A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

A_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
A_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
aboutAction - Variable in class org.virion.jam.framework.Application
 
AboutBox - Class in org.virion.jam.framework
 
AboutBox(String, String, Icon) - Constructor for class org.virion.jam.framework.AboutBox
Creates an AboutBox with a given title, message and icon and centers it over the parent component.
AbstractController - Class in org.virion.jam.controlpalettes
 
AbstractController() - Constructor for class org.virion.jam.controlpalettes.AbstractController
 
AbstractFrame - Class in org.virion.jam.framework
 
AbstractFrame() - Constructor for class org.virion.jam.framework.AbstractFrame
 
AbstractPainter<T> - Class in jebl.gui.trees.treeviewer.painters
 
AbstractPainter() - Constructor for class jebl.gui.trees.treeviewer.painters.AbstractPainter
 
AbstractPainter<T> - Class in jebl.gui.trees.treeviewer_dev.painters
 
AbstractPainter() - Constructor for class jebl.gui.trees.treeviewer_dev.painters.AbstractPainter
 
AbstractRateMatrix - Class in jebl.evolution.substmodel
abstract base class for all rate matrices
AbstractRateMatrix(int) - Constructor for class jebl.evolution.substmodel.AbstractRateMatrix
 
AbstractTreeLayout - Class in jebl.gui.trees.treeviewer.treelayouts
 
AbstractTreeLayout() - Constructor for class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
AbstractTreeLayout - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
AbstractTreeLayout() - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
ActionPanel - Class in org.virion.jam.panels
Creates a panel consisting of three buttons: an add button, a remove button and an action button.
ActionPanel() - Constructor for class org.virion.jam.panels.ActionPanel
 
ActionPanel(boolean) - Constructor for class org.virion.jam.panels.ActionPanel
 
actionPerformed(ActionEvent) - Method in class org.virion.jam.framework.RecentFileList
 
actionPerformed(ActionEvent) - Method in class org.virion.jam.table.ColorEditor
Handles events from the editor button and from the dialog's OK button.
add(Sequence) - Method in interface jebl.evolution.io.ImmediateSequenceImporter.Callback
 
add(RootedTree) - Method in class jebl.evolution.trees.CladeSystem
adds all the clades in the tree
add(File) - Method in class org.virion.jam.framework.RecentFileList
Add a file to the list
add(String) - Method in class org.virion.jam.framework.RecentFileList
Add a file to the list
add(SimpleListener) - Method in class org.virion.jam.util.SimpleListenerManager
 
addActionListener(ActionListener) - Method in class org.virion.jam.framework.RecentFileList
 
addChangeListener(ChangeListener) - Method in class org.virion.jam.components.RealNumberField
 
addChangeListener(ChangeListener) - Method in class org.virion.jam.components.WholeNumberField
 
addCharacter(char, int) - Method in class jebl.evolution.align.ProfileCharacter
 
addCoalescentEvent(double) - Method in class jebl.evolution.coalescent.Intervals
 
addComponent(JComponent) - Method in class org.virion.jam.panels.OptionsPanel
 
addComponent(JComponent, boolean) - Method in class org.virion.jam.panels.OptionsPanel
 
addComponent(JComponent) - Method in class org.virion.jam.toolbar.Toolbar
 
addComponents(JComponent, JComponent) - Method in class org.virion.jam.panels.OptionsPanel
 
addComponents(JComponent, boolean, JComponent, boolean) - Method in class org.virion.jam.panels.OptionsPanel
 
addComponentWithLabel(String, JComponent) - Method in class org.virion.jam.panels.OptionsPanel
 
addComponentWithLabel(String, JComponent, boolean) - Method in class org.virion.jam.panels.OptionsPanel
 
addController(Controller) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
addController(int, Controller) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
addController(Controller) - Method in interface org.virion.jam.controlpalettes.ControlPalette
install a Controller into the palette
addControllerListener(ControllerListener) - Method in class org.virion.jam.controlpalettes.AbstractController
Add a ControllerListener to this controllers list of listeners The main listener will be the ControlPalette itself which will use this to resize the panels if the components changed
addControllerListener(ControllerListener) - Method in interface org.virion.jam.controlpalettes.Controller
Add a ControllerListener to this controllers list of listeners The main listener will be the ControlPalette itself which will use this to resize the panels if the components changed
addControlPaletteListener(ControlPaletteListener) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
addControlPaletteListener(ControlPaletteListener) - Method in interface org.virion.jam.controlpalettes.ControlPalette
Add a listener to this palette
addControlPanelListener(ControlPaletteListener) - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
addControlPanelListener(ControlPaletteListener) - Method in interface org.virion.jam.controlpanels.ControlPalette
 
addControlsProvider(ControlsProvider, boolean) - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
addControlsProvider(ControlsProvider, boolean) - Method in interface org.virion.jam.controlpanels.ControlPalette
 
addDisclosureListener(DisclosureListener) - Method in class org.virion.jam.disclosure.DisclosureButton
 
addDisclosureListener(DisclosureListener) - Method in class org.virion.jam.disclosure.DisclosurePanel
 
addEdge(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
Add a new edge between two existing nodes.
addFlexibleSpace() - Method in class org.virion.jam.toolbar.Toolbar
 
addGaps(int) - Method in class jebl.evolution.align.ProfileCharacter
 
addLabel(String) - Method in class org.virion.jam.panels.OptionsPanel
 
addLayoutComponent(Component, Object) - Method in class org.virion.jam.layouts.CompassLayout
Adds the specified named component to the layout.
addLayoutComponent(String, Component) - Method in class org.virion.jam.layouts.CompassLayout
Deprecated. replaced by addLayoutComponent(Component, Object).
addListener(RootedTreeComponent.Listener) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Add a plot listener
addMenuFactory(MenuFactory) - Method in class org.virion.jam.framework.Application
 
addMigrationEvent(double, int) - Method in class jebl.evolution.coalescent.Intervals
 
addNothingEvent(double) - Method in class jebl.evolution.coalescent.Intervals
 
addOverrideProvider(StatusProvider) - Method in interface org.virion.jam.panels.StatusProvider
 
addOverrideProvider(StatusProvider) - Method in class org.virion.jam.panels.StatusProvider.Helper
 
addPainterListener(PainterListener) - Method in class jebl.gui.trees.treeviewer.painters.AbstractPainter
 
addPainterListener(PainterListener) - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
addPainterListener(PainterListener) - Method in class jebl.gui.trees.treeviewer_dev.painters.AbstractPainter
 
addPainterListener(PainterListener) - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
 
addPreferencesSection(PreferencesSection) - Method in class org.virion.jam.framework.Application
 
addProfileCharacter(ProfileCharacter) - Method in class jebl.evolution.align.ProfileCharacter
 
addProgress(double) - Method in class jebl.util.CompositeProgressListener
 
addProgressListener(ProgressListener) - Method in interface jebl.evolution.aligners.Aligner
 
addProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
addProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
 
addProgressListener(ProgressListener) - Method in interface jebl.evolution.trees.TreeBuilder
 
addRecentFile(File) - Method in class org.virion.jam.framework.Application
 
AddRemovePanel - Class in org.virion.jam.panels
OptionsPanel.
AddRemovePanel() - Constructor for class org.virion.jam.panels.AddRemovePanel
 
