Hierarchy For All Packages

Package Hierarchies:

com.jgoodies.looks.demo, com.jgoodies.uif_lite.component, com.jgoodies.uif_lite.panel, edu.sdsc.mbt, edu.sdsc.mbt.filters, edu.sdsc.mbt.image, edu.sdsc.mbt.util, edu.sdsc.mbt.viewables, edu.sdsc.mbt.viewers.GLViewerImpl, edu.sdsc.mbt.viewers.GLViewerImpl.util, edu.sdsc.mbt.viewers.StructureViewerImpl.pdb, edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io, edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util, edu.sdsc.mbt.viewers.StructureViewerImpl.util, edu.sdsc.mbt.viewers.StructureViewerImpl.vec, edu.sdsc.sirius.builder, edu.sdsc.sirius.dialogs, edu.sdsc.sirius.dialogs.TableImpl, edu.sdsc.sirius.export, edu.sdsc.sirius.io, edu.sdsc.sirius.monitors, edu.sdsc.sirius.rasmol, edu.sdsc.sirius.ray, edu.sdsc.sirius.util, edu.sdsc.sirius.viewers, edu.sdsc.sirius.viewers.RamachandranViewerImpl, edu.sdsc.sirius.viewers.SequenceViewerImpl, edu.sdsc.sirius.viewers.TreeViewer, edu.sdsc.sirius.workbench

Class Hierarchy

• class java.lang.Object
  • class javax.swing.text.AbstractDocument (implements javax.swing.text.Document, java.io.Serializable)
    • class javax.swing.text.PlainDocument
      • class edu.sdsc.sirius.util.LimitedLengthDocument
  • class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
  • class edu.sdsc.mbt.util.Algebra
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentService
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings
  • class edu.sdsc.sirius.io.AlnEntryLoader (implements edu.sdsc.sirius.io.FileEntryLoader)
  • class edu.sdsc.mbt.util.AminoAcidInfo
  • class edu.sdsc.sirius.rasmol.AminoColorScheme (implements edu.sdsc.sirius.rasmol.ColorScheme)
  • class edu.sdsc.mbt.AnnotationComponent (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.ArrowComponent
    • class edu.sdsc.mbt.HydrogenBondComponent
    • class edu.sdsc.mbt.LabelComponent
    • class edu.sdsc.mbt.MonitorComponent
    • class edu.sdsc.mbt.ResidueLabelComponent
    • class edu.sdsc.mbt.StericBumpComponent
  • class edu.sdsc.mbt.AnnotationComponentRegistry
  • class edu.sdsc.mbt.viewers.GLViewerImpl.AnnotationGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.ArrowGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.LabelGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.ResidueLabelGeometry
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom
  • class edu.sdsc.mbt.viewables.AtomColorByCharge (implements edu.sdsc.mbt.viewables.AtomColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.AtomColorByElement (implements edu.sdsc.mbt.viewables.AtomColor)
  • class edu.sdsc.mbt.viewables.AtomColorFactory (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.AtomColorRegistry
  • class edu.sdsc.mbt.viewables.AtomColorUniform (implements edu.sdsc.mbt.viewables.AtomColor, java.io.Serializable)
  • class edu.sdsc.mbt.filters.AtomFilter (implements edu.sdsc.mbt.filters.StructureComponentFilter)
    • class edu.sdsc.mbt.filters.CAlphaAtomFilter
  • class edu.sdsc.mbt.viewables.AtomLabelByAtomCompound (implements edu.sdsc.mbt.viewables.AtomLabel)
  • class edu.sdsc.mbt.viewables.AtomLabelByAtomElement (implements edu.sdsc.mbt.viewables.AtomLabel)
  • class edu.sdsc.mbt.viewables.AtomLabelByAtomName (implements edu.sdsc.mbt.viewables.AtomLabel)
  • class edu.sdsc.mbt.viewables.AtomLabelByChainId (implements edu.sdsc.mbt.viewables.AtomLabel)
  • class edu.sdsc.mbt.viewables.AtomLabelNone (implements edu.sdsc.mbt.viewables.AtomLabel)
  • class edu.sdsc.mbt.viewables.AtomLabelRegistry
  • class edu.sdsc.mbt.viewables.AtomRadiusByConstant (implements edu.sdsc.mbt.viewables.AtomRadius)
  • class edu.sdsc.mbt.viewables.AtomRadiusByCpk (implements edu.sdsc.mbt.viewables.AtomRadius)
  • class edu.sdsc.mbt.viewables.AtomRadiusByScaledCpk (implements edu.sdsc.mbt.viewables.AtomRadius)
  • class edu.sdsc.mbt.viewables.AtomRadiusRegistry
  • class edu.sdsc.mbt.util.AtomStats
  • class edu.sdsc.mbt.viewers.GLViewerImpl.BackboneLine
  • class edu.sdsc.sirius.util.BlastSettings
  • class edu.sdsc.mbt.viewables.BondColorByAtomColor (implements edu.sdsc.mbt.viewables.BondColor)
  • class edu.sdsc.mbt.viewables.BondColorByElement (implements edu.sdsc.mbt.viewables.BondColor)
  • class edu.sdsc.mbt.viewables.BondColorRegistry
  • class edu.sdsc.mbt.util.BondFactory
  • class edu.sdsc.mbt.viewables.BondFormOrder (implements edu.sdsc.mbt.viewables.BondForm)
  • class edu.sdsc.mbt.viewables.BondFormRegistry
