Hierarchy For All Packages

Package Hierarchies:

• demo,
• org.biojava.nbio.structure.align.gui,
• org.biojava.nbio.structure.align.gui.aligpanel,
• org.biojava.nbio.structure.align.gui.autosuggest,
• org.biojava.nbio.structure.align.gui.jmol,
• org.biojava.nbio.structure.align.webstart,
• org.biojava.nbio.structure.gui,
• org.biojava.nbio.structure.gui.events,
• org.biojava.nbio.structure.gui.util,
• org.biojava.nbio.structure.gui.util.color,
• org.biojava.nbio.structure.symmetry.gui,
• org.biojava.nbio.structure.symmetry.jmolScript

Class Hierarchy

• java.lang.Object
  • org.biojava.nbio.structure.align.gui.AboutDialog
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • org.biojava.nbio.structure.align.gui.ChooseDirAction
  • org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol (implements java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener)
    • org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol
    • org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol (implements javax.swing.event.ChangeListener)
  • org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
  • demo.AFPFromFasta
  • org.biojava.nbio.structure.gui.util.AlignedPosition
  • org.biojava.nbio.structure.align.gui.AlignmentCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.nbio.structure.gui.util.AlignmentCalc (implements java.lang.Runnable)
  • org.biojava.nbio.structure.align.gui.AlignmentCalcDB (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • demo.AlignmentGuiDemo
  • org.biojava.nbio.structure.align.gui.aligpanel.AligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.nbio.structure.align.webstart.AligUIManager
  • org.biojava.nbio.structure.align.gui.jmol.AtomInfo
  • org.biojava.nbio.structure.align.gui.jmol.AtomInfoParser
  • org.biojava.nbio.structure.gui.BiojavaJmol
  • org.biojava.nbio.structure.align.webstart.BrowserOpener
  • org.biojava.nbio.structure.symmetry.jmolScript.ColorConverter
  • java.awt.color.ColorSpace (implements java.io.Serializable)
    • org.biojava.nbio.structure.gui.util.color.HSVColorSpace
  • org.biojava.nbio.structure.gui.util.color.ColorUtils
  • 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.JPanel (implements javax.accessibility.Accessible)
          • org.biojava.nbio.structure.align.gui.ConfigPDBInstallPanel
          • org.biojava.nbio.structure.align.gui.DBSearchGUI
          • org.biojava.nbio.structure.gui.util.color.GradientPanel
          • org.biojava.nbio.structure.align.gui.GUIAlignmentProgressListener (implements java.awt.event.ActionListener, org.biojava.nbio.structure.align.events.AlignmentProgressListener)
          • org.biojava.nbio.structure.gui.JMatrixPanel
          • org.biojava.nbio.structure.align.gui.JPrintPanel (implements java.awt.event.ActionListener, java.awt.print.Printable)
            • org.biojava.nbio.structure.align.gui.AlignmentTextPanel
            • org.biojava.nbio.structure.align.gui.aligpanel.AligPanel (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
            • org.biojava.nbio.structure.align.gui.jmol.JmolPanel (implements java.awt.event.ActionListener)
            • org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
          • org.biojava.nbio.structure.align.gui.MemoryMonitor
          • org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface (implements java.lang.Runnable)
          • org.biojava.nbio.structure.gui.util.PDBDirPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.util.PDBServerPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.util.PDBUploadPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.ScaleableMatrixPanel (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
            • org.biojava.nbio.structure.align.gui.DotPlotPanel
          • org.biojava.nbio.structure.gui.ScaleableMatrixPanel.GradientRenderer (implements javax.swing.ListCellRenderer<E>)
          • org.biojava.nbio.structure.gui.util.ScopSelectPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.util.SelectMultiplePanel
          • org.biojava.nbio.structure.align.gui.SelectPDBPanel (implements org.biojava.nbio.structure.gui.util.StructurePairSelector)
          • org.biojava.nbio.structure.gui.SequenceDisplay (implements javax.swing.event.ChangeListener)
          • org.biojava.nbio.structure.gui.util.SequenceScalePanel
        • javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • javax.swing.JTextField (implements javax.swing.SwingConstants)
            • org.biojava.nbio.structure.align.gui.autosuggest.JAutoSuggest
            • org.biojava.nbio.structure.align.gui.aligpanel.MultipleStatusDisplay (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
            • org.biojava.nbio.structure.align.gui.aligpanel.StatusDisplay (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener, java.awt.event.WindowListener)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.biojava.nbio.structure.align.gui.AlignmentGui
            • org.biojava.nbio.structure.gui.util.AlternativeAlignmentFrame
            • org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI
            • org.biojava.nbio.structure.align.gui.ParameterGUI
            • org.biojava.nbio.structure.symmetry.gui.SymmetryGui
  • org.biojava.nbio.structure.gui.util.color.ContinuousColorMapperTransform (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper)
    • org.biojava.nbio.structure.gui.util.color.LogColorMapper
    • org.biojava.nbio.structure.gui.util.color.SqrtColorMapper
  • demo.CookBook
  • org.biojava.nbio.structure.gui.util.CoordManager