AddRemovePanel(JPanel[]) - Constructor for class org.virion.jam.panels.AddRemovePanel
 
addSampleEvent(double) - Method in class jebl.evolution.coalescent.Intervals
 
addSearchPanelListener(SearchPanelListener) - Method in class org.virion.jam.panels.SearchPanel
 
addSection(PreferencesSection) - Method in class org.virion.jam.preferences.PreferencesDialog
 
addSelectedClade(Node) - Method in class jebl.gui.trees.treeviewer.TreePane
 
addSelectedClade(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
addSelectedNode(Node) - Method in class jebl.gui.trees.treeviewer.TreePane
 
addSelectedNode(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
addSelectedTaxa(Node) - Method in class jebl.gui.trees.treeviewer.TreePane
 
addSelectedTaxon(Taxon) - Method in class jebl.gui.trees.treeviewer.TreePane
 
addSelectedTip(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
addSelectedTips(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
addSeparator() - Method in class org.virion.jam.panels.OptionsPanel
 
addSeperator() - Method in class org.virion.jam.panels.OptionsPanel
Deprecated.  
addSeperator() - Method in class org.virion.jam.toolbar.Toolbar
 
addSequence(Sequence) - Method in class jebl.evolution.alignments.BasicAlignment
Adds a sequence to this alignment
addSpace() - Method in class org.virion.jam.toolbar.Toolbar
 
addSpanningComponent(JComponent) - Method in class org.virion.jam.panels.OptionsPanel
 
addStatusListener(StatusListener) - Method in interface org.virion.jam.panels.StatusProvider
Status providers must be able to store a list of StatusListeners.
addStatusListener(StatusListener) - Method in class org.virion.jam.panels.StatusProvider.Helper
 
addTaxa(Set<Taxon>) - Method in class jebl.evolution.characters.ContinuousCharacter
set the taxa for this character with a previously constructed Set
addTaxon(Taxon) - Method in interface jebl.evolution.characters.Character
add a taxon with this character
addTaxon(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
 
addTaxon(Taxon) - Method in class jebl.evolution.characters.DiscreteCharacter
 
addTree(Tree) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
addTreeLayoutListener(TreeLayoutListener) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
addTreeLayoutListener(TreeLayoutListener) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Add a listener for this layout
addTreeLayoutListener(TreeLayoutListener) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
addTreeLayoutListener(TreeLayoutListener) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Add a listener for this layout
addTreePaneListener(TreePaneListener) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
addTrees(Collection<? extends Tree>) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
addTreeSelectionListener(TreeSelectionListener) - Method in class jebl.gui.trees.treeviewer.TreePane
 
addTreeSelectionListener(TreeSelectionListener) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
addTreeViewerListener(TreeViewerListener) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
AdvancedTableUI - Class in org.virion.jam.table
 
AdvancedTableUI() - Constructor for class org.virion.jam.table.AdvancedTableUI
 
alias - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
Align - Class in jebl.evolution.align
 
Align(Scores, float) - Constructor for class jebl.evolution.align.Align
 
align(List<Sequence>, ProgressListener, boolean, boolean) - Method in class jebl.evolution.align.BartonSternberg
 
AlignCommand - Class in jebl.evolution.align
A command line interface for the algorithms in jebl.evolution.align.
AlignCommand() - Constructor for class jebl.evolution.align.AlignCommand
 
AlignCommand(String, String) - Constructor for class jebl.evolution.align.AlignCommand
 
Aligner - Interface in jebl.evolution.aligners
 
alignment - Variable in class jebl.evolution.align.PairwiseAligner.Result
 
Alignment - Interface in jebl.evolution.alignments
 
alignment - Variable in class jebl.evolution.alignments.ResampledAlignment
 
AlignmentExporter - Interface in jebl.evolution.io
 
AlignmentImporter - Interface in jebl.evolution.io
 
AlignmentTreeBuilderFactory - Class in jebl.evolution.align
 
AlignmentTreeBuilderFactory() - Constructor for class jebl.evolution.align.AlignmentTreeBuilderFactory
 
AlignmentTreeBuilderFactory.Result - Class in jebl.evolution.align
 
alignSequences(Collection<Sequence>) - Method in interface jebl.evolution.aligners.Aligner
 
allocateMatrices(int, int) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
allocateMatrices(int, int) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
ALT_YEAST - Static variable in class jebl.evolution.sequences.GeneticCode
 
AMINO_ACID - Static variable in interface jebl.evolution.sequences.SequenceType
 
AminoAcidModel - Class in jebl.evolution.substmodel
base class of rate matrices for amino acids
AminoAcidModel(double[]) - Constructor for class jebl.evolution.substmodel.AminoAcidModel
 
AminoAcids - Class in jebl.evolution.sequences
 
AminoAcids() - Constructor for class jebl.evolution.sequences.AminoAcids
 
AminoAcidScores - Class in jebl.evolution.align.scores
 
AminoAcidScores() - Constructor for class jebl.evolution.align.scores.AminoAcidScores
 
AminoAcidScores(float, float) - Constructor for class jebl.evolution.align.scores.AminoAcidScores
 
AminoAcidState - Class in jebl.evolution.sequences
 
annotateSelectedNodes(String, Object) - Method in class jebl.gui.trees.treeviewer.TreePane
 
annotateSelectedNodes(String, Object) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
annotateSelectedTaxa(String, Object) - Method in class jebl.gui.trees.treeviewer.TreePane
 
annotateSelectedTips(String, Object) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
append(char) - Method in class jebl.evolution.io.ByteBuilder
 
appendMatch(AlignmentResult, AlignmentResult) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
Application - Class in org.virion.jam.framework
 
Application(MenuBarFactory, String, String, Icon) - Constructor for class org.virion.jam.framework.Application
 
Application(MenuBarFactory, String, String, Icon, String, String) - Constructor for class org.virion.jam.framework.Application
 
AREA_ATTRIBUTE - Static variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
ARGUMENT_CHARACTER - Static variable in class org.virion.jam.app.Arguments
 
Arguments - Class in org.virion.jam.app
 
Arguments(Arguments.Option[]) - Constructor for class org.virion.jam.app.Arguments
Parse a list of arguments ready for accessing
Arguments(Arguments.Option[], boolean) - Constructor for class org.virion.jam.app.Arguments
 
Arguments.ArgumentException - Exception in org.virion.jam.app
 
Arguments.ArgumentException() - Constructor for exception org.virion.jam.app.Arguments.ArgumentException
 
Arguments.ArgumentException(String) - Constructor for exception org.virion.jam.app.Arguments.ArgumentException
 
Arguments.IntegerArrayOption - Class in org.virion.jam.app
 
Arguments.IntegerArrayOption(String, String) - Constructor for class org.virion.jam.app.Arguments.IntegerArrayOption
 
Arguments.IntegerArrayOption(String, int, String) - Constructor for class org.virion.jam.app.Arguments.IntegerArrayOption
 
Arguments.IntegerArrayOption(String, int, int, String) - Constructor for class org.virion.jam.app.Arguments.IntegerArrayOption
 
Arguments.IntegerArrayOption(String, int, int, int, String) - Constructor for class org.virion.jam.app.Arguments.IntegerArrayOption
 
Arguments.IntegerOption - Class in org.virion.jam.app
 
Arguments.IntegerOption(String, String) - Constructor for class org.virion.jam.app.Arguments.IntegerOption
 
Arguments.IntegerOption(String, int, int, String) - Constructor for class org.virion.jam.app.Arguments.IntegerOption
 
Arguments.Option - Class in org.virion.jam.app
 
Arguments.Option(String, String) - Constructor for class org.virion.jam.app.Arguments.Option
 
Arguments.RealArrayOption - Class in org.virion.jam.app
 
Arguments.RealArrayOption(String, String) - Constructor for class org.virion.jam.app.Arguments.RealArrayOption
 
Arguments.RealArrayOption(String, int, String) - Constructor for class org.virion.jam.app.Arguments.RealArrayOption
 
Arguments.RealArrayOption(String, double, double, String) - Constructor for class org.virion.jam.app.Arguments.RealArrayOption
 
Arguments.RealArrayOption(String, int, double, double, String) - Constructor for class org.virion.jam.app.Arguments.RealArrayOption
 
Arguments.RealOption - Class in org.virion.jam.app
 
Arguments.RealOption(String, String) - Constructor for class org.virion.jam.app.Arguments.RealOption
 