  • class edu.sdsc.mbt.viewables.BondFormSimple (implements edu.sdsc.mbt.viewables.BondForm)
  • class edu.sdsc.mbt.viewables.BondFormSplit (implements edu.sdsc.mbt.viewables.BondForm)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils
  • class edu.sdsc.mbt.util.BondInfo
  • class edu.sdsc.mbt.viewables.BondLabelByDistance (implements edu.sdsc.mbt.viewables.BondLabel)
  • class edu.sdsc.mbt.viewables.BondLabelNone (implements edu.sdsc.mbt.viewables.BondLabel)
  • class edu.sdsc.mbt.viewables.BondLabelRegistry
  • class edu.sdsc.mbt.viewables.BondRadiusAsStick (implements edu.sdsc.mbt.viewables.BondRadius)
  • class edu.sdsc.mbt.viewables.BondRadiusAsWire (implements edu.sdsc.mbt.viewables.BondRadius)
  • class edu.sdsc.mbt.viewables.BondRadiusByAtomRadius (implements edu.sdsc.mbt.viewables.BondRadius)
  • class edu.sdsc.mbt.viewables.BondRadiusByScaledAtomRadius (implements edu.sdsc.mbt.viewables.BondRadius)
  • class edu.sdsc.mbt.viewables.BondRadiusRegistry
  • class edu.sdsc.sirius.util.BrowserControl
  • class edu.sdsc.sirius.util.BrowserLauncher
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell (implements java.lang.Comparable)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain
  • class edu.sdsc.mbt.viewables.ChainColorById (implements edu.sdsc.mbt.viewables.ChainColor)
  • class edu.sdsc.mbt.viewables.ChainColorRegistry
  • class edu.sdsc.mbt.util.CodonInfo
  • class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f
  • class edu.sdsc.sirius.dialogs.ColorEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.sirius.rasmol.ColorManager
  • class edu.sdsc.sirius.dialogs.TableImpl.ColumnData
  • 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.AbstractButton (implements java.awt.ItemSelectable, javax.swing.SwingConstants)
          • class javax.swing.JButton (implements javax.accessibility.Accessible)
            • class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtButton
            • class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtButton
        • class javax.swing.JFileChooser (implements javax.accessibility.Accessible)
          • class edu.sdsc.sirius.dialogs.ImageFileChooser
        • class edu.sdsc.sirius.dialogs.JFontChooser (implements java.awt.event.ActionListener, javax.swing.event.ListSelectionListener)
        • class javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • class edu.sdsc.sirius.viewers.ProgressPanel
          • class edu.sdsc.sirius.util.TabListCellRenderer (implements javax.swing.ListCellRenderer)
        • class javax.swing.JPanel (implements javax.accessibility.Accessible)
          • class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel
          • class edu.sdsc.sirius.builder.BuilderPanel
          • class edu.sdsc.sirius.builder.CustomFragmentPanel (implements edu.sdsc.sirius.builder.FragmentGroupPanel)
          • class edu.sdsc.sirius.dialogs.ElementSelectionPanel
          • class edu.sdsc.sirius.dialogs.ElementStylesEditor
          • class edu.sdsc.sirius.builder.FragmentButton
          • class edu.sdsc.sirius.builder.GeneralFragmentPanel (implements edu.sdsc.sirius.builder.FragmentGroupPanel)
          • class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer (implements javax.media.opengl.GLEventListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
          • class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer
          • class edu.sdsc.sirius.dialogs.JFontPreviewPanel
          • class edu.sdsc.sirius.monitors.MonitorPanel
          • class edu.sdsc.sirius.builder.ProteinFragmentPanel (implements edu.sdsc.sirius.builder.FragmentGroupPanel)
          • class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel
          • class edu.sdsc.sirius.viewers.RamachandranViewer (implements edu.sdsc.mbt.StructureComponentEventListener, edu.sdsc.mbt.viewables.StructureStylesEventListener, edu.sdsc.sirius.viewers.Viewer)
          • class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
          • class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
          • class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel
          • class edu.sdsc.sirius.viewers.SequenceViewer (implements edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEventListener, edu.sdsc.mbt.StructureComponentEventListener, edu.sdsc.mbt.viewables.StructureStylesEventListener, edu.sdsc.sirius.viewers.Viewer)
