Hierarchy For All Packages

Package Hierarchies:

org.biojava.spice, org.biojava.spice.alignment, org.biojava.spice.config, org.biojava.spice.das, org.biojava.spice.feature, org.biojava.spice.gui, org.biojava.spice.gui.aligchooser, org.biojava.spice.gui.alignment, org.biojava.spice.gui.alignmentchooser, org.biojava.spice.gui.logging, org.biojava.spice.gui.msdkeyword, org.biojava.spice.jmol, org.biojava.spice.manypanel, org.biojava.spice.manypanel.drawable, org.biojava.spice.manypanel.eventmodel, org.biojava.spice.manypanel.managers, org.biojava.spice.manypanel.renderer, org.biojava.spice.server, org.biojava.spice.utils

Class Hierarchy

• class java.lang.Object
  • class org.biojava.spice.manypanel.managers.AbstractAlignmentManager
    • class org.biojava.spice.manypanel.managers.AlignmentManager
  • class org.biojava.spice.manypanel.managers.AbstractChainManager (implements org.biojava.spice.manypanel.managers.ObjectManager)
    • class org.biojava.spice.manypanel.managers.SequenceManager (implements org.biojava.spice.manypanel.managers.ObjectManager)
    • class org.biojava.spice.manypanel.managers.StructureManager (implements org.biojava.spice.manypanel.managers.ObjectManager)
  • class org.biojava.spice.feature.AbstractFeature (implements java.lang.Cloneable, org.biojava.spice.feature.Feature)
    • class org.biojava.spice.feature.FeatureImpl (implements org.biojava.spice.feature.Feature)
    • class org.biojava.spice.feature.HistogramFeature
  • class org.biojava.spice.gui.AbstractPopupFrame (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
    • class org.biojava.spice.gui.logging.LogPopupFrame
    • class org.biojava.spice.manypanel.renderer.SegmentPopupFrame (implements org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener)
  • class org.biojava.spice.feature.AbstractSegment (implements java.lang.Cloneable, org.biojava.spice.feature.Segment)
    • class org.biojava.spice.feature.HistogramSegment
    • class org.biojava.spice.feature.SegmentImpl
  • class javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • class org.biojava.spice.config.DasSourcePanelTableModel
  • class org.biojava.spice.gui.aligchooser.AligLabel
  • class org.biojava.spice.gui.alignment.AlignmentCalc (implements java.lang.Runnable)
  • class org.biojava.spice.gui.alignmentchooser.AlignmentChooser
  • class org.biojava.spice.gui.aligchooser.AlignmentFilterActionListener (implements java.awt.event.ActionListener)
  • class org.biojava.spice.gui.aligchooser.AlignmentItemListener
  • class org.biojava.spice.manypanel.renderer.AlignmentPanelMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • class org.biojava.spice.gui.AlignmentServerSwitcher
  • class org.biojava.spice.gui.aligchooser.AlignmentSortPopup (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  • class org.biojava.spice.manypanel.AlignmentTool
  • class org.biojava.spice.das.AlignmentTools
  • class org.biojava.spice.gui.alignmentchooser.AligPanelListener (implements java.awt.event.ComponentListener)
  • class org.biojava.spice.jmol.AtomInfo
  • class org.biojava.spice.jmol.AtomInfoParser
  • class BioException
    • class org.biojava.spice.config.ConfigurationException
  • class org.biojava.spice.gui.BrowseMenuListener (implements java.awt.event.ActionListener)
  • class org.biojava.spice.utils.BrowserOpener
  • class org.biojava.spice.manypanel.renderer.ChainRendererMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • class org.biojava.spice.utils.CliTools
  • class org.biojava.spice.gui.CloseableTabbedPane.ClosingIcon (implements javax.swing.Icon)
  • class org.biojava.spice.utils.CollectTools
  • class org.biojava.spice.utils.ColorTools
  • class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • class java.awt.Container
      • class javax.swing.JComponent (implements java.io.Serializable)
        • class javax.swing.JLayeredPane (implements javax.accessibility.Accessible)
          • class org.biojava.spice.manypanel.renderer.DasScrollPaneColumnHeader
        • class javax.swing.JPanel (implements javax.accessibility.Accessible)
          • class org.biojava.spice.manypanel.renderer.AbstractChainRenderer (implements org.biojava.spice.manypanel.eventmodel.DasSourceListener, org.biojava.spice.manypanel.eventmodel.FeatureListener, org.biojava.spice.manypanel.renderer.ObjectRenderer)
            • class org.biojava.spice.manypanel.renderer.SequenceRenderer
            • class org.biojava.spice.manypanel.renderer.StructureRenderer
          • class org.biojava.spice.manypanel.renderer.AlignmentCursorPanel
          • class org.biojava.spice.manypanel.renderer.AlignmentPanel
