Hierarchy For All Packages

Package Hierarchies:

jebl.evolution.align, jebl.evolution.align.scores, jebl.evolution.aligners, jebl.evolution.alignments, jebl.evolution.characterReconstruction, jebl.evolution.characters, jebl.evolution.coalescent, jebl.evolution.distances, jebl.evolution.graphs, jebl.evolution.io, jebl.evolution.parsimony, jebl.evolution.sequences, jebl.evolution.substmodel, jebl.evolution.taxa, jebl.evolution.trees, jebl.gui.trees.treecomponent, jebl.gui.trees.treeviewer, jebl.gui.trees.treeviewer_dev, jebl.gui.trees.treeviewer_dev.decorators, jebl.gui.trees.treeviewer_dev.painters, jebl.gui.trees.treeviewer_dev.treelayouts, jebl.gui.trees.treeviewer.decorators, jebl.gui.trees.treeviewer.painters, jebl.gui.trees.treeviewer.treelayouts, jebl.math, jebl.util, org.virion.jam.app, org.virion.jam.components, org.virion.jam.console, org.virion.jam.controlpalettes, org.virion.jam.controlpanels, org.virion.jam.demo, org.virion.jam.demo.menus, org.virion.jam.disclosure, org.virion.jam.framework, org.virion.jam.html, org.virion.jam.layouts, org.virion.jam.mac, org.virion.jam.maconly, org.virion.jam.panels, org.virion.jam.preferences, org.virion.jam.table, org.virion.jam.toolbar, org.virion.jam.util

Class Hierarchy

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • org.virion.jam.toolbar.ToolbarAction
  • javax.swing.AbstractCellEditor (implements javax.swing.CellEditor, java.io.Serializable)
    • org.virion.jam.table.ColorEditor (implements java.awt.event.ActionListener, javax.swing.table.TableCellEditor)
    • javax.swing.DefaultCellEditor (implements javax.swing.table.TableCellEditor, javax.swing.tree.TreeCellEditor)
      • org.virion.jam.table.RealNumberCellEditor
      • org.virion.jam.table.WholeNumberCellEditor
  • org.virion.jam.controlpalettes.AbstractController (implements org.virion.jam.controlpalettes.Controller)
    • jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
    • jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
    • jebl.gui.trees.treeviewer_dev.painters.NodeBarController
    • jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
    • jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
    • jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
    • jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
    • jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
    • jebl.gui.trees.treeviewer_dev.TreeAppearanceController
    • jebl.gui.trees.treeviewer_dev.TreePaneController
    • jebl.gui.trees.treeviewer_dev.TreeViewerController
  • jebl.gui.trees.treeviewer.painters.AbstractPainter<T> (implements jebl.gui.trees.treeviewer.painters.Painter<T>)
    • jebl.gui.trees.treeviewer.painters.BasicLabelPainter
    • jebl.gui.trees.treeviewer.painters.ScaleBarPainter
  • jebl.gui.trees.treeviewer_dev.painters.AbstractPainter<T> (implements jebl.gui.trees.treeviewer_dev.painters.Painter<T>)
    • jebl.gui.trees.treeviewer_dev.painters.LabelPainter<T>
      • jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
      • jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
    • jebl.gui.trees.treeviewer_dev.painters.NodePainter
      • jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
      • jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
  • jebl.evolution.substmodel.AbstractRateMatrix (implements jebl.evolution.substmodel.RateMatrix)
    • jebl.evolution.substmodel.AminoAcidModel
      • jebl.evolution.substmodel.WAG
  • jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout (implements jebl.gui.trees.treeviewer.treelayouts.TreeLayout)
    • jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
    • jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
    • jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
  • jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout (implements jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout)
    • jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
    • jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
    • jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
  • jebl.evolution.align.Align
    • jebl.evolution.align.MaximalSegmentPair
    • jebl.evolution.align.NeedlemanWunsch
    • jebl.evolution.align.NeedlemanWunschAffine
    • jebl.evolution.align.NeedlemanWunschLinearSpace
    • jebl.evolution.align.NeedlemanWunschLinearSpaceAffine (implements jebl.evolution.align.PairwiseAligner)
    • jebl.evolution.align.NonOverlapMultipleLocalAffine
    • jebl.evolution.align.OldNeedlemanWunschAffine
    • jebl.evolution.align.OverlapAlign
    • jebl.evolution.align.SmithWaterman
    • jebl.evolution.align.SmithWatermanLinearSpace
    • jebl.evolution.align.SmithWatermanLinearSpaceAffine
  • jebl.evolution.align.AlignCommand
  • jebl.evolution.align.AlignmentTreeBuilderFactory
  • jebl.evolution.align.AlignmentTreeBuilderFactory.Result
  • jebl.evolution.sequences.AminoAcids
  • org.virion.jam.framework.Application
    • org.virion.jam.console.ConsoleApplication
    • org.virion.jam.framework.MultiDocApplication
      • org.virion.jam.demo.DemoApplication
    • org.virion.jam.framework.SingleDocApplication
  • ApplicationAdapter
    • org.virion.jam.maconly.OSXAdapter
  • org.virion.jam.app.Arguments
  • org.virion.jam.app.Arguments.Option
    • org.virion.jam.app.Arguments.IntegerOption
      • org.virion.jam.app.Arguments.IntegerArrayOption
    • org.virion.jam.app.Arguments.RealOption
      • org.virion.jam.app.Arguments.RealArrayOption
    • org.virion.jam.app.Arguments.StringOption
  • jebl.util.Attributable.Utils
  • jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator (implements jebl.gui.trees.treeviewer_dev.decorators.Decorator)
  • jebl.util.AttributableHelper (implements jebl.util.Attributable)
  • jebl.gui.trees.treeviewer.decorators.AttributeBranchDecorator (implements jebl.gui.trees.treeviewer.decorators.BranchDecorator)
  • jebl.evolution.align.BartonSternberg (implements jebl.evolution.align.MultipleAligner)
  • jebl.evolution.alignments.BasicAlignment (implements jebl.evolution.alignments.Alignment)
  • jebl.evolution.distances.BasicDistanceMatrix (implements jebl.evolution.distances.DistanceMatrix)
    • jebl.evolution.distances.F84DistanceMatrix
    • jebl.evolution.distances.HKYDistanceMatrix
    • jebl.evolution.distances.JukesCantorDistanceMatrix
    • jebl.evolution.align.SequenceAlignmentsDistanceMatrix
    • jebl.evolution.distances.TamuraNeiDistanceMatrix
  • jebl.evolution.sequences.BasicSequence (implements jebl.evolution.sequences.Sequence)
  • jebl.math.Binomial
  • org.virion.jam.util.BrowserLauncher
  • jebl.evolution.io.ByteBuilder (implements java.lang.CharSequence)
  • jebl.evolution.trees.CladeSystem
  • jebl.evolution.trees.ClusteringTreeBuilder<T> (implements jebl.evolution.trees.TreeBuilder<T>)
    • jebl.evolution.trees.NeighborJoiningTreeBuilder
  • jebl.evolution.coalescent.Coalescent (implements jebl.math.MultivariateFunction)
  • jebl.evolution.coalescent.CoalescentIntervalGenerator (implements jebl.evolution.trees.IntervalGenerator)
  • jebl.evolution.sequences.Codons
  • jebl.evolution.trees.CompactRootedTree (implements jebl.evolution.trees.RootedTree)
  • org.virion.jam.layouts.CompassLayout (implements java.awt.LayoutManager2)
  • 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)
            • org.virion.jam.toolbar.ToolbarButton (implements org.virion.jam.toolbar.ToolbarItem)
          • javax.swing.JToggleButton (implements javax.accessibility.Accessible)
            • org.virion.jam.disclosure.DisclosureButton
            • org.virion.jam.controlpalettes.PinnedButton
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • org.virion.jam.table.ColorRenderer (implements javax.swing.table.TableCellRenderer)
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • org.virion.jam.table.HeaderRenderer
            • org.virion.jam.table.TableRenderer
          • org.virion.jam.components.JVerticalLabel