          • class com.jgoodies.uif_lite.panel.SimpleInternalFrame
          • class edu.sdsc.sirius.viewers.StatusPanel (implements edu.sdsc.mbt.util.StatusListener)
          • class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser (implements edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEventListener, edu.sdsc.mbt.StructureComponentEventListener, edu.sdsc.mbt.viewables.StructureStylesEventListener, edu.sdsc.sirius.viewers.Viewer)
          • class edu.sdsc.sirius.viewers.StructureViewer (implements edu.sdsc.sirius.dialogs.DisplayDialogListener, edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEventListener, edu.sdsc.mbt.viewers.GLViewerImpl.MoveEventListener, edu.sdsc.mbt.StructureComponentEventListener, edu.sdsc.mbt.viewables.StructureStylesEventListener, edu.sdsc.sirius.viewers.Viewer)
          • class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
          • class edu.sdsc.sirius.workbench.WBListPanel
        • class javax.swing.JSplitPane (implements javax.accessibility.Accessible)
          • class com.jgoodies.uif_lite.component.UIFSplitPane
        • class 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)
          • class edu.sdsc.sirius.dialogs.TableImpl.ColorTable
          • class edu.sdsc.sirius.dialogs.TableImpl.ResultTable
      • class java.awt.Panel (implements javax.accessibility.Accessible)
        • class java.applet.Applet
          • class AppletLauncher3D
          • class SiriusAppletLauncher
          • class Viewer (implements edu.sdsc.mbt.util.ElementSettable, edu.sdsc.sirius.util.Manager)
      • 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 edu.sdsc.sirius.dialogs.AboutDialog
            • class edu.sdsc.sirius.dialogs.AlignmentSettingsDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.AngleDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.AngleMonitorDialog
            • class edu.sdsc.sirius.dialogs.AtomDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.AtomRenameDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.BondOrderDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.BreakBondDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.builder.BuilderDialog
            • class edu.sdsc.sirius.dialogs.BumpDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.CenterDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ChargeDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ColorDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.rasmol.CommandPanel
            • class edu.sdsc.sirius.dialogs.ComponentColorDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ComponentRenderingDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ComponentRibbonDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.CreateBondDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.CreateSequenceDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.DataListerDialog (implements edu.sdsc.sirius.dialogs.ListerDialog, edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable)
            • class edu.sdsc.sirius.dialogs.DataWBListerDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog, edu.sdsc.sirius.dialogs.ListerDialog, edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable)
            • class edu.sdsc.sirius.dialogs.DihedralDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.DistanceDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.DistributionViewer
            • class edu.sdsc.sirius.dialogs.ElementSelectionDialog
            • class edu.sdsc.sirius.dialogs.ElementStylesDialog
            • class edu.sdsc.sirius.dialogs.EntryListerDialog (implements edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable)
            • class edu.sdsc.sirius.dialogs.FogDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.HBDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.HybridizationDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.HydrogenDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ImageExportDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.ray.ImagePreviewPanel
            • class edu.sdsc.sirius.dialogs.LabelDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.MessageDialog
            • class edu.sdsc.sirius.monitors.MonitorDialog
            • class edu.sdsc.sirius.dialogs.MotifDialog
            • class edu.sdsc.sirius.dialogs.MotionDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.PdbDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.PdbLoadDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.PreferencesDialog (implements javax.swing.event.ChangeListener)