          • class org.biojava.spice.manypanel.renderer.AlignmentRenderer
          • class org.biojava.spice.manypanel.renderer.ArrowPanel
          • class org.biojava.spice.manypanel.BrowserPane (implements javax.swing.event.ChangeListener, org.biojava.spice.manypanel.eventmodel.DasSourceListener)
          • class org.biojava.spice.gui.ConfigPanel (implements org.biojava.spice.config.ConfigurationListener)
          • class org.biojava.spice.manypanel.renderer.CursorPanel (implements org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener)
          • class org.biojava.spice.manypanel.renderer.DasScrollPaneRowHeader (implements org.biojava.spice.manypanel.eventmodel.DasSourceListener)
          • class org.biojava.spice.manypanel.renderer.DasSourcePanel (implements org.biojava.spice.manypanel.eventmodel.FeatureListener, org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener)
            • class org.biojava.spice.manypanel.renderer.DasSourcePanelHeader
          • class org.biojava.spice.gui.logging.LoggingPanel
          • class org.biojava.spice.gui.MemoryMonitor
          • class org.biojava.spice.gui.MemoryMonitor.Surface (implements java.lang.Runnable)
          • class org.biojava.spice.gui.SelectionPanel
          • class org.biojava.spice.manypanel.renderer.SequenceScalePanel
            • class org.biojava.spice.manypanel.renderer.StructureScalePanel
          • class org.biojava.spice.gui.alignmentchooser.ShowAligPanel
          • class org.biojava.spice.SpiceApplication (implements org.biojava.spice.config.ConfigurationListener, org.biojava.spice.SPICEFrame)
          • class org.biojava.spice.gui.StatusPanel (implements org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener)
          • class org.biojava.spice.manypanel.renderer.StatusPanel
          • class org.biojava.spice.jmol.StructurePanel (implements org.biojava.spice.jmol.JmolCommander)
        • class javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          • class org.biojava.spice.gui.aligchooser.StructureAlignmentChooser (implements org.biojava.spice.manypanel.eventmodel.StructureAlignmentListener)
        • class org.biojava.spice.manypanel.renderer.JScrollPaneCorner
        • class javax.swing.JTabbedPane (implements javax.accessibility.Accessible, java.io.Serializable, javax.swing.SwingConstants)
          • class org.biojava.spice.gui.CloseableTabbedPane
            • class org.biojava.spice.gui.SpiceTabbedPane (implements java.awt.event.WindowListener)
        • class javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • class javax.swing.JTextField (implements javax.swing.SwingConstants)
            • class org.biojava.spice.gui.StructureCommandPanel
      • class java.awt.Window (implements javax.accessibility.Accessible)
        • class java.awt.Dialog
          • class javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class org.biojava.spice.gui.AboutDialog
            • class org.biojava.spice.gui.DasSourceDialog
            • class org.biojava.spice.gui.OpenDialog
            • class org.biojava.spice.gui.TechInfoDialog
        • class java.awt.Frame (implements java.awt.MenuContainer)
          • class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class org.biojava.spice.gui.alignment.AlignmentGui
            • class org.biojava.spice.gui.alignment.AlternativeAlignmentFrame
  • class org.biojava.spice.manypanel.renderer.ComponentResizedChainListener (implements java.awt.event.ComponentListener)
  • class org.biojava.spice.config.ConfigGui
  • class org.biojava.spice.manypanel.renderer.CoordManager
  • class Das1Source
    • class org.biojava.spice.das.SpiceDasSource
  • class org.biojava.spice.config.DasSourceConfigPanel
  • class org.biojava.spice.manypanel.eventmodel.DasSourceEvent
  • class org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • class org.biojava.spice.config.ConfigXMLHandler
    • class org.biojava.spice.gui.msdkeyword.MSDContentHandler
  • class org.biojava.spice.gui.msdkeyword.Deposition
  • class org.biojava.spice.manypanel.drawable.DrawableDasSource (implements org.biojava.spice.manypanel.drawable.Drawable, org.biojava.spice.manypanel.eventmodel.FeatureListener)
  • class org.biojava.spice.manypanel.drawable.DrawableSequence (implements org.biojava.spice.manypanel.drawable.Drawable)
    • class org.biojava.spice.manypanel.drawable.DrawableStructure
  • class org.biojava.spice.manypanel.renderer.DrawUtils
  • class org.biojava.spice.feature.FeatureComparator (implements java.util.Comparator)
  • class org.biojava.spice.manypanel.managers.FeatureManager (implements org.biojava.spice.manypanel.managers.ObjectManager)