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.virion.jam.panels.ActionPanel
          • org.virion.jam.panels.AddRemovePanel
          • org.virion.jam.controlpalettes.BasicControlPalette (implements org.virion.jam.controlpalettes.ControlPalette)
          • org.virion.jam.controlpanels.BasicControlPalette (implements org.virion.jam.controlpanels.ControlPalette)
          • org.virion.jam.disclosure.DisclosurePanel
          • org.virion.jam.toolbar.GenericToolbarItem (implements org.virion.jam.toolbar.ToolbarItem)
          • org.virion.jam.panels.OptionsPanel
          • org.virion.jam.panels.RulesPanel
          • org.virion.jam.panels.SearchPanel
          • org.virion.jam.panels.StatusPanel (implements org.virion.jam.panels.StatusListener)
            • org.virion.jam.panels.StatusBar
          • jebl.gui.trees.treeviewer.TreeViewer (implements java.awt.print.Printable)
            • jebl.gui.trees.treeviewer.MultipleTreeViewer
          • jebl.gui.trees.treeviewer_dev.TreeViewer (implements java.awt.print.Printable)
            • jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
          • jebl.gui.trees.treeviewer_dev.TreeViewerPanel
        • javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • javax.swing.JTextField (implements javax.swing.SwingConstants)
            • org.virion.jam.components.RealNumberField (implements javax.swing.event.DocumentListener, java.awt.event.FocusListener)
            • org.virion.jam.components.WholeNumberField (implements javax.swing.event.DocumentListener, java.awt.event.FocusListener)
        • javax.swing.JToolBar (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • org.virion.jam.toolbar.Toolbar
        • jebl.gui.trees.treecomponent.RootedTreeComponent (implements java.awt.print.Printable)
        • jebl.gui.trees.treeviewer.TreePane (implements org.virion.jam.controlpanels.ControlsProvider, jebl.gui.trees.treeviewer.painters.PainterListener, java.awt.print.Printable)
        • jebl.gui.trees.treeviewer_dev.TreePane (implements jebl.gui.trees.treeviewer_dev.painters.PainterListener, java.awt.print.Printable)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.virion.jam.util.JExceptionDialog
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.virion.jam.framework.AbstractFrame (implements org.virion.jam.framework.Exportable)
              • org.virion.jam.framework.AboutBox
              • org.virion.jam.framework.AuxilaryFrame
              • org.virion.jam.framework.DocumentFrame
                • org.virion.jam.console.ConsoleFrame
                • org.virion.jam.demo.DemoFrame (implements org.virion.jam.demo.menus.DemoMenuHandler)
            • org.virion.jam.html.HTMLViewer
  • javax.swing.plaf.ComponentUI
    • javax.swing.plaf.TableUI
      • javax.swing.plaf.basic.BasicTableUI
        • org.virion.jam.table.AdvancedTableUI
  • jebl.evolution.alignments.ConsensusSequence (implements jebl.evolution.sequences.Sequence)
  • jebl.evolution.trees.ConsensusTreeBuilder<T> (implements jebl.evolution.trees.TreeBuilder<T>)
    • jebl.evolution.trees.GreedyRootedConsensusTreeBuilder
    • jebl.evolution.trees.GreedyUnrootedConsensusTreeBuilder
    • jebl.evolution.trees.MRCACConsensusTreeBuilder
  • jebl.evolution.coalescent.ConstantPopulation (implements jebl.evolution.coalescent.DemographicFunction)
    • jebl.evolution.coalescent.ExponentialGrowth
      • jebl.evolution.coalescent.CataclysmicDemographic
      • jebl.evolution.coalescent.ConstExponential
      • jebl.evolution.coalescent.Expansion
      • jebl.evolution.coalescent.LogisticGrowth
        • jebl.evolution.coalescent.ConstLogistic
  • jebl.evolution.characters.ContinuousCharacter (implements jebl.evolution.characters.Character)
  • jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator (implements jebl.gui.trees.treeviewer_dev.decorators.Decorator)
  • org.virion.jam.controlpanels.Controls