            • class edu.sdsc.sirius.viewers.RamachandranViewerImpl.RamachandranViewerDialog
            • class edu.sdsc.sirius.dialogs.RayTracerDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.RenderingDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ReplaceAtomDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog, edu.sdsc.mbt.util.ElementSettable)
            • class edu.sdsc.sirius.dialogs.ReplaceResidueDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ResidueLabelDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.ResidueRenameDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame (implements edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable)
            • class edu.sdsc.sirius.dialogs.RibbonColorDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.RibbonDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.RotateBondDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.builder.SaveFragmentDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.SelectionAreaDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.SelectListDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.SequenceRenameDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.StructureAlignmentDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.StructureEditDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.StructureRenameDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.StructureSelectionDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.StructureSetDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.StructureSuperpositionAlignDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.SuperimposeDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.VisibilityDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.workbench.WBListDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.workbench.WBSaveDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
            • class edu.sdsc.sirius.dialogs.WeightDialog (implements edu.sdsc.sirius.dialogs.DisplayDialog)
        • class edu.sdsc.sirius.util.SplashWindow
  • class edu.sdsc.mbt.viewables.ConservationColorMap (implements edu.sdsc.mbt.viewables.ColorMap, java.io.Serializable)
  • class edu.sdsc.mbt.util.Coordinate
  • class edu.sdsc.sirius.rasmol.CpkColorScheme (implements edu.sdsc.sirius.rasmol.ColorScheme)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionBuilder
  • class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle
  • class edu.sdsc.sirius.dialogs.TableImpl.DataBlock (implements java.io.Serializable)
    • class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock (implements java.io.Serializable)
  • class edu.sdsc.sirius.util.DataService
  • class edu.sdsc.sirius.dialogs.TableImpl.DataSet (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug
  • class edu.sdsc.sirius.util.DeletionInfo
  • class edu.sdsc.mbt.util.DerivedInformation
  • class edu.sdsc.sirius.dialogs.DialogConstants
  • class edu.sdsc.sirius.util.DialogLayout (implements java.awt.LayoutManager)
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters
  • class edu.sdsc.sirius.util.DNAProperties
  • class edu.sdsc.mbt.util.DoubleRange (implements edu.sdsc.mbt.util.Range, java.io.Serializable)
  • class edu.sdsc.mbt.util.Element
  • class edu.sdsc.mbt.viewables.ElementPreferences
  • class edu.sdsc.mbt.util.ElementProperties
  • class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtListener (implements java.awt.event.ActionListener)
  • class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtListener (implements java.awt.event.ActionListener)
  • class edu.sdsc.sirius.io.Entry
    • class edu.sdsc.sirius.io.SequenceEntry (implements java.io.Serializable)
    • class edu.sdsc.sirius.io.StructureEntry (implements java.io.Serializable)
      • class edu.sdsc.sirius.io.FragmentEntry (implements java.io.Serializable)
  • class edu.sdsc.sirius.io.EntryFactory
  • class edu.sdsc.sirius.util.ExtensionLayout (implements java.awt.LayoutManager)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion
  • class com.jgoodies.uif_lite.component.Factory
  • class edu.sdsc.sirius.io.FastaEntryLoader (implements edu.sdsc.sirius.io.FileEntryLoader)
  • class edu.sdsc.sirius.util.FileCloseListener (implements java.awt.event.ActionListener)