Arguments.RealOption(String, double, double, String) - Constructor for class org.virion.jam.app.Arguments.RealOption
 
Arguments.StringOption - Class in org.virion.jam.app
 
Arguments.StringOption(String, String, String) - Constructor for class org.virion.jam.app.Arguments.StringOption
 
Arguments.StringOption(String, String[], boolean, String) - Constructor for class org.virion.jam.app.Arguments.StringOption
 
ASCIDIAN_MT - Static variable in class jebl.evolution.sequences.GeneticCode
 
asText(Tree, int) - Static method in class jebl.evolution.trees.Utils
 
Attributable - Interface in jebl.util
Interface for associating attributeNames with an object.
Attributable.Utils - Class in jebl.util
 
Attributable.Utils() - Constructor for class jebl.util.Attributable.Utils
 
AttributableDecorator - Class in jebl.gui.trees.treeviewer_dev.decorators
 
AttributableDecorator() - Constructor for class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
AttributableHelper - Class in jebl.util
 
AttributableHelper() - Constructor for class jebl.util.AttributableHelper
 
attribute - Variable in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
AttributeBranchDecorator - Class in jebl.gui.trees.treeviewer.decorators
 
AttributeBranchDecorator(String, Map<Object, Paint>) - Constructor for class jebl.gui.trees.treeviewer.decorators.AttributeBranchDecorator
 
attributeName - Variable in class jebl.gui.trees.treeviewer.decorators.AttributeBranchDecorator
 
attributes - Variable in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
attributes - Variable in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
attributes - Variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
AuxilaryFrame - Class in org.virion.jam.framework
 
AuxilaryFrame(DocumentFrame) - Constructor for class org.virion.jam.framework.AuxilaryFrame
 
AuxilaryFrame(DocumentFrame, JPanel) - Constructor for class org.virion.jam.framework.AuxilaryFrame
 

B

B_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
B_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
BACTERIAL - Static variable in class jebl.evolution.sequences.GeneticCode
 
BartonSternberg - Class in jebl.evolution.align
 
BartonSternberg(Scores, float, float, int, boolean, boolean) - Constructor for class jebl.evolution.align.BartonSternberg
 
baseTime - Variable in class jebl.util.CompositeProgressListener
 
BasicAlignment - Class in jebl.evolution.alignments
A basic implementation of the Alignment interface.
BasicAlignment() - Constructor for class jebl.evolution.alignments.BasicAlignment
Constructs a basic alignment with no sequences.
BasicAlignment(Collection<? extends Sequence>) - Constructor for class jebl.evolution.alignments.BasicAlignment
Constructs a basic alignment from a collection of sequences.
BasicAlignment(Sequence[]) - Constructor for class jebl.evolution.alignments.BasicAlignment
Constructs a basic alignment from an array of sequences.
BasicControlPalette - Class in org.virion.jam.controlpalettes
 
BasicControlPalette(int) - Constructor for class org.virion.jam.controlpalettes.BasicControlPalette
 
BasicControlPalette(int, BasicControlPalette.DisplayMode) - Constructor for class org.virion.jam.controlpalettes.BasicControlPalette
 
BasicControlPalette(int, BasicControlPalette.DisplayMode, int) - Constructor for class org.virion.jam.controlpalettes.BasicControlPalette
 
BasicControlPalette - Class in org.virion.jam.controlpanels
 
BasicControlPalette(int) - Constructor for class org.virion.jam.controlpanels.BasicControlPalette
 
BasicControlPalette(int, BasicControlPalette.DisplayMode, boolean) - Constructor for class org.virion.jam.controlpanels.BasicControlPalette
todo We should probably dump this constructor.
BasicControlPalette(int, BasicControlPalette.DisplayMode, int) - Constructor for class org.virion.jam.controlpanels.BasicControlPalette
 
BasicControlPalette.DisplayMode - Enum in org.virion.jam.controlpalettes
 
BasicControlPalette.DisplayMode - Enum in org.virion.jam.controlpanels
 
BasicDistanceMatrix - Class in jebl.evolution.distances
 
BasicDistanceMatrix(Collection<Taxon>, double[][]) - Constructor for class jebl.evolution.distances.BasicDistanceMatrix
 
BasicLabelPainter - Class in jebl.gui.trees.treeviewer.painters
 
BasicLabelPainter(String, RootedTree, BasicLabelPainter.PainterIntent) - Constructor for class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
BasicLabelPainter(String, RootedTree, BasicLabelPainter.PainterIntent, int) - Constructor for class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
BasicLabelPainter - Class in jebl.gui.trees.treeviewer_dev.painters
A simple implementation of LabelPainter that can be used to display tip, node or branch labels.
BasicLabelPainter(BasicLabelPainter.PainterIntent) - Constructor for class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
BasicLabelPainter.PainterIntent - Enum in jebl.gui.trees.treeviewer.painters
 
BasicLabelPainter.PainterIntent - Enum in jebl.gui.trees.treeviewer_dev.painters
 
BasicSequence - Class in jebl.evolution.sequences
A default implementation of the Sequence interface.
BasicSequence(SequenceType, Taxon, CharSequence) - Constructor for class jebl.evolution.sequences.BasicSequence
Creates a sequence with a name corresponding to the taxon name.
BasicSequence(SequenceType, Taxon, State[]) - Constructor for class jebl.evolution.sequences.BasicSequence
Creates a sequence with a name corresponding to the taxon name
beginNextSubtask(String) - Method in class jebl.util.CompositeProgressListener
Convenience method to start the next operation AND set a new message.
beginNextSubtask() - Method in class jebl.util.CompositeProgressListener
begins the next subtask.
beginSubtask() - Method in class jebl.util.CompositeProgressListener
Used as an alternative to CompositeProgressListener.beginNextSubtask().
beginSubtask(String) - Method in class jebl.util.CompositeProgressListener
Used as an alternative to CompositeProgressListener.beginNextSubtask().
besti - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
bestj - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
bg1 - Variable in class org.virion.jam.table.TableRenderer
 
bg2 - Variable in class org.virion.jam.table.TableRenderer
 
Binomial - Class in jebl.math
Binomial coefficients
Binomial() - Constructor for class jebl.math.Binomial
 
BLEPHARISMA_NUC - Static variable in class jebl.evolution.sequences.GeneticCode
 
Blosum45 - Class in jebl.evolution.align.scores
 
Blosum45() - Constructor for class jebl.evolution.align.scores.Blosum45
 
Blosum50 - Class in jebl.evolution.align.scores
 
Blosum50() - Constructor for class jebl.evolution.align.scores.Blosum50
 
Blosum55 - Class in jebl.evolution.align.scores
 
Blosum55() - Constructor for class jebl.evolution.align.scores.Blosum55
 
Blosum60 - Class in jebl.evolution.align.scores
 
Blosum60() - Constructor for class jebl.evolution.align.scores.Blosum60
 
Blosum62 - Class in jebl.evolution.align.scores
 
Blosum62() - Constructor for class jebl.evolution.align.scores.Blosum62
 
Blosum65 - Class in jebl.evolution.align.scores
 
Blosum65() - Constructor for class jebl.evolution.align.scores.Blosum65
 
Blosum70 - Class in jebl.evolution.align.scores
 
Blosum70() - Constructor for class jebl.evolution.align.scores.Blosum70
 
Blosum75 - Class in jebl.evolution.align.scores
 
Blosum75() - Constructor for class jebl.evolution.align.scores.Blosum75
 
Blosum80 - Class in jebl.evolution.align.scores
 
Blosum80() - Constructor for class jebl.evolution.align.scores.Blosum80
 
Blosum85 - Class in jebl.evolution.align.scores
 
Blosum85() - Constructor for class jebl.evolution.align.scores.Blosum85
 
Blosum90 - Class in jebl.evolution.align.scores
 
Blosum90() - Constructor for class jebl.evolution.align.scores.Blosum90
 
BootrappedAlignment - Class in jebl.evolution.alignments
Date: 15/01/2006 Time: 10:13:50
BootrappedAlignment(Alignment) - Constructor for class jebl.evolution.alignments.BootrappedAlignment
 
