file.bash5.BaseH5FileBase
    • com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileBase
      • com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5FileData
        • com.pacbio.secondary.vis.io.hdf.file.cmph5.CMPH5File
  • com.pacbio.secondary.vis.io.hdf.hyperslabinfo.HDF5HyperslabInfo
  • com.pacbio.secondary.vis.svc.server.HDFService
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceCallbackHandler
    • com.pacbio.secondary.vis.svc.hdf.client.HDFServiceCallbackImpl
  • com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex
  • com.pacbio.secondary.vis.svc.server.hdf.HDFServiceExperienceIndex.ExperienceIndexMetrics
  • com.pacbio.secondary.vis.svc.server.test.HDFServiceLocalTest
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.ExtensionMapper
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertions.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedInsertionsResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResults.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetAnnotatedResultsResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequence.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetConsensusSequenceResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNames.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetContigNamesResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeader.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetFileHeaderResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensus.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetIPDConsensusResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceExperienceIndexResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse
  • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub.GetServiceInfoResponse.Factory
  • com.pacbio.secondary.vis.svc.hdf.client.HDFServiceWrapper
  • com.pacbio.secondary.vis.io.hdf.test.HDFTest
  • org.apache.log4j.HTMLLayout
    • com.pacbio.secondary.vis.common.utils.SMRTHTMLLayout
  • com.pacbio.secondary.vis.data.db.IdeogramDB (implements java.io.Serializable)
  • com.pacbio.secondary.vis.gui.draw.print.IdeogramViewPrintingHelper (implements java.awt.print.Printable)
  • com.pacbio.secondary.vis.io.importer.ImportDataHelper
  • com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder
  • javax.swing.InputVerifier
    • com.pacbio.secondary.vis.gui.dialogs.FormattedDoubleInputVerifier
    • com.pacbio.secondary.vis.gui.dialogs.FormattedFieldInputVerifier
  • com.pacbio.secondary.vis.data.interval.Interval (implements com.pacbio.secondary.vis.data.interval.IntervalScale<T>)
  • com.pacbio.secondary.vis.data.interval.IntervalTree
  • com.pacbio.secondary.vis.data.interval.IntervalTreeNode
  • com.pacbio.secondary.vis.data.interval.IntervalTreeQuery
  • com.pacbio.secondary.vis.data.interval.IntervalTreeQuery.FilterVisitor (implements com.pacbio.secondary.vis.data.interval.IntervalTreeVisitor)
  • com.pacbio.secondary.vis.data.session.IPDConsensusStorage
  • com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileBuilder
  • com.pacbio.secondary.vis.svc.server.jnlp.JNLPFileWrapper
  • com.pacbio.secondary.vis.svc.server.JNLPService
  • com.pacbio.secondary.vis.svc.server.threads.JobInfo
  • com.pacbio.secondary.vis.data.xmlinfo.JobMetadataInfo
  • pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIcon (implements java.lang.Cloneable, javax.swing.Icon)
  • pub.vlsolutions.swing.tabbedpane.JTabbedPaneSmartIconManager (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelKeyListener
  • com.pacbio.secondary.vis.svc.server.data.KineticsComparator (implements java.util.Comparator<T>)
  • com.pacbio.secondary.vis.io.hdf.constants.LibraryConstants
  • com.pacbio.secondary.vis.data.filesystem.LocalFileNode
  • com.pacbio.secondary.vis.data.locus.Locus (implements java.lang.Comparable<T>)
  • com.pacbio.secondary.vis.common.utils.LoggerUtils
  • com.pacbio.secondary.vis.data.marker.Marker (implements java.lang.Comparable<T>)
  • com.pacbio.secondary.vis.data.marker.MarkerCollection
  • com.pacbio.secondary.vis.data.marker.MarkerComparator (implements java.util.Comparator<T>)
  • com.pacbio.secondary.vis.common.utils.constants.MathConstants
  • com.pacbio.secondary.vis.common.collection.MathUtility
  • com.pacbio.secondary.vis.gui.control.treetable.MergeSort
  • com.pacbio.secondary.vis.common.utils.MessageUtils
  • com.pacbio.secondary.vis.data.db.MotifData
  • com.pacbio.secondary.vis.data.db.MotifsDB
  • com.pacbio.secondary.vis.io.motifs.MotifsReader
  • java.awt.event.MouseAdapter (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener)