  • org.virion.jam.framework.DefaultEditMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • org.virion.jam.framework.DefaultFileMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • org.virion.jam.framework.DefaultHelpMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • org.virion.jam.framework.DefaultMenuBarFactory (implements org.virion.jam.framework.MenuBarFactory)
    • org.virion.jam.console.ConsoleMenuBarFactory
    • org.virion.jam.demo.DemoMenuBarFactory
    • org.virion.jam.framework.MultiDocMenuBarFactory
    • org.virion.jam.framework.SingleDocMenuBarFactory
  • jebl.evolution.coalescent.DemographicFunction.Utils
  • org.virion.jam.demo.menus.DemoMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • jebl.evolution.characters.DiscreteCharacter (implements jebl.evolution.characters.Character)
  • jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator (implements jebl.gui.trees.treeviewer_dev.decorators.Decorator)
  • jebl.evolution.io.FastaExporter (implements jebl.evolution.io.SequenceExporter)
  • jebl.evolution.io.FastaImporter (implements jebl.evolution.io.ImmediateSequenceImporter, jebl.evolution.io.SequenceImporter)
  • jebl.evolution.trees.FilteredRootedTree (implements jebl.evolution.trees.RootedTree)
    • jebl.evolution.trees.SortedRootedTree
    • jebl.evolution.trees.TransformedRootedTree
  • jebl.evolution.sequences.FilteredSequence (implements jebl.evolution.sequences.Sequence)
    • jebl.evolution.sequences.GaplessSequence
    • jebl.evolution.sequences.TranslatedSequence
  • jebl.evolution.parsimony.FitchParsimony (implements jebl.evolution.parsimony.ParsimonyCriterion)
  • jebl.util.FixedBitSet
  • jebl.math.GammaFunction
  • jebl.evolution.sequences.GeneticCode
  • jebl.evolution.graphs.Graph.Utils
  • org.virion.jam.util.IconUtils
  • jebl.evolution.io.ImportHelper
  • jebl.evolution.coalescent.IntervalList.Utils
  • jebl.evolution.coalescent.Intervals (implements jebl.evolution.coalescent.IntervalList)
  • org.virion.jam.util.LongTask
    • org.virion.jam.util.SimpleLongTask
  • org.virion.jam.util.LongTaskMonitor
  • org.virion.jam.mac.MacFileMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • org.virion.jam.mac.MacHelpMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • jebl.math.MachineAccuracy
  • org.virion.jam.mac.MacWindowMenuFactory (implements org.virion.jam.framework.MenuFactory)
  • jebl.math.MatrixCalc
  • jebl.evolution.substmodel.MatrixExponential (implements java.lang.Cloneable, java.io.Serializable)
  • jebl.evolution.io.MEGAExporter (implements jebl.evolution.io.AlignmentExporter)
  • jebl.math.MinimiserMonitor.Utils
  • jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
  • jebl.evolution.distances.ModelBasedDistanceMatrix
  • java.awt.event.MouseAdapter (implements java.awt.event.MouseListener)
    • jebl.gui.trees.treecomponent.RootedTreeComponent.MListener
  • jebl.math.MultivariateMinimum
    • jebl.math.OrthogonalSearch
  • jebl.evolution.trees.MutableRootedTree (implements jebl.evolution.trees.RootedTree)
  • jebl.evolution.io.NewickExporter (implements jebl.evolution.io.TreeExporter)
  • jebl.evolution.io.NewickImporter (implements jebl.evolution.io.TreeImporter)
  • jebl.evolution.io.NexusExporter (implements jebl.evolution.io.AlignmentExporter, jebl.evolution.io.SequenceExporter, jebl.evolution.io.TreeExporter)
  • jebl.evolution.io.NexusImporter (implements jebl.evolution.io.AlignmentImporter, jebl.evolution.io.DistanceMatrixImporter, jebl.evolution.io.SequenceImporter, jebl.evolution.io.TreeImporter)
  • jebl.evolution.sequences.Nucleotides
  • jebl.util.NumberFormatter
  • jebl.math.NumericalDerivative
  • jebl.math.OrderEnumerator.Utils
  • jebl.math.OrthogonalHints.Utils
  • jebl.math.OrthogonalLineFunction (implements jebl.math.UnivariateFunction)
  • jebl.evolution.align.Output
  • jebl.evolution.align.PairwiseAligner.Result
  • jebl.evolution.io.PHYLIPExporter (implements jebl.evolution.io.AlignmentExporter)
  • jebl.evolution.io.PhylipSequentialImporter (implements jebl.evolution.io.SequenceImporter)