BRANCH_LENGTHS - Static variable in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
BRANCH_LENGTHS - Static variable in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
branchColouringAttribute - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
BranchDecorator - Interface in jebl.gui.trees.treeviewer.decorators
 
branchLabelPaths - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
branchLabelPaths - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
branchPaths - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
branchPaths - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
brighten(Icon) - Static method in class org.virion.jam.util.IconUtils
Returns a slightly brighter version of the icon.
BrowserLauncher - Class in org.virion.jam.util
BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
build(Alignment, TreeBuilderFactory.Method, TreeBuilderFactory.DistanceModel, ProgressListener) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
 
build(List<Sequence>, TreeBuilderFactory.Method, PairwiseAligner, ProgressListener) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
 
build(List<Sequence>, TreeBuilderFactory.Method, MultipleAligner, ProgressListener) - Static method in class jebl.evolution.align.AlignmentTreeBuilderFactory
 
build() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
build() - Method in class jebl.evolution.trees.GreedyRootedConsensusTreeBuilder
 
build() - Method in class jebl.evolution.trees.GreedyUnrootedConsensusTreeBuilder
 
build() - Method in class jebl.evolution.trees.MRCACConsensusTreeBuilder
 
build() - Method in interface jebl.evolution.trees.TreeBuilder
 
buildMenu(JMenu) - Method in class org.virion.jam.framework.RecentFileList
Adds the recent file list to a menu.
buildRooted(RootedTree[], double, TreeBuilderFactory.ConsensusMethod) - Static method in class jebl.evolution.trees.TreeBuilderFactory
 
buildRooted(Tree[], double, TreeBuilderFactory.ConsensusMethod) - Static method in class jebl.evolution.trees.TreeBuilderFactory
convenience method.
buildScores(float[][]) - Method in class jebl.evolution.align.scores.Scores
 
buildUnRooted(Tree[], Taxon, double, TreeBuilderFactory.ConsensusMethod) - Static method in class jebl.evolution.trees.TreeBuilderFactory
 
ByteBuilder - Class in jebl.evolution.io
 
ByteBuilder(int) - Constructor for class jebl.evolution.io.ByteBuilder
 

C

C_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
C_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
calculateAnalyticalLogLikelihood(IntervalList) - Static method in class jebl.evolution.coalescent.Coalescent
Calculates the log likelihood of this set of coalescent intervals, using an analytical integration over theta.
calculateBranchLengths() - Method in class jebl.evolution.trees.MutableRootedTree
Calculate branch lengths from the current node heights.
calculateBranchLengths() - Method in class jebl.evolution.trees.SimpleRootedTree
Calculate branch lengths from the current node heights.
calculateLogLikelihood() - Method in class jebl.evolution.coalescent.Coalescent
Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
calculateLogLikelihood(IntervalList, DemographicFunction) - Static method in class jebl.evolution.coalescent.Coalescent
Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
calculateScaleRange() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
calibrate(Graphics2D, Node) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
calibrate(Graphics2D, T) - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
calibrate(Graphics2D, TreePane) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
calibrate(Graphics2D, Node) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
calibrate(Graphics2D, Node) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
calibrate(Graphics2D, Node) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
calibrate(Graphics2D, T) - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
Called to calibrate the painters for a given graphics context.
calibrate(Graphics2D, TreePane) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
calloutPaths - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
calloutPaths - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.AminoAcids
 
CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.Codons
 
CANONICAL_STATE_COUNT - Static variable in class jebl.evolution.sequences.Nucleotides
 
CANONICAL_STATES - Static variable in class jebl.evolution.sequences.AminoAcids
 
CANONICAL_STATES - Static variable in class jebl.evolution.sequences.Codons
 
CANONICAL_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
 
cardinality() - Method in class jebl.util.FixedBitSet
 
CataclysmicDemographic - Class in jebl.evolution.coalescent
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
CataclysmicDemographic() - Constructor for class jebl.evolution.coalescent.CataclysmicDemographic
Construct demographic model with default settings
CataclysmicDemographic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.CataclysmicDemographic
Construct demographic model with given settings
CENTER - Static variable in interface org.virion.jam.framework.MenuFactory
 
centerComponent(Component, Component) - Static method in class org.virion.jam.util.Utils
Center a component in reference to another, if the reference is null or not visible the screen is used as reference
changedUpdate(DocumentEvent) - Method in class org.virion.jam.components.RealNumberField
 
changedUpdate(DocumentEvent) - Method in class org.virion.jam.components.WholeNumberField
 
changeListeners - Variable in class org.virion.jam.components.RealNumberField
 
changeListeners - Variable in class org.virion.jam.components.WholeNumberField
 
Character - Interface in jebl.evolution.characters
 
characters - Variable in class jebl.evolution.align.ProfileCharacter
 
CharacterType - Interface in jebl.evolution.characters
 
charAt(int) - Method in class jebl.evolution.io.ByteBuilder
 
CHEMICAL_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids
 
choleskyFactor(double[][]) - Static method in class jebl.math.MatrixCalc
Cholesky factorization (aka Cholesky Decomposition) This factorization can be used when square matrix is symmetric and positive definite.
choleskySolve(double[][], double[]) - Static method in class jebl.math.MatrixCalc
Cholesky solve Once the matrix is decomposed with the above routine, one can solve the triangular factor with backsubstitution.
choose(double, double) - Static method in class jebl.math.Binomial
Binomial coefficient n choose k
choose2(int) - Static method in class jebl.math.Binomial
get n choose 2
CILIATE - Static variable in class jebl.evolution.sequences.GeneticCode
 
CladeSystem - Class in jebl.evolution.trees
Stores a set of unique clades for a tree
CladeSystem() - Constructor for class jebl.evolution.trees.CladeSystem
 
CladeSystem(RootedTree) - Constructor for class jebl.evolution.trees.CladeSystem
 
clear() - Method in class jebl.evolution.align.ProfileCharacter
 
clear(int) - Method in class jebl.util.FixedBitSet
 
clearAllProgress() - Method in class jebl.util.CompositeProgressListener
Clear all progress, including that of previous subtasks.
clearDirty() - Method in class org.virion.jam.framework.AbstractFrame
 
clearFile() - Method in class org.virion.jam.framework.DocumentFrame
 
clearLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
 
clearSelectedTaxa() - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
clearSelectedTaxa() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
clearSelection() - Method in class jebl.gui.trees.treeviewer.TreePane
 
clearSelection() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
close() - Method in class org.virion.jam.framework.AboutBox
Sets the visibility to false and disposes the frame.
closed(Component) - Method in interface org.virion.jam.disclosure.DisclosureListener
 
closeReader() - Method in class jebl.evolution.io.ImportHelper
 
closeWindowAction - Variable in class org.virion.jam.framework.AbstractFrame
 
closing(Component) - Method in interface org.virion.jam.disclosure.DisclosureListener
 
CLUSTALW - Static variable in class jebl.evolution.align.scores.NucleotideScores
 
ClusteringTreeBuilder<T extends Tree> - Class in jebl.evolution.trees
An abstract base class for clustering algorithms from pairwise distances
ClusteringTreeBuilder(DistanceMatrix, int) - Constructor for class jebl.evolution.trees.ClusteringTreeBuilder
Constructor
clusters - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
Coalescent - Class in jebl.evolution.coalescent
A likelihood function for the coalescent.
Coalescent(RootedTree, DemographicFunction) - Constructor for class jebl.evolution.coalescent.Coalescent
 