  • class javax.swing.filechooser.FileFilter
    • class edu.sdsc.sirius.util.FileNameFilter
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper (implements edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper)
  • class edu.sdsc.sirius.io.FileTransfer
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtom (implements edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter)
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByChain
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByType
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidue (implements edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter)
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidueByName
  • class edu.sdsc.mbt.viewables.FragmentColorByType (implements edu.sdsc.mbt.viewables.FragmentColor)
  • class edu.sdsc.mbt.viewables.FragmentColorRegistry
  • class edu.sdsc.mbt.viewables.FragmentFormCartoon (implements edu.sdsc.mbt.viewables.FragmentForm)
  • class edu.sdsc.mbt.viewables.FragmentFormCylinder (implements edu.sdsc.mbt.viewables.FragmentForm)
  • class edu.sdsc.mbt.viewables.FragmentFormLadder (implements edu.sdsc.mbt.viewables.FragmentForm)
  • class edu.sdsc.mbt.viewables.FragmentFormRegistry
  • class edu.sdsc.mbt.viewables.FragmentFormRibbon (implements edu.sdsc.mbt.viewables.FragmentForm)
  • class edu.sdsc.mbt.viewables.FragmentFormTube (implements edu.sdsc.mbt.viewables.FragmentForm)
  • class edu.sdsc.mbt.viewables.FragmentFormWireframe (implements edu.sdsc.mbt.viewables.FragmentForm)
  • class edu.sdsc.sirius.io.FragmentLoader
  • class edu.sdsc.sirius.builder.FragmentRecord
  • class edu.sdsc.sirius.builder.FragmentRegistry
  • class edu.sdsc.sirius.builder.FragmentUtil
  • class edu.sdsc.mbt.util.FrameRegistry
  • class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.AtomGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.AtomLineGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry
    • class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry
  • class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity
    • class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry
      • class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry
      • class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry
      • class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry
  • class edu.sdsc.sirius.dialogs.GeometryEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.GlAxesRenderable (implements edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion
  • class edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEvent
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
  • class edu.sdsc.sirius.dialogs.HydrogenEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.mbt.image.ImageHandler
  • class edu.sdsc.mbt.image.ImageUtils
  • class edu.sdsc.mbt.viewables.InterpolatedColorMap (implements edu.sdsc.mbt.viewables.ColorMap)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator
  • class edu.sdsc.mbt.util.IntRange (implements edu.sdsc.mbt.util.Range, java.io.Serializable)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
  • class edu.sdsc.sirius.util.IOHandler
  • class edu.sdsc.sirius.dialogs.LabelEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.sirius.dialogs.TableImpl.LineData
    • class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData
    • class edu.sdsc.sirius.dialogs.TableImpl.PubmedLineData
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.Loader
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FileLoader
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlLoader
  • class edu.sdsc.sirius.util.Location
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.LogicalGroup (implements edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable (implements edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable)
  • class edu.sdsc.sirius.io.MetaData
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model
  • class edu.sdsc.sirius.io.Mol2EntryLoader (implements edu.sdsc.sirius.io.FileEntryLoader, java.io.Serializable)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable (implements edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent
  • class edu.sdsc.sirius.io.MsfEntryLoader (implements edu.sdsc.sirius.io.FileEntryLoader)
  • class edu.sdsc.mbt.util.NucleicAcidInfo
  • class edu.sdsc.mbt.util.Octree
  • class edu.sdsc.mbt.util.OctreeAtomItem (implements edu.sdsc.mbt.util.OctreeDataItem)