  • org.virion.jam.preferences.PreferencesDialog
  • org.virion.jam.util.PrintUtilities (implements java.awt.print.Printable)
  • jebl.evolution.align.ProfileCharacter
  • jebl.util.ProgressListener
    • jebl.util.CompositeProgressListener
  • jebl.math.Random
  • org.virion.jam.framework.RecentFileList (implements java.awt.event.ActionListener)
  • jebl.evolution.alignments.ResampledAlignment (implements jebl.evolution.alignments.Alignment)
    • jebl.evolution.alignments.BootrappedAlignment
    • jebl.evolution.alignments.JackknifedAlignment
  • jebl.evolution.trees.RootedFromUnrooted (implements jebl.evolution.trees.RootedTree)
  • jebl.gui.trees.treecomponent.RootedTreeComponent.Adaptor (implements jebl.gui.trees.treecomponent.RootedTreeComponent.Listener)
  • jebl.evolution.trees.RootedTreeUtils
  • jebl.evolution.align.scores.Scores (implements jebl.evolution.align.scores.ScoreMatrix)
    • jebl.evolution.align.scores.AminoAcidScores
      • jebl.evolution.align.scores.Blosum45
      • jebl.evolution.align.scores.Blosum50
      • jebl.evolution.align.scores.Blosum55
      • jebl.evolution.align.scores.Blosum60
      • jebl.evolution.align.scores.Blosum62
      • jebl.evolution.align.scores.Blosum65
      • jebl.evolution.align.scores.Blosum70
      • jebl.evolution.align.scores.Blosum75
      • jebl.evolution.align.scores.Blosum80
      • jebl.evolution.align.scores.Blosum85
      • jebl.evolution.align.scores.Blosum90
      • jebl.evolution.align.scores.Pam100
      • jebl.evolution.align.scores.Pam110
      • jebl.evolution.align.scores.Pam120
      • jebl.evolution.align.scores.Pam130
      • jebl.evolution.align.scores.Pam140
      • jebl.evolution.align.scores.Pam150
      • jebl.evolution.align.scores.Pam160
      • jebl.evolution.align.scores.Pam170
      • jebl.evolution.align.scores.Pam180
      • jebl.evolution.align.scores.Pam190
      • jebl.evolution.align.scores.Pam200
      • jebl.evolution.align.scores.Pam210
      • jebl.evolution.align.scores.Pam220
      • jebl.evolution.align.scores.Pam230
      • jebl.evolution.align.scores.Pam240
      • jebl.evolution.align.scores.Pam250
    • jebl.evolution.align.scores.NucleotideScores
      • jebl.evolution.align.scores.Hamming
      • jebl.evolution.align.scores.JukesCantor
    • jebl.evolution.align.scores.SubstScoreMatrix
  • jebl.evolution.align.scores.ScoresFactory
  • jebl.evolution.align.SequenceShuffler
  • jebl.evolution.sequences.SequenceTester
  • jebl.evolution.sequences.SequenceType.Utils
  • org.virion.jam.html.SimpleLinkListener (implements javax.swing.event.HyperlinkListener)
  • org.virion.jam.util.SimpleListenerManager
  • jebl.evolution.trees.SimpleRootedTree (implements jebl.evolution.trees.RootedTree)
  • jebl.evolution.trees.SimpleTree (implements jebl.evolution.trees.Tree)
  • jebl.evolution.trees.SplitSystem
  • jebl.evolution.trees.SplitUtils
  • jebl.gui.trees.treecomponent.SquareTreePainter (implements jebl.gui.trees.treecomponent.RootedTreePainter)
  • jebl.evolution.sequences.State (implements java.lang.Comparable<T>)
    • jebl.evolution.sequences.AminoAcidState
    • jebl.evolution.sequences.CodonState
    • jebl.evolution.sequences.NucleotideState
  • jebl.evolution.sequences.StateClassification.Default (implements jebl.evolution.sequences.StateClassification)
  • org.virion.jam.panels.StatusProvider.Helper (implements org.virion.jam.panels.StatusProvider)
  • org.virion.jam.util.SwingWorker
  • jebl.evolution.io.TabDelimitedImporter (implements jebl.evolution.io.DistanceMatrixImporter)
  • jebl.evolution.taxa.Taxon (implements jebl.util.Attributable, java.lang.Comparable<T>)
  • jebl.evolution.taxa.TaxonomicLevel
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.virion.jam.app.Arguments.ArgumentException
      • jebl.evolution.graphs.Graph.NoEdgeException
      • jebl.evolution.io.ImportException
        • jebl.evolution.io.ImportException.BadFormatException