Coalescent(IntervalList, DemographicFunction) - Constructor for class jebl.evolution.coalescent.Coalescent
 
CoalescentIntervalGenerator - Class in jebl.evolution.coalescent
This is a class that draws coalescent intervals under the given demographic function.
CoalescentIntervalGenerator(DemographicFunction) - Constructor for class jebl.evolution.coalescent.CoalescentIntervalGenerator
 
CODON - Static variable in interface jebl.evolution.sequences.SequenceType
 
Codons - Class in jebl.evolution.sequences
 
Codons() - Constructor for class jebl.evolution.sequences.Codons
 
CodonState - Class in jebl.evolution.sequences
 
COLLAPSE_ATTRIBUTE_NAME - Variable in class jebl.gui.trees.treeviewer_dev.TreePane
 
collapseAttributeName - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
collapsedShapes - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
collapseSelected() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
collapseSelectedNodes() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
ColorEditor - Class in org.virion.jam.table
 
ColorEditor() - Constructor for class org.virion.jam.table.ColorEditor
 
ColorRenderer - Class in org.virion.jam.table
 
ColorRenderer(boolean) - Constructor for class org.virion.jam.table.ColorRenderer
 
Command - Interface in org.virion.jam.framework
 
CompactRootedTree - Class in jebl.evolution.trees
A memory efficient rooted tree.
CompactRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.CompactRootedTree
Do all the hard work.
compareTo(Object) - Method in class jebl.evolution.alignments.ConsensusSequence
Sequences are compared by their taxa
compareTo(Object) - Method in class jebl.evolution.sequences.AminoAcidState
 
compareTo(Object) - Method in class jebl.evolution.sequences.BasicSequence
Sequences are compared by their taxa
compareTo(Object) - Method in class jebl.evolution.sequences.FilteredSequence
 
compareTo(Object) - Method in class jebl.evolution.sequences.NucleotideState
 
compareTo(Object) - Method in class jebl.evolution.sequences.State
 
compareTo(Object) - Method in class jebl.evolution.taxa.Taxon
 
CompassLayout - Class in org.virion.jam.layouts
A layout manager similar to BorderLayout but with 8 compass directions.
CompassLayout() - Constructor for class org.virion.jam.layouts.CompassLayout
Constructs a new CompassLayout.
CompassLayout(int, int) - Constructor for class org.virion.jam.layouts.CompassLayout
Constructs a CompassLayout with the specified gaps.
complement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
 
complement(FixedBitSet) - Static method in class jebl.util.FixedBitSet
 
complement() - Method in class jebl.util.FixedBitSet
 
COMPLEMENTARY_STATES - Static variable in class jebl.evolution.sequences.Nucleotides
 
CompositeProgressListener - Class in jebl.util
 
CompositeProgressListener(ProgressListener, double[]) - Constructor for class jebl.util.CompositeProgressListener
 
computeEpsilon() - Static method in class jebl.math.MachineAccuracy
compute EPSILON from scratch
conceptuallyUnrooted() - Method in class jebl.evolution.trees.CompactRootedTree
 
conceptuallyUnrooted() - Method in class jebl.evolution.trees.FilteredRootedTree
 
conceptuallyUnrooted() - Method in class jebl.evolution.trees.MutableRootedTree
 
conceptuallyUnrooted() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
conceptuallyUnrooted() - Method in interface jebl.evolution.trees.RootedTree
Deprecated. This should be removed. If this is a rooted tree then it is rooted. This can really only confuse things. Trees are unrooted, RootedTrees are rooted. This is not an implementation limitation. It may be that a RootedTree has an arbitrary root but it is still rooted. With a rooted tree, it is convenient to store branch information at the node (i.e., for the branch above the node) because there is no "branch" object. Andrew.
conceptuallyUnrooted() - Method in class jebl.evolution.trees.SimpleRootedTree
 
ConsensusSequence - Class in jebl.evolution.alignments
 
ConsensusSequence(Taxon, Alignment) - Constructor for class jebl.evolution.alignments.ConsensusSequence
Creates a FilteredSequence wrapper to the given source sequence.
ConsensusTreeBuilder<T extends Tree> - Class in jebl.evolution.trees
Build a consensus tree for a set of trees.
ConsensusTreeBuilder.Method - Enum in jebl.evolution.trees
Supported consesus methods.
ConsoleApplication - Class in org.virion.jam.console
 
ConsoleApplication(String, String, Icon, boolean) - Constructor for class org.virion.jam.console.ConsoleApplication
 
ConsoleApplication(MenuBarFactory, String, String, Icon, boolean) - Constructor for class org.virion.jam.console.ConsoleApplication
 
ConsoleFrame - Class in org.virion.jam.console
 
ConsoleFrame() - Constructor for class org.virion.jam.console.ConsoleFrame
 
ConsoleMenuBarFactory - Class in org.virion.jam.console
 
ConsoleMenuBarFactory() - Constructor for class org.virion.jam.console.ConsoleMenuBarFactory
 
ConstantPopulation - Class in jebl.evolution.coalescent
This class models coalescent intervals for a constant population (parameter: N0=present-day population size).
ConstantPopulation() - Constructor for class jebl.evolution.coalescent.ConstantPopulation
Construct demographic model with default settings
ConstantPopulation(double) - Constructor for class jebl.evolution.coalescent.ConstantPopulation
Construct demographic model with given settings
ConstExponential - Class in jebl.evolution.coalescent
This class models exponential growth from an initial population size.
ConstExponential() - Constructor for class jebl.evolution.coalescent.ConstExponential
Construct demographic model with default settings
ConstExponential(double, double, double) - Constructor for class jebl.evolution.coalescent.ConstExponential
Construct demographic model with given settings
ConstLogistic - Class in jebl.evolution.coalescent
This class models logistic growth from an initial population size.
ConstLogistic() - Constructor for class jebl.evolution.coalescent.ConstLogistic
Construct demographic model with default settings
ConstLogistic(double, double, double, double) - Constructor for class jebl.evolution.coalescent.ConstLogistic
Construct demographic model with given settings
construct() - Method in class org.virion.jam.util.SwingWorker
Compute the value to be returned by the get method.
constructConsensus(Alignment) - Static method in class jebl.evolution.alignments.ConsensusSequence
 
contains(int) - Method in class jebl.util.FixedBitSet
 
CONTINUOUS - Static variable in interface jebl.evolution.characters.CharacterType
 
ContinuousCharacter - Class in jebl.evolution.characters
 
ContinuousCharacter(String, String) - Constructor for class jebl.evolution.characters.ContinuousCharacter
Constructs a basic ContinuousCharacter object with no taxa added yet
ContinuousCharacter(String, String, Set<Taxon>) - Constructor for class jebl.evolution.characters.ContinuousCharacter
Constructs a basic ContinuousCharacter object with taxa added
ContinuousColorDecorator - Class in jebl.gui.trees.treeviewer_dev.decorators
This decorator takes an attribute name and a set of attibutable Objects.
ContinuousColorDecorator(String, Set<? extends Attributable>, Color, Color) - Constructor for class jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator
 
Controller - Interface in org.virion.jam.controlpalettes
 
ControllerListener - Interface in org.virion.jam.controlpalettes
 
ControlPalette - Interface in org.virion.jam.controlpalettes
Date: 20/03/2006 Time: 10:23:21
ControlPalette - Interface in org.virion.jam.controlpanels
Date: 20/03/2006 Time: 10:23:21
ControlPaletteListener - Interface in org.virion.jam.controlpalettes
 
ControlPaletteListener - Interface in org.virion.jam.controlpanels
 
Controls - Class in org.virion.jam.controlpanels
 
Controls(String, JPanel, boolean) - Constructor for class org.virion.jam.controlpanels.Controls
 