  • org.biojava.nbio.structure.align.gui.DBResultTable (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.autosuggest.DefaultAutoSuggestProvider (implements org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider)
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
  • org.biojava.nbio.structure.gui.util.color.DefaultMatrixMapper (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper)
  • demo.DemoAlignmentFromFasta
  • demo.DemoCE
  • demo.DemoCeSymm
  • demo.DemoFATCAT
  • demo.DemoMultipleMC
  • demo.DemoNWALignment
  • demo.DemoQuatSymmetryJmol
  • demo.DemoRotationAxis
  • demo.DemoShowBiolAssembly
  • demo.DemoShowCATHDomain
  • demo.DemoShowLargeAssembly
  • demo.DemoShowValidationResults
  • demo.DemoStructureFromFasta
  • demo.DemoSW3DAligner
  • org.biojava.nbio.structure.align.gui.DisplayAFP
  • java.awt.FlowLayout (implements java.awt.LayoutManager, java.io.Serializable)
    • org.biojava.nbio.structure.gui.WrapLayout
  • org.biojava.nbio.structure.gui.util.color.GradientMapper (implements org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper, java.util.Map<K,V>)
  • org.biojava.nbio.structure.align.gui.GUIFarmJobRunnable (implements java.lang.Runnable)
  • org.biojava.nbio.structure.align.gui.HelpDialog
  • org.biojava.nbio.structure.gui.events.JmolAlignedPositionListener (implements org.biojava.nbio.structure.gui.events.AlignmentPositionListener)
  • org.biojava.nbio.structure.align.gui.jmol.JmolPanel.JmolLoggerAdapter (implements org.jmol.util.LoggerInterface)
  • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator
    • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorH
    • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorC1
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorCn
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorDn
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorI
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorO
      • org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorT
  • org.biojava.nbio.structure.align.gui.jmol.JmolTools
  • org.biojava.nbio.structure.gui.JmolViewerImpl (implements org.biojava.nbio.structure.gui.StructureViewer)
  • org.biojava.nbio.structure.align.webstart.JNLPProxy
  • java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • org.biojava.nbio.structure.align.gui.jmol.RasmolCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  • org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator (implements org.biojava.nbio.structure.gui.util.color.ColorInterpolator)
  • org.biojava.nbio.structure.align.gui.MenuCreator
  • org.biojava.nbio.structure.gui.util.MenuCreator
  • org.biojava.nbio.structure.align.gui.MenuCreator.DotPlotListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MultipleAlignmentCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
  • org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay
  • org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanelMouseMotionListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.nbio.structure.align.gui.MyAlignmentLoadListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MyDistMaxListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MyExportListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.jmol.MyJmolStatusListener (implements org.jmol.api.JmolStatusListener)
  • org.biojava.nbio.structure.align.gui.MyOpenPdbFileListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.MySaveFileListener (implements java.awt.event.ActionListener)
  • javax.swing.RowSorter<M>
    • javax.swing.DefaultRowSorter<M,I>
      • javax.swing.table.TableRowSorter<M>
        • org.biojava.nbio.structure.align.gui.MyTableRowSorter
  • org.biojava.nbio.structure.align.gui.autosuggest.SCOPAutoSuggestProvider (implements org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider)
  • org.biojava.nbio.structure.gui.util.ScopInstallationInstance
  • org.biojava.nbio.structure.gui.SelectionImpl (implements org.biojava.nbio.structure.gui.Selection)
  • org.biojava.nbio.structure.gui.util.SequenceMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.biojava.nbio.structure.align.gui.ShowPDBIDListener (implements java.awt.event.ActionListener)
  • demo.ShowStructureInJmol
  • org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay
  • javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
    • org.biojava.nbio.structure.align.gui.StructureLoaderThread
  • org.biojava.nbio.structure.symmetry.gui.SymmetryCalc (implements org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable)
  • org.biojava.nbio.structure.symmetry.gui.SymmetryDisplay
  • org.biojava.nbio.structure.symmetry.gui.SymmetryListener (implements java.awt.event.ActionListener)
  • org.biojava.nbio.structure.align.gui.SystemInfo
  • demo.WebStartClientDemo
  • org.biojava.nbio.structure.align.webstart.WebStartDBSearch
  • org.biojava.nbio.structure.align.webstart.WebStartDBSearchResults
  • org.biojava.nbio.structure.align.webstart.WebStartMain

Interface Hierarchy

• org.biojava.nbio.structure.gui.events.AlignmentPositionListener
• org.biojava.nbio.structure.align.gui.autosuggest.AutoSuggestProvider
• org.biojava.nbio.structure.gui.util.color.ColorInterpolator
• org.biojava.nbio.structure.gui.util.color.ContinuousColorMapper
• java.lang.Runnable
  • org.biojava.nbio.structure.align.gui.AlignmentCalculationRunnable
• org.biojava.nbio.structure.gui.Selection
• org.biojava.nbio.structure.gui.util.StructurePairSelector
• org.biojava.nbio.structure.gui.StructureViewer

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.nbio.structure.gui.util.color.LinearColorInterpolator.InterpolationDirection
    • org.biojava.nbio.structure.gui.RenderStyle