        • jebl.evolution.io.ImportException.DuplicateFieldException
        • jebl.evolution.io.ImportException.DuplicateTaxaException
        • jebl.evolution.io.ImportException.MissingFieldException
        • jebl.evolution.io.ImportException.ShortSequenceException
        • jebl.evolution.io.ImportException.TooFewTaxaException
        • jebl.evolution.io.ImportException.UnknownTaxonException
        • jebl.evolution.io.ImportException.UnparsableDataException
        • jebl.evolution.io.NexusImporter.MissingBlockException
      • jebl.math.MatrixCalcException
        • jebl.math.MatrixCalcException.NotSquareMatrixException
        • jebl.math.MatrixCalcException.PositiveDefiniteException
      • jebl.evolution.sequences.SequenceStateException
    • jebl.evolution.taxa.MissingTaxonException
  • org.virion.jam.toolbar.ToolbarOptions
  • jebl.evolution.align.Traceback
  • jebl.evolution.trees.TreeBuilderFactory
  • jebl.gui.trees.treeviewer.TreePaneRuler (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • jebl.gui.trees.treeviewer_dev.TreePaneRuler (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • jebl.gui.trees.treeviewer.TreePaneSelector (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • jebl.gui.trees.treeviewer_dev.TreePaneSelector (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • jebl.evolution.trees.TreeSimulator
  • jebl.math.UnivariateMinimum
  • jebl.evolution.graphs.Utils
  • jebl.evolution.sequences.Utils
  • jebl.evolution.trees.Utils
  • jebl.util.Utils
  • org.virion.jam.app.Utils
  • org.virion.jam.mac.Utils
  • org.virion.jam.util.Utils

Interface Hierarchy

• jebl.evolution.aligners.Aligner
• jebl.evolution.io.AlignmentExporter
• jebl.evolution.io.AlignmentImporter
• jebl.util.Attributable
  • jebl.evolution.graphs.Edge
  • jebl.evolution.graphs.Graph
    • jebl.evolution.trees.RootedTree
    • jebl.evolution.trees.Tree
      • jebl.evolution.trees.RootedTree
  • jebl.evolution.graphs.Node
  • jebl.evolution.trees.RootedTree
  • jebl.evolution.sequences.Sequence (also extends java.lang.Comparable<T>)
  • jebl.evolution.trees.Tree
    • jebl.evolution.trees.RootedTree
• jebl.gui.trees.treeviewer.decorators.BranchDecorator
• jebl.evolution.characters.Character
• jebl.evolution.characters.CharacterType
• java.lang.Cloneable
  • jebl.evolution.substmodel.RateMatrix (also extends java.io.Serializable)
• org.virion.jam.framework.Command
• java.lang.Comparable<T>
  • jebl.evolution.sequences.Sequence (also extends jebl.util.Attributable)
• org.virion.jam.controlpalettes.Controller
• org.virion.jam.controlpalettes.ControllerListener
• org.virion.jam.controlpalettes.ControlPalette
• org.virion.jam.controlpanels.ControlPalette
• org.virion.jam.controlpalettes.ControlPaletteListener
• org.virion.jam.controlpanels.ControlPaletteListener
• org.virion.jam.controlpanels.ControlsProvider
  • jebl.gui.trees.treeviewer.painters.Painter<T>
  • jebl.gui.trees.treeviewer.treelayouts.TreeLayout
• org.virion.jam.controlpanels.ControlsSettings
• jebl.gui.trees.treeviewer_dev.decorators.Decorator
• jebl.evolution.coalescent.DemographicFunction
• org.virion.jam.demo.menus.DemoMenuHandler
• org.virion.jam.disclosure.DisclosureListener
• jebl.evolution.distances.DistanceMatrix
• jebl.evolution.io.DistanceMatrixImporter
• org.virion.jam.framework.DocumentFrameFactory
• org.virion.jam.framework.Exportable
• jebl.evolution.io.ImmediateSequenceImporter
• jebl.evolution.io.ImmediateSequenceImporter.Callback
• jebl.evolution.trees.IntervalGenerator
• jebl.evolution.coalescent.IntervalList
• java.lang.Iterable<T>
  • jebl.evolution.io.TreeImporter
• org.virion.jam.util.ListItemView
• org.virion.jam.framework.MenuBarFactory
• org.virion.jam.framework.MenuFactory
• jebl.math.MinimiserMonitor
• jebl.evolution.align.MultipleAligner
• jebl.math.MultivariateFunction
• jebl.math.MultivariateMinimum.Factory
• jebl.math.OrderEnumerator
• jebl.math.OrderEnumerator.OEFactory
• jebl.math.OrthogonalHints