Controls(String, JPanel, boolean, boolean, JCheckBox) - Constructor for class org.virion.jam.controlpanels.Controls
 
controlsChanged() - Method in interface org.virion.jam.controlpalettes.ControllerListener
 
controlsChanged() - Method in interface org.virion.jam.controlpalettes.ControlPaletteListener
 
controlsChanged() - Method in interface org.virion.jam.controlpanels.ControlPaletteListener
 
ControlsProvider - Interface in org.virion.jam.controlpanels
 
ControlsSettings - Interface in org.virion.jam.controlpanels
 
copy(double[], double[]) - Static method in class jebl.math.MultivariateMinimum
Copy source vector into target vector
copy(double[][], double[][]) - Static method in class jebl.util.Utils
Copies all of source into dest - assumes dest to be large enough
copyIntervals(Intervals) - Method in class jebl.evolution.coalescent.Intervals
 
copyMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
copy one matrix into another
count - Variable in class jebl.evolution.align.ProfileCharacter
 
createDefaultModel() - Method in class org.virion.jam.components.RealNumberField
 
createDefaultModel() - Method in class org.virion.jam.components.WholeNumberField
 
createDocumentFrame(Application, MenuBarFactory) - Method in interface org.virion.jam.framework.DocumentFrameFactory
 
createDocumentFrame() - Method in class org.virion.jam.framework.MultiDocApplication
 
createExternalNode(Taxon) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
createExternalNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
Creates a new external node with the given taxon.
createExternalNode(Taxon) - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
 
createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
Creates a new external node with the given taxon.
createExternalNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
Creates a new external node with the given taxon.
createInternalNode(Node[], double[]) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.MutableRootedTree
Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
createInternalNode(Node[], double[]) - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
Creates a new internal node that will have the specified nodes as its children
createInternalNode(List<? extends Node>) - Method in class jebl.evolution.trees.SimpleRootedTree
Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
createInternalNode(List<Node>) - Method in class jebl.evolution.trees.SimpleTree
Once a SimpleTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode.
createMouseInputListener() - Method in class org.virion.jam.table.AdvancedTableUI
 
createNodeDensityComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
 
createNodeDensityMinNodeHeightComparator(RootedTree) - Static method in class jebl.evolution.trees.Utils
 
createNodes(RootedTree, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
Clones the entire tree structure from the given RootedTree.
createNodes(Tree, Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
Clones the entire tree structure from the given (unrooted) Tree.
createNullMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
Creates a MinimiserMonitor that looses all output
createOrderEnumerator(int) - Method in interface jebl.math.OrderEnumerator.OEFactory
For generating an ordering from 0..size-1.
createPanel() - Method in class org.virion.jam.panels.AddRemovePanel
 
createSimpleMonitor(PrintWriter) - Static method in class jebl.math.MinimiserMonitor.Utils
Creates a MinimiserMonitor that outputs current minimum to a print stream
createSplitMonitor(MinimiserMonitor, MinimiserMonitor) - Static method in class jebl.math.MinimiserMonitor.Utils
creates a monitor such that all information sent to monitor is based on two sub monitors
createStringMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
Creates a MinimiserMonitor that Stores output (use toString() to access current results)
createSystemErrorMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
Creates a MinimiserMonitor that outputs current minimum to a System.err
createSystemOuptutMonitor() - Static method in class jebl.math.MinimiserMonitor.Utils
Creates a MinimiserMonitor that outputs current minimum to a System.out
current - Variable in class org.virion.jam.util.SimpleLongTask
 
currentOperationNum - Variable in class jebl.util.CompositeProgressListener
 
currentOperationProgress - Variable in class jebl.util.CompositeProgressListener
 

D

D_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
D_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
darken(Icon) - Static method in class org.virion.jam.util.IconUtils
Returns a slightly darker version of the icon.
debug(Object) - Method in class jebl.math.OrthogonalSearch
 
DEBUGsubTreeRep(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
 
Decorator - Interface in jebl.gui.trees.treeviewer_dev.decorators
 
DEFAULT_OPENING_SPEED - Static variable in class org.virion.jam.controlpalettes.BasicControlPalette
 
DEFAULT_PAINTS - Static variable in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
DEFAULT_SUPPORT_ATTRIBUTE_NAME - Static variable in class jebl.evolution.trees.ConsensusTreeBuilder
Name of attribute specifing amount of support for branch
DefaultEditMenuFactory - Class in org.virion.jam.framework
 
DefaultEditMenuFactory() - Constructor for class org.virion.jam.framework.DefaultEditMenuFactory
 
DefaultFileMenuFactory - Class in org.virion.jam.framework
 
DefaultFileMenuFactory(boolean) - Constructor for class org.virion.jam.framework.DefaultFileMenuFactory
 
DefaultHelpMenuFactory - Class in org.virion.jam.framework
 
DefaultHelpMenuFactory() - Constructor for class org.virion.jam.framework.DefaultHelpMenuFactory
 
DefaultMenuBarFactory - Class in org.virion.jam.framework
 
DefaultMenuBarFactory() - Constructor for class org.virion.jam.framework.DefaultMenuBarFactory
 
deleteMatrixColumn(double[][], int) - Static method in class jebl.math.MatrixCalc
takes a matrix and deletes a column
deleteMatrixRow(double[][], int) - Static method in class jebl.math.MatrixCalc
takes a matrix and deletes a row
DemoApplication - Class in org.virion.jam.demo
 
DemoApplication(MenuBarFactory, String, String, Icon) - Constructor for class org.virion.jam.demo.DemoApplication
 
DemoFrame - Class in org.virion.jam.demo
 
DemoFrame(String) - Constructor for class org.virion.jam.demo.DemoFrame
 
demographicFunction - Variable in class jebl.evolution.coalescent.CoalescentIntervalGenerator
 
DemographicFunction - Interface in jebl.evolution.coalescent
This interface provides methods that describe a demographic function.
DemographicFunction.Utils - Class in jebl.evolution.coalescent
 
DemographicFunction.Utils() - Constructor for class jebl.evolution.coalescent.DemographicFunction.Utils
 
DemoMenuBarFactory - Class in org.virion.jam.demo
 
DemoMenuBarFactory() - Constructor for class org.virion.jam.demo.DemoMenuBarFactory
 
DemoMenuFactory - Class in org.virion.jam.demo.menus
 
DemoMenuFactory() - Constructor for class org.virion.jam.demo.menus.DemoMenuFactory
 
DemoMenuHandler - Interface in org.virion.jam.demo.menus
 
deregisterMenuFactories() - Method in class org.virion.jam.framework.DefaultMenuBarFactory
 
deregisterMenuFactories() - Method in interface org.virion.jam.framework.MenuBarFactory
 
description - Variable in class org.virion.jam.util.SimpleLongTask
 
descriptionPropertyName - Static variable in class jebl.evolution.io.FastaImporter
Name of Jebl sequence property which stores sequence description (i.e.
destroyDocumentFrame(DocumentFrame) - Method in class org.virion.jam.framework.MultiDocApplication
 
detachChildren(Node, List<Integer>) - Method in class jebl.evolution.trees.MutableRootedTree
 
diagonalHessian(MultivariateFunction, double[]) - Static method in class jebl.math.NumericalDerivative
determine diagonal of Hessian
disableDoubleBuffering(Component) - Static method in class org.virion.jam.util.PrintUtilities
The speed and quality of printing suffers dramatically if any of the containers have double buffering turned on.
DisclosureButton - Class in org.virion.jam.disclosure
 
DisclosureButton() - Constructor for class org.virion.jam.disclosure.DisclosureButton
 
DisclosureButton(int) - Constructor for class org.virion.jam.disclosure.DisclosureButton
 
DisclosureListener - Interface in org.virion.jam.disclosure
 
DisclosurePanel - Class in org.virion.jam.disclosure
 
DisclosurePanel(String, JPanel, boolean) - Constructor for class org.virion.jam.disclosure.DisclosurePanel
 