  • class org.biojava.spice.feature.FeatureMapComparator (implements java.util.Comparator)
  • class org.biojava.spice.manypanel.renderer.FeatureRenderer
  • class org.biojava.spice.manypanel.renderer.HistogramPainter
  • class JmolAdapter
    • class org.biojava.spice.jmol.SpiceJmolAdapter
  • class org.biojava.spice.jmol.JmolSpiceTranslator
  • class org.biojava.spice.jmol.JmolUtils
  • class org.biojava.spice.utils.JNLPProxy
  • class java.awt.event.KeyAdapter (implements java.awt.event.KeyListener)
    • class org.biojava.spice.gui.StructureCommandListener (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
  • class org.biojava.spice.gui.logging.LoggingPanel.Column
  • class org.biojava.spice.gui.LoggingPanelManager
  • class org.biojava.spice.gui.aligchooser.MenuAlignmentListener
  • class org.biojava.spice.gui.MenuCreator
  • class java.awt.event.MouseAdapter (implements java.awt.event.MouseListener)
    • class org.biojava.spice.gui.CloseableTabbedPane.ClosingListener
    • class org.biojava.spice.gui.SelectionLockPopupListener
  • class org.biojava.spice.gui.msdkeyword.MSDKeywordSearch
  • class org.biojava.spice.gui.msdkeyword.MSDWindow
  • class org.biojava.spice.manypanel.renderer.PDB2SeqPositionMapper
  • class org.biojava.spice.config.PersistentConfig
  • class org.biojava.spice.gui.RainbowPainter
  • class org.biojava.spice.config.RegistryConfigIO (implements org.biojava.spice.config.ConfigurationListener, java.lang.Runnable)
  • class org.biojava.spice.config.RegistryConfiguration
  • class org.biojava.spice.ResourceManager
  • class org.biojava.spice.manypanel.renderer.RowHeaderMouseListener (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • class org.biojava.spice.gui.SaveLoadSession
  • class org.biojava.spice.manypanel.eventmodel.ScaleEvent
  • class org.biojava.spice.config.SearchDasSourceManager
  • class org.biojava.spice.feature.SegmentComparator (implements java.util.Comparator)
  • class org.biojava.spice.gui.SelectionLockMenuListener (implements java.awt.event.ActionListener)
  • class org.biojava.spice.utils.SendEmail
  • class org.biojava.spice.gui.SendEmailGui
  • class org.biojava.spice.manypanel.renderer.SeqToolTipListener (implements org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener)
  • class org.biojava.spice.Spice
  • class org.biojava.spice.gui.SpiceChainDisplay (implements javax.swing.event.ListSelectionListener)
  • class org.biojava.spice.server.SpiceClient
  • class org.biojava.spice.config.SpiceDefaults
  • class org.biojava.spice.manypanel.eventmodel.SpiceFeatureEvent
  • class org.biojava.spice.manypanel.SpiceLayeredPanel
  • class org.biojava.spice.gui.SpiceMenuListener (implements java.awt.event.ActionListener)
  • class org.biojava.spice.server.SpiceProtocol
  • class org.biojava.spice.server.SpiceServer
  • class org.biojava.spice.SpiceStartParameters
  • class org.biojava.spice.StartParameterFilter
  • class org.biojava.spice.alignment.StructureAlignment
  • class org.biojava.spice.alignment.StructureAlignmentBuilder
  • class org.biojava.spice.alignment.StructureAlignmentComparator (implements java.util.Comparator)
  • class org.biojava.spice.StructureBuilder
  • class org.biojava.spice.jmol.StructurePanelListener (implements org.biojava.spice.jmol.JmolCommander, org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener)
  • class org.biojava.spice.gui.TabEvent
  • class java.lang.Thread (implements java.lang.Runnable)
    • class org.biojava.spice.das.SingleFeatureThread
    • class org.biojava.spice.server.SpiceMultiServerThread
  • class org.biojava.spice.utils.UniProtAccessionCodeTools
  • class org.biojava.spice.server.UserChoosesSpiceDialog

Interface Hierarchy

• interface org.biojava.spice.config.ConfigurationListener
• interface org.biojava.spice.manypanel.eventmodel.DasSourceListener
• interface org.biojava.spice.manypanel.drawable.Drawable
• interface org.biojava.spice.feature.Feature
• interface org.biojava.spice.manypanel.eventmodel.FeatureListener
• interface org.biojava.spice.jmol.JmolCommander
• interface org.biojava.spice.manypanel.managers.ObjectManager
• interface org.biojava.spice.manypanel.Scaleable
  • interface org.biojava.spice.manypanel.renderer.ObjectRenderer
• interface org.biojava.spice.manypanel.eventmodel.ScaleListener
• interface org.biojava.spice.feature.Segment
• interface org.biojava.spice.manypanel.eventmodel.SpiceFeatureListener
• interface org.biojava.spice.SPICEFrame
• interface org.biojava.spice.manypanel.eventmodel.StructureAlignmentListener
• interface org.biojava.spice.gui.TabListener