• jebl.math.OrthogonalSearch.RoundOptimiser
• jebl.gui.trees.treeviewer_dev.painters.Painter<T>
• jebl.gui.trees.treeviewer.painters.PainterListener
• jebl.gui.trees.treeviewer_dev.painters.PainterListener
• jebl.evolution.align.PairwiseAligner
• jebl.evolution.parsimony.ParsimonyCriterion
• jebl.evolution.alignments.Pattern
• jebl.evolution.alignments.Patterns
  • jebl.evolution.alignments.Alignment (also extends jebl.evolution.sequences.Sequences)
• org.virion.jam.preferences.PreferencesSection
• jebl.gui.trees.treecomponent.RootedTreeComponent.Listener
• jebl.gui.trees.treecomponent.RootedTreePainter
• org.virion.jam.panels.RuleModel
• org.virion.jam.panels.RulesPanel.Rule
• jebl.evolution.align.scores.ScoreMatrix
• org.virion.jam.panels.SearchPanelListener
• jebl.evolution.io.SequenceExporter
• jebl.evolution.io.SequenceImporter
• jebl.evolution.sequences.Sequences
  • jebl.evolution.alignments.Alignment (also extends jebl.evolution.alignments.Patterns)
• jebl.evolution.sequences.SequenceType
• java.io.Serializable
  • jebl.evolution.substmodel.RateMatrix (also extends java.lang.Cloneable)
• org.virion.jam.util.SimpleListener
• jebl.evolution.sequences.StateClassification
• org.virion.jam.panels.StatusListener
• org.virion.jam.panels.StatusProvider
• org.virion.jam.util.TaskListener
• jebl.gui.trees.treeviewer.decorators.TaxonDecorator
• org.virion.jam.toolbar.ToolbarItem
• jebl.evolution.align.TracebackPlotter
• jebl.evolution.trees.TreeBuilder<T>
• jebl.evolution.io.TreeExporter
• jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
• jebl.gui.trees.treeviewer.treelayouts.TreeLayoutListener
• jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayoutListener
• jebl.gui.trees.treeviewer_dev.TreePaneListener
• jebl.gui.trees.treeviewer.TreeSelectionListener
• jebl.gui.trees.treeviewer_dev.TreeSelectionListener
• jebl.gui.trees.treeviewer_dev.TreeViewerListener
• jebl.math.UnivariateFunction

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • jebl.evolution.coalescent.IntervalList.IntervalType
    • jebl.evolution.io.DistanceMatrixImporter.Triangle
    • jebl.evolution.io.NexusImporter.NexusBlock
    • jebl.evolution.trees.ConsensusTreeBuilder.Method
    • jebl.evolution.trees.SortedRootedTree.BranchOrdering
    • jebl.evolution.trees.TransformedRootedTree.Transform
    • jebl.evolution.trees.TreeBuilderFactory.Method
    • jebl.evolution.trees.TreeBuilderFactory.DistanceModel
    • jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
    • jebl.gui.trees.treeviewer.TreePaneSelector.SelectionMode
    • jebl.gui.trees.treeviewer.TreePaneSelector.DragMode
    • jebl.gui.trees.treeviewer.TreeViewer.TreeLayoutType
    • jebl.gui.trees.treeviewer.TreeViewer.SearchType
    • jebl.gui.trees.treeviewer.painters.BasicLabelPainter.PainterIntent
    • jebl.gui.trees.treeviewer.painters.Painter.Orientation
    • jebl.gui.trees.treeviewer.painters.Painter.Justification
    • jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout.TaxonLabelPosition
    • jebl.gui.trees.treeviewer.treelayouts.TreeLayout.AxisType
    • jebl.gui.trees.treeviewer_dev.TreePaneSelector.SelectionMode
    • jebl.gui.trees.treeviewer_dev.TreePaneSelector.DragMode
    • jebl.gui.trees.treeviewer_dev.TreeViewer.SearchType
    • jebl.gui.trees.treeviewer_dev.TreeViewerController.TreeLayoutType
    • jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter.PainterIntent
    • jebl.gui.trees.treeviewer_dev.painters.NodeShapeController.NodePainterType
    • jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter.NodeShape
    • jebl.gui.trees.treeviewer_dev.painters.Painter.Orientation
    • jebl.gui.trees.treeviewer_dev.painters.Painter.Justification
    • jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout.TipLabelPosition
    • jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout.AxisType
    • org.virion.jam.controlpalettes.BasicControlPalette.DisplayMode
    • org.virion.jam.controlpanels.BasicControlPalette.DisplayMode