DisclosurePanel(JComponent, JPanel, boolean, int) - Constructor for class org.virion.jam.disclosure.DisclosurePanel
 
DISCRETE - Static variable in interface jebl.evolution.characters.CharacterType
 
DiscreteCharacter - Class in jebl.evolution.characters
 
DiscreteCharacter(String, String, int) - Constructor for class jebl.evolution.characters.DiscreteCharacter
Constructs a basic DiscreteCharacter object with no taxa added yet
DiscreteCharacter(String, String, int, Set<Taxon>) - Constructor for class jebl.evolution.characters.DiscreteCharacter
Constructs a basic DiscreteCharacter object with taxa
DiscreteColorDecorator - Class in jebl.gui.trees.treeviewer_dev.decorators
This decorator takes an attribute name and a set of attibutable Objects.
DiscreteColorDecorator() - Constructor for class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
DiscreteColorDecorator(Color[]) - Constructor for class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
DiscreteColorDecorator(String, Set<? extends Attributable>) - Constructor for class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
DiscreteColorDecorator(String, Set<? extends Attributable>, Color[]) - Constructor for class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
displayAttribute - Variable in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
displayAttributes - Variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
displayURL(String) - Method in class org.virion.jam.framework.Application
 
displayValues - Variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
distance - Variable in class jebl.evolution.align.AlignmentTreeBuilderFactory.Result
 
distance - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
DistanceMatrix - Interface in jebl.evolution.distances
 
distanceMatrix - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
DistanceMatrixImporter - Interface in jebl.evolution.io
 
DistanceMatrixImporter.Triangle - Enum in jebl.evolution.io
 
doAbout() - Method in class org.virion.jam.framework.Application
 
doAlign(List<Sequence>, RootedTree, ProgressListener) - Method in class jebl.evolution.align.BartonSternberg
 
doAlign(Alignment, Alignment, ProgressListener) - Method in class jebl.evolution.align.BartonSternberg
 
doAlign(Alignment, Sequence, ProgressListener) - Method in class jebl.evolution.align.BartonSternberg
 
doAlign(List<Sequence>, RootedTree, ProgressListener) - Method in interface jebl.evolution.align.MultipleAligner
 
doAlign(Alignment, Alignment, ProgressListener) - Method in interface jebl.evolution.align.MultipleAligner
 
doAlign(Alignment, Sequence, ProgressListener) - Method in interface jebl.evolution.align.MultipleAligner
 
doAlignment(String, String) - Method in class jebl.evolution.align.Align
Performs the alignment, abstract.
doAlignment(String, String) - Method in class jebl.evolution.align.MaximalSegmentPair
 
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunsch
 
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
doAlignment(String, String, int, int) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
doAlignment(Profile, Profile, int, int, int, int, int, int) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
doAlignment(Profile, Profile, int, int, int, int, int, int, boolean, boolean) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
 
doAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
doAlignment(String, String, ProgressListener, boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
doAlignment(String, String, ProgressListener) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
doAlignment(Profile, Profile, ProgressListener, boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
doAlignment(Sequence, Sequence, ProgressListener) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
doAlignment(String, String) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
 
doAlignment(String, String) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
 
doAlignment(String, String) - Method in class jebl.evolution.align.OverlapAlign
 
doAlignment(Sequence, Sequence, ProgressListener) - Method in interface jebl.evolution.align.PairwiseAligner
 
doAlignment(String, String, ProgressListener) - Method in class jebl.evolution.align.SmithWaterman
 
doAlignment(String, String) - Method in class jebl.evolution.align.SmithWaterman
 
doAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
 
doAlignment(String, String, ProgressListener) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
 
doAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
 
doCloseWindow() - Method in class org.virion.jam.console.ConsoleApplication
 
doCloseWindow() - Method in class org.virion.jam.framework.AbstractFrame
 
doCloseWindow() - Method in class org.virion.jam.framework.AuxilaryFrame
 
doCloseWindow() - Method in class org.virion.jam.framework.SingleDocApplication
 
doCopy() - Method in class org.virion.jam.console.ConsoleFrame
 
doCopy() - Method in class org.virion.jam.demo.DemoFrame
 
doCopy() - Method in class org.virion.jam.framework.AbstractFrame
 
DocumentFrame - Class in org.virion.jam.framework
 
DocumentFrame() - Constructor for class org.virion.jam.framework.DocumentFrame
 
DocumentFrameFactory - Interface in org.virion.jam.framework
 
doCut() - Method in class org.virion.jam.framework.AbstractFrame
 
doDelete() - Method in class org.virion.jam.framework.AbstractFrame
 
doExport() - Method in class org.virion.jam.framework.AbstractFrame
 
doFind() - Method in class org.virion.jam.demo.DemoFrame
 
doFind() - Method in class org.virion.jam.framework.AbstractFrame
 
doFindAgain() - Method in class org.virion.jam.demo.DemoFrame
 
doHelp() - Method in class org.virion.jam.framework.Application
 
doImport() - Method in class org.virion.jam.framework.AbstractFrame
 
doMatch(Output, String, boolean) - Method in class jebl.evolution.align.Align
Print the score, the F matrix, and the alignment
doMatch(Output, String) - Method in class jebl.evolution.align.Align
Print the score and the alignment
doMinimizeWindow() - Method in class org.virion.jam.framework.AbstractFrame
 
done() - Method in class org.virion.jam.util.LongTask
Called to find out if the task has completed.
doNew() - Method in class org.virion.jam.console.ConsoleApplication
 
doNew() - Method in class org.virion.jam.framework.Application
 
doNew() - Method in class org.virion.jam.framework.MultiDocApplication
 
doNew() - Method in class org.virion.jam.framework.SingleDocApplication
 
doOpen() - Method in class org.virion.jam.framework.Application
 
doOpen(String) - Method in class org.virion.jam.framework.Application
 
doOpenFile(File) - Method in class org.virion.jam.console.ConsoleApplication
 
doOpenFile(File) - Method in class org.virion.jam.framework.Application
 
doOpenFile(File) - Method in class org.virion.jam.framework.MultiDocApplication
 
doOpenFile(File) - Method in class org.virion.jam.framework.SingleDocApplication
 
doPageSetup() - Method in class org.virion.jam.framework.Application
 
doPaste() - Method in class org.virion.jam.framework.AbstractFrame
 
doPreferences() - Method in class org.virion.jam.console.ConsoleApplication
 
doPreferences() - Method in class org.virion.jam.framework.Application
 
doPrint() - Method in class org.virion.jam.framework.AbstractFrame
 
doPrint(boolean) - Method in class org.virion.jam.framework.AbstractFrame
 
doQuit() - Method in class org.virion.jam.console.ConsoleApplication
 
doQuit() - Method in class org.virion.jam.framework.Application
 
doQuit() - Method in class org.virion.jam.framework.MultiDocApplication
 
doQuit() - Method in class org.virion.jam.framework.SingleDocApplication
 
doRound(double[], UnivariateMinimum, double, double, MinimiserMonitor) - Method in interface jebl.math.OrthogonalSearch.RoundOptimiser
 
doSave() - Method in class org.virion.jam.framework.DocumentFrame
 
doSaveAs() - Method in class org.virion.jam.framework.DocumentFrame
 
doSelectAll() - Method in class org.virion.jam.console.ConsoleFrame
 
doSelectAll() - Method in class org.virion.jam.framework.AbstractFrame
 
doStop() - Method in class org.virion.jam.console.ConsoleApplication
 
doWebsite() - Method in class org.virion.jam.framework.Application
 
doWork() - Method in class org.virion.jam.util.LongTask
Does the actual work and returns some kind of result.
doZoomWindow() - Method in class org.virion.jam.framework.AbstractFrame
 
drawHorizontals(boolean) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
 
drawLabels(boolean) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
 
drawTree(Graphics2D, double, double) - Method in class jebl.gui.trees.treeviewer.TreePane
 
drawTree(Graphics2D, double, double) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
drawVerticals(boolean) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
 
duplicate(Scores) - Static method in class jebl.evolution.align.scores.Scores
 

E

E_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
ECHINODERM_MT - Static variable in class jebl.evolution.sequences.GeneticCode
 