  • class edu.sdsc.sirius.util.PagePrintable (implements java.awt.print.Printable)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb
  • class edu.sdsc.sirius.io.PdbEntryLoader (implements edu.sdsc.sirius.io.FileEntryLoader, java.io.Serializable)
  • class edu.sdsc.mbt.util.PeriodicTable
  • class edu.sdsc.mbt.util.PickUtils
  • class edu.sdsc.mbt.viewers.GLViewerImpl.util.Point3f
  • class edu.sdsc.sirius.dialogs.PreferencesCache
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Priestle
  • class edu.sdsc.sirius.util.ProteinProperties
  • class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f
  • class edu.sdsc.mbt.util.RangeMap
  • class edu.sdsc.sirius.rasmol.RasmolReader
  • class edu.sdsc.sirius.ray.RayTraceUtil
  • class edu.sdsc.mbt.filters.RelationFilter (implements edu.sdsc.mbt.filters.StructureComponentFilter)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Renderable
  • class edu.sdsc.sirius.dialogs.RenderingEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue
  • class edu.sdsc.mbt.viewables.ResidueAnnotation
  • class edu.sdsc.mbt.viewables.ResidueColorByCharge (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorByElement (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorByType (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorDefault (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorFactory (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorRegistry (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorScaled (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.ResidueColorUniform (implements edu.sdsc.mbt.viewables.ResidueColor, java.io.Serializable)
  • class edu.sdsc.mbt.viewables.RibbonColorDefault (implements edu.sdsc.mbt.viewables.RibbonColor, java.io.Serializable)
  • class edu.sdsc.sirius.dialogs.RibbonColorEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.mbt.viewables.RibbonColorFactory (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.RibbonColorUniform (implements edu.sdsc.mbt.viewables.RibbonColor, java.io.Serializable)
  • class edu.sdsc.sirius.dialogs.RibbonEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.sirius.io.SDFEntryLoader (implements edu.sdsc.sirius.io.FileEntryLoader)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Selection
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfAtoms
    • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfResidues
  • class edu.sdsc.mbt.Sequence
  • class edu.sdsc.sirius.viewers.SequenceComparator (implements java.util.Comparator)
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles (implements java.io.Serializable)
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent
  • class com.jgoodies.looks.demo.Settings
  • class edu.sdsc.sirius.io.SideChain
  • class edu.sdsc.sirius.export.StateHandler
  • class edu.sdsc.sirius.export.StateObject (implements java.io.Serializable)
  • class edu.sdsc.mbt.util.Status
  • class edu.sdsc.mbt.util.StatusEvent
  • class edu.sdsc.sirius.dialogs.StericEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Strain
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.util.StringLib
  • class edu.sdsc.sirius.util.StringUtils
  • class edu.sdsc.mbt.Structure (implements java.io.Serializable)
  • class edu.sdsc.sirius.rasmol.StructureColorScheme (implements edu.sdsc.sirius.rasmol.ColorScheme)
  • class edu.sdsc.mbt.StructureComponent (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.Atom (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.Bond (implements java.lang.Cloneable)
    • class edu.sdsc.mbt.Chain (implements java.lang.Cloneable)
    • class edu.sdsc.mbt.Conformation (implements java.lang.Cloneable, java.io.Serializable)
      • class edu.sdsc.mbt.Coil (implements java.lang.Cloneable, java.io.Serializable)
      • class edu.sdsc.mbt.Helix (implements java.lang.Cloneable, java.io.Serializable)
      • class edu.sdsc.mbt.Strand (implements java.lang.Cloneable, java.io.Serializable)
      • class edu.sdsc.mbt.Turn (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.Fragment (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.Residue (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.StructureInfo (implements java.lang.Cloneable, java.io.Serializable)
    • class edu.sdsc.mbt.Symmetry (implements java.lang.Cloneable, java.io.Serializable)
  • class edu.sdsc.mbt.StructureComponentEvent (implements java.io.Serializable)