    • com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel.DeNovoTablePanelMouseListener
    • com.pacbio.secondary.vis.gui.panels.GenomicTablePanel.GenomicTablePanelMouseListener
    • com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseListener
    • com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel.SelectionInfoPanelMouseListener
  • java.awt.event.MouseMotionAdapter (implements java.awt.event.MouseMotionListener)
    • com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents.GenomicViewMouseMotionListener
      • com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect.GenomicViewInspectMouseMotionListener
  • com.pacbio.secondary.vis.common.collection.MultiIterator<T> (implements java.util.Iterator<E>)
  • com.pacbio.secondary.vis.gui.dialogs.OpenRemoteDataHelper
  • com.pacbio.secondary.vis.common.utils.constants.PanelConstants
  • com.pacbio.secondary.vis.common.utils.PerformanceUtils
  • com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog.myActionListener (implements java.awt.event.ActionListener)
  • com.pacbio.secondary.vis.common.utils.constants.ProgramConstants
  • com.pacbio.secondary.vis.common.utils.ProgramGlobals
  • com.pacbio.secondary.vis.common.utils.ProgramUtils
  • com.pacbio.secondary.vis.common.utils.PropertiesHelper (implements java.io.Serializable)
  • com.pacbio.secondary.vis.io.hdf.data.RawRead
  • com.pacbio.secondary.vis.data.read.ReadInfo
    • com.pacbio.secondary.vis.data.read.EpiProReadInfo
  • com.pacbio.secondary.vis.data.xmlinfo.ReferenceInfo
  • com.pacbio.secondary.vis.data.session.ReferenceSequenceStorage
  • com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.RegionsOfInterestHyperlinkListener (implements javax.swing.event.HyperlinkListener)
  • com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest (implements java.io.Serializable)
  • pub.vlsolutions.swing.docking.RelativeDockablePosition
  • com.pacbio.secondary.vis.data.filesystem.RemoteFile
  • com.pacbio.secondary.vis.data.filesystem.RemoteFileNode
  • com.pacbio.secondary.vis.common.utils.ResourceUtils
  • pub.vlsolutions.swing.toolbars.RolloverIcon (implements javax.swing.Icon)
  • pub.vlsolutions.swing.toolbars.RoundedBorder (implements javax.swing.border.Border)
  • com.pacbio.secondary.vis.svc.server.data.RStartComparator (implements java.util.Comparator<T>)
  • com.pacbio.secondary.vis.common.utils.RuntimeConfigUtils
  • com.pacbio.secondary.vis.data.xmlinfo.SampleInfo
  • com.pacbio.secondary.vis.common.utils.ScreenCaptureUtils
  • com.pacbio.secondary.vis.svc.server.utils.ServiceUtils
  • com.pacbio.secondary.vis.data.session.SessionDataHelper (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.session.timer.SessionDataTimer
  • pub.vlsolutions.swing.docking.ShadowBorder (implements javax.swing.border.Border)
  • pub.vlsolutions.swing.tabbedpane.SmartIconJButton (implements javax.swing.Icon, java.beans.PropertyChangeListener)
  • com.pacbio.secondary.vis.update.SMRTViewUpdater
  • com.pacbio.secondary.vis.common.collection.SortedMultiIterator<T> (implements java.util.Iterator<E>)
  • com.pacbio.secondary.vis.svc.server.data.StrandComparator (implements java.util.Comparator<T>)
  • com.pacbio.secondary.vis.io.hdf.streaming.StreamingDataConsumer
    • com.pacbio.secondary.vis.io.hdf.streaming.UCharStreamingDataConsumer
    • com.pacbio.secondary.vis.io.hdf.streaming.UIntStreamingDataConsumer
  • com.pacbio.secondary.vis.common.utils.StringUtils
  • org.apache.axis2.client.Stub
    • com.pacbio.secondary.vis.svc.hdf.client.auto.HDFServiceStub
  • org.apache.axis2.client.Stub
    • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub
  • com.pacbio.secondary.vis.common.collection.SweepLineIterator<T> (implements java.util.Iterator<E>)
  • com.pacbio.secondary.vis.common.collection.SweepLineIterator.CutLine (implements com.pacbio.secondary.vis.data.interval.IntervalScale<T>)
  • javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
    • com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper.UpdateDetailsThreadHelper
    • com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper.UpdateInsertionsThreadHelper
    • com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper.ThreadHelper
    • com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper.ThreadHelper
  • pub.vlsolutions.swing.docking.TabbedContainerActions
  • com.pacbio.secondary.vis.data.xmlinfo.TemplateInfo
  • com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer
    • com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer
    • com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer
  • java.lang.Thread (implements java.lang.Runnable)
    • com.pacbio.secondary.vis.gui.frame.VioletFrameChanges.setOptimumZoomFactorsThreaded
    • com.pacbio.secondary.vis.svc.server.threads.VisWorkerThread
    • com.pacbio.secondary.vis.svc.server.threads.VisWorkSenderThread
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • com.pacbio.secondary.vis.common.utils.exception.FileFormatException
      • com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx
      • com.pacbio.secondary.vis.common.utils.exception.IntervalTreeException
        • com.pacbio.secondary.vis.common.utils.exception.InsertNodeException
      • pub.vlsolutions.swing.docking.ws.WorkspaceException
  • java.util.TimerTask (implements java.lang.Runnable)
    • com.pacbio.secondary.vis.data.session.timer.SessionDataTimerTask
  • pub.vlsolutions.swing.toolbars.ToolBarButtonBorder (implements javax.swing.border.Border)
  • pub.vlsolutions.swing.toolbars.ToolBarConstraints
  • pub.vlsolutions.swing.toolbars.ToolBarIO
  • pub.vlsolutions.swing.toolbars.ToolBarIOReadInfo
  • pub.vlsolutions.swing.toolbars.ToolBarPanelBorder (implements javax.swing.border.Border)
  • pub.vlsolutions.swing.toolbars.ToolBarPanelLayout (implements java.awt.LayoutManager2)
  • pub.vlsolutions.swing.toolbars.ToolBarPersistence (implements java.lang.Runnable)
  • com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo
  • com.pacbio.secondary.vis.gui.draw.track.TrackDrawInfo
  • com.pacbio.secondary.vis.data.session.tracks.TracksDataInfoList
  • com.pacbio.secondary.vis.io.hdf.data.UCharMatrixArray
    • com.pacbio.secondary.vis.io.hdf.data.ConsensusCallsTable
  • com.pacbio.secondary.vis.io.hdf.data.UIntMatrixArray
    • com.pacbio.secondary.vis.io.hdf.data.AlignmentIndexTable
    • com.pacbio.secondary.vis.io.hdf.data.IPDConsensusTable
    • com.pacbio.secondary.vis.io.hdf.data.SortedRefIndexTable
  • com.pacbio.secondary.vis.common.collection.UndoIterator<T> (implements java.util.Iterator<E>)
  • com.pacbio.secondary.vis.io.update.UpdateDetailsDataHelper
  • com.pacbio.secondary.vis.io.update.UpdateInsertionsDataHelper
  • com.pacbio.secondary.vis.io.update.UpdateModificationsDataHelper
  • com.pacbio.secondary.vis.update.UpdaterUtils
  • com.pacbio.secondary.vis.io.update.UpdateVariantsDataHelper
  • com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue (implements java.io.Serializable)
  • com.pacbio.secondary.vis.data.variableresolution.record.VariableValuesTypeDefs
  • com.pacbio.secondary.vis.svc.server.VersionService
  • com.pacbio.secondary.vis.gui.draw.views.ViewLayoutInfo
  • com.pacbio.secondary.vis.gui.app.VioletAppBase
    • com.pacbio.secondary.vis.gui.app.VioletApp
      • com.pacbio.secondary.vis.gui.app.DesktopApp
      • com.pacbio.secondary.vis.gui.app.LocalTestApp
      • com.pacbio.secondary.vis.gui.app.WebStartApp
  • com.pacbio.secondary.vis.io.importer.VioletFileAnalyzer
  • com.pacbio.secondary.vis.svc.server.VisService
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceCallbackHandler
    • com.pacbio.secondary.vis.svc.vis.client.VisServiceCallbackImpl
  • com.pacbio.secondary.vis.svc.server.test.VisServiceLocalTest
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.ExtensionMapper
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDefaultDirectoryResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryList.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetDirectoryListResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequence.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFastaSequenceResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFile.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFileResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformation.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetFilesInformationResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFile.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetGZippedFileResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetMetadataInfoResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetReferenceInfoResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetServiceInfoResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.GetTracksListInfoResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFile.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.PutFileResponse.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsContigInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsFileInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsJobMetadataInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsReferenceInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo
  • com.pacbio.secondary.vis.svc.vis.client.auto.VisServiceStub.WsTrackInfo.Factory
  • com.pacbio.secondary.vis.svc.vis.client.VisServiceWrapper
  • com.pacbio.secondary.vis.svc.server.threads.VisThreadPool
  • com.pacbio.secondary.vis.svc.server.threads.VisWorkDoneQueue
  • com.pacbio.secondary.vis.svc.server.threads.VisWorkToDoQueue
  • pub.vlsolutions.swing.toolbars.VLToolBarLayout (implements java.awt.LayoutManager2)
  • com.pacbio.secondary.vis.common.utils.WebBrowserUtils
  • com.pacbio.secondary.vis.gui.panels.WholeGenomePanel.CtgInfo (implements java.lang.Comparable<T>)
  • pub.vlsolutions.swing.docking.ws.Workspace
  • com.pacbio.secondary.vis.gui.desktop.WorkspaceManager
  • com.pacbio.secondary.vis.svc.server.data.WsContigInfo (implements java.lang.Comparable<T>, java.io.Serializable)
  • pub.vlsolutions.swing.docking.ws.WSDesktop
  • pub.vlsolutions.swing.docking.ws.WSDockKey
  • com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsFileInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc (implements java.lang.Comparable<T>, java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsRead (implements java.lang.Comparable<T>, java.io.Serializable)
    • com.pacbio.secondary.vis.svc.server.data.WsReadEx (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsResults (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsResultsInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.WsTrackInfo (implements java.io.Serializable)
  • com.pacbio.secondary.vis.svc.server.data.parser.XMLInfoBaseParser
    • com.pacbio.secondary.vis.svc.server.data.parser.MetadataInfoParser
    • com.pacbio.secondary.vis.svc.server.data.parser.ReferenceInfoParser
    • com.pacbio.secondary.vis.svc.server.data.parser.TrackInfoParser
  • com.pacbio.secondary.vis.common.utils.constants.XMLInfoConstants
  • com.pacbio.secondary.vis.common.utils.XMLObjectSerializerUtils

Interface Hierarchy

• pub.vlsolutions.swing.docking.animation.AnimationListener
• pub.vlsolutions.swing.toolbars.BackgroundPainter
• java.lang.Comparable<T>
  • com.pacbio.secondary.vis.data.interval.IntervalScale<T>
• pub.vlsolutions.swing.docking.Dockable
• pub.vlsolutions.swing.docking.DockableContainer
  • pub.vlsolutions.swing.docking.SingleDockableContainer
  • pub.vlsolutions.swing.docking.TabbedDockableContainer
• pub.vlsolutions.swing.docking.DockableDragSource
• pub.vlsolutions.swing.docking.DockableResolver
• pub.vlsolutions.swing.docking.event.DockableSelectionListener
• pub.vlsolutions.swing.docking.event.DockableStateChangeListener
• pub.vlsolutions.swing.docking.event.DockableStateWillChangeListener
• pub.vlsolutions.swing.docking.DockDropReceiver
• pub.vlsolutions.swing.docking.event.DockingActionListener
• java.util.EventListener
  • pub.vlsolutions.swing.docking.DragControler (also extends java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • java.awt.event.MouseListener
    • pub.vlsolutions.swing.docking.DragControler (also extends java.awt.event.MouseMotionListener)
  • java.awt.event.MouseMotionListener
    • pub.vlsolutions.swing.docking.DragControler (also extends java.awt.event.MouseListener)
• pub.vlsolutions.swing.docking.FloatingDockableContainer
• com.pacbio.secondary.vis.gui.evt.IChangeNotifier
  • com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer (also extends java.lang.Iterable<T>)
• com.pacbio.secondary.vis.data.interval.IntervalTreeVisitor
• com.pacbio.secondary.vis.gui.evt.IProgressNotifier
• java.lang.Iterable<T>
  • com.pacbio.secondary.vis.data.variableresolution.model.IVariableResolutionDataModelServer (also extends com.pacbio.secondary.vis.gui.evt.IChangeNotifier)
• javax.swing.tree.TreeModel
  • com.pacbio.secondary.vis.gui.control.treetable.TreeTableModel

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • com.pacbio.secondary.vis.data.base.BaseDataModel.eDataType
    • com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo.eTrackStatus
    • com.pacbio.secondary.vis.data.session.tracks.TrackDataInfo.eTrackSource
    • com.pacbio.secondary.vis.gui.app.VioletAppBase.APP_TYPE
    • com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent.GenomicViewEventType
    • com.pacbio.secondary.vis.io.importer.DataFileInfo.eFileType
    • com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader.vcf_version
    • pub.vlsolutions.swing.docking.AutoHidePolicy.ExpandMode
    • pub.vlsolutions.swing.docking.DockableContainerFactory.ParentType
    • pub.vlsolutions.swing.docking.DockableState.Location