Edge - Interface in jebl.evolution.graphs
Represents a node in a graph or tree.
EDIT - Static variable in class org.virion.jam.table.ColorEditor
 
EMPTY - Static variable in class jebl.util.ProgressListener
A ProgressListener that ignores all events and always returns false from ProgressListener.isCanceled().
enableDoubleBuffering(Component) - Static method in class org.virion.jam.util.PrintUtilities
Re-enables double buffering globally.
enablePrefs(boolean) - Static method in class org.virion.jam.maconly.OSXAdapter
 
EPSILON - Static variable in class jebl.math.MachineAccuracy
machine accuracy constant
equal(RootedTree, RootedTree) - Static method in class jebl.evolution.trees.RootedTreeUtils
Compares 2 trees and returns true if they have the same topology.
equals(Object) - Method in class jebl.evolution.sequences.State
 
equals(Taxon) - Method in class jebl.evolution.taxa.Taxon
 
equals(Object) - Method in class jebl.util.FixedBitSet
 
ERROR - Static variable in class org.virion.jam.panels.StatusPanel
 
errorMsg() - Method in class org.virion.jam.components.RealNumberField
 
errorMsg() - Method in class org.virion.jam.components.WholeNumberField
 
escapePressed() - Method in class org.virion.jam.console.ConsoleFrame
 
EUPLOTID_NUC - Static variable in class jebl.evolution.sequences.GeneticCode
 
evaluate(double[]) - Method in class jebl.evolution.coalescent.Coalescent
 
evaluate(double[]) - Method in interface jebl.math.MultivariateFunction
compute function value
evaluate(double) - Method in class jebl.math.OrthogonalLineFunction
 
evaluate(double) - Method in interface jebl.math.UnivariateFunction
compute function value
exitAction - Variable in class org.virion.jam.framework.Application
 
Expansion - Class in jebl.evolution.coalescent
This class models exponential growth from an initial ancestral population size.
Expansion() - Constructor for class jebl.evolution.coalescent.Expansion
Construct demographic model with default settings
Expansion(double, double, double) - Constructor for class jebl.evolution.coalescent.Expansion
Construct demographic model with given settings
ExponentialGrowth - Class in jebl.evolution.coalescent
This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).
ExponentialGrowth() - Constructor for class jebl.evolution.coalescent.ExponentialGrowth
Construct demographic model with default settings
ExponentialGrowth(double, double) - Constructor for class jebl.evolution.coalescent.ExponentialGrowth
Construct demographic model with given settings
Exportable - Interface in org.virion.jam.framework
 
exportAlignment(Alignment) - Method in interface jebl.evolution.io.AlignmentExporter
exportAlignment.
exportAlignment(Alignment) - Method in class jebl.evolution.io.MEGAExporter
 
exportAlignment(Alignment) - Method in class jebl.evolution.io.NexusExporter
exportAlignment.
exportAlignment(Alignment) - Method in class jebl.evolution.io.PHYLIPExporter
 
exportMatrix(DistanceMatrix) - Method in class jebl.evolution.io.NexusExporter
 
exportSequences(Collection<? extends Sequence>) - Method in class jebl.evolution.io.FastaExporter
export alignment or set of sequences.
exportSequences(Collection<? extends Sequence>) - Method in class jebl.evolution.io.NexusExporter
export alignment.
exportSequences(Collection<? extends Sequence>) - Method in interface jebl.evolution.io.SequenceExporter
exportSequences.
exportTree(Tree) - Method in class jebl.evolution.io.NewickExporter
Export a single tree
exportTree(Tree) - Method in class jebl.evolution.io.NexusExporter
Export a single tree
exportTree(Tree) - Method in interface jebl.evolution.io.TreeExporter
Export a single tree
exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.NewickExporter
Export a collection of trees
exportTrees(Collection<? extends Tree>) - Method in class jebl.evolution.io.NexusExporter
export trees
exportTrees(Collection<? extends Tree>) - Method in interface jebl.evolution.io.TreeExporter
Export a collection of trees
exportTreesWithTranslation(Collection<? extends Tree>, Map<String, String>) - Method in class jebl.evolution.io.NexusExporter
 

F

f2minx - Variable in class jebl.math.UnivariateMinimum
curvature at minimum
F84DistanceMatrix - Class in jebl.evolution.distances
 
F84DistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.F84DistanceMatrix
 
F84DistanceMatrix(Alignment) - Constructor for class jebl.evolution.distances.F84DistanceMatrix
 
F_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
FastaExporter - Class in jebl.evolution.io
Class for exporting a fasta file format.
FastaExporter(Writer) - Constructor for class jebl.evolution.io.FastaExporter
Constructor
FastaImporter - Class in jebl.evolution.io
Class for importing Fasta sequential file format.
FastaImporter(File, SequenceType) - Constructor for class jebl.evolution.io.FastaImporter
Use this constructor if you are reading from a file.
FastaImporter(Reader, SequenceType) - Constructor for class jebl.evolution.io.FastaImporter
Deprecated. 
FilteredRootedTree - Class in jebl.evolution.trees
 
FilteredRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.FilteredRootedTree
 
FilteredSequence - Class in jebl.evolution.sequences
 
FilteredSequence(Sequence) - Constructor for class jebl.evolution.sequences.FilteredSequence
Creates a FilteredSequence wrapper to the given source sequence.
filterSequence(Sequence) - Method in class jebl.evolution.sequences.FilteredSequence
 
filterSequence(Sequence) - Method in class jebl.evolution.sequences.GaplessSequence
 
filterSequence(Sequence) - Method in class jebl.evolution.sequences.TranslatedSequence
 
findEndBlock() - Method in class jebl.evolution.io.NexusImporter
Finds the end of the current block.
findMinimum(MultivariateFunction, double[]) - Method in class jebl.math.MultivariateMinimum
Find minimum close to vector x
findMinimum(MultivariateFunction, double[], int, int) - Method in class jebl.math.MultivariateMinimum
Find minimum close to vector x (desired fractional digits for each parameter is specified)
findMinimum(MultivariateFunction, double[], int, int, MinimiserMonitor) - Method in class jebl.math.MultivariateMinimum
Find minimum close to vector x (desired fractional digits for each parameter is specified)
findMinimum(double, UnivariateFunction) - Method in class jebl.math.UnivariateMinimum
Find minimum (first estimate given)
findMinimum(double, UnivariateFunction, int) - Method in class jebl.math.UnivariateMinimum
Find minimum (first estimate given, desired number of fractional digits specified)
findMinimum(UnivariateFunction) - Method in class jebl.math.UnivariateMinimum
Find minimum (no first estimate given)
findMinimum(UnivariateFunction, int) - Method in class jebl.math.UnivariateMinimum
Find minimum (no first estimate given, desired number of fractional digits specified)
findNextBlock() - Method in class jebl.evolution.io.NexusImporter
This function returns an integer to specify what the next block in the file is.
findNextPair() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
Find next two clusters to join.
findNextPair() - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
 
findNodeAtPoint(Point2D) - Method in interface jebl.gui.trees.treecomponent.RootedTreePainter
Find the node under point.
findNodeAtPoint(Point2D) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Find the node under point.
finish() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
finish() - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
 
finished() - Method in class org.virion.jam.util.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
finishedTraceBack() - Method in interface jebl.evolution.align.TracebackPlotter
 
fire() - Method in class org.virion.jam.util.SimpleListenerManager
 
fireActionPerformed(ActionEvent) - Method in class org.virion.jam.