  • class edu.sdsc.mbt.StructureComponentIterator (implements java.io.Serializable)
  • class edu.sdsc.mbt.StructureComponentRegistry (implements java.io.Serializable)
  • class edu.sdsc.mbt.StructureComponentRelation (implements java.io.Serializable)
    • class edu.sdsc.mbt.Relation_Conformation_Atom (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.StructureDocument (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.StructureDocumentEvent (implements java.io.Serializable)
  • class edu.sdsc.sirius.dialogs.StructureEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.sirius.dialogs.StructureEventRegistry
  • class edu.sdsc.sirius.util.StructureItem (implements java.io.Serializable)
  • class edu.sdsc.mbt.StructureMap
  • class edu.sdsc.sirius.util.StructureMath
  • class edu.sdsc.mbt.viewables.StructureStyles (implements java.io.Serializable, edu.sdsc.mbt.StructureComponentEventListener)
  • class edu.sdsc.mbt.viewables.StructureStylesEvent
  • class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
  • class edu.sdsc.sirius.export.StyleMap (implements java.io.Serializable)
  • class edu.sdsc.mbt.viewables.StylesPreferences
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class edu.sdsc.mbt.viewers.GLViewerImpl.FragmentTooShortException
      • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.MalformedPathException
  • class edu.sdsc.mbt.image.TileRenderer
  • class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable (implements edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.Trihedron
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper (implements edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper)
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.vec.Vec3d
  • class edu.sdsc.mbt.viewers.StructureViewerImpl.vec.Vec3f
  • class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f
  • class edu.sdsc.sirius.util.VectorSet
  • class edu.sdsc.sirius.export.ViewerParameters (implements java.io.Serializable)
  • class edu.sdsc.sirius.dialogs.ViewEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2
  • class edu.sdsc.sirius.dialogs.VisibilityEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)
  • class edu.sdsc.sirius.workbench.WBEntry
  • class edu.sdsc.sirius.workbench.WBManager
  • class edu.sdsc.sirius.dialogs.WeightEvent (implements edu.sdsc.sirius.dialogs.DisplayDialogEvent)

Interface Hierarchy

• interface edu.sdsc.mbt.viewables.AtomColor
• interface edu.sdsc.mbt.viewables.AtomLabel
• interface edu.sdsc.mbt.viewables.AtomRadius
• interface edu.sdsc.mbt.viewables.BondColor
• interface edu.sdsc.mbt.viewables.BondForm
• interface edu.sdsc.mbt.viewables.BondLabel
• interface edu.sdsc.mbt.viewables.BondRadius
• interface edu.sdsc.mbt.viewables.ChainColor
• interface edu.sdsc.mbt.viewables.ColorMap
• interface edu.sdsc.sirius.rasmol.ColorScheme
• interface edu.sdsc.sirius.dialogs.DisplayDialog
• interface edu.sdsc.sirius.dialogs.DisplayDialogEvent
• interface edu.sdsc.sirius.dialogs.DisplayDialogListener
• interface edu.sdsc.mbt.util.ElementSettable
• interface edu.sdsc.sirius.io.EntryLoader
  • interface edu.sdsc.sirius.io.FileEntryLoader
• interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter
• interface edu.sdsc.mbt.viewables.FragmentColor
• interface edu.sdsc.mbt.viewables.FragmentForm
• interface edu.sdsc.sirius.builder.FragmentGroupPanel
• interface edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable
• interface edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEventListener
• interface edu.sdsc.sirius.dialogs.ListerDialog
• interface edu.sdsc.sirius.util.Manager
• interface edu.sdsc.mbt.viewers.GLViewerImpl.MoveEventListener
• interface edu.sdsc.mbt.util.OctreeDataItem
• interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
• interface edu.sdsc.mbt.util.Range
• interface edu.sdsc.mbt.viewables.ResidueColor
• interface edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable
• interface edu.sdsc.mbt.viewables.RibbonColor
• interface edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEventListener
• interface java.io.Serializable
  • interface edu.sdsc.mbt.StructureComponentEventListener
  • interface edu.sdsc.mbt.filters.StructureComponentFilter
• interface edu.sdsc.mbt.util.Settable
• interface edu.sdsc.mbt.util.StatusListener
• interface edu.sdsc.mbt.viewables.StructureStylesEventListener
• interface edu.sdsc.sirius.viewers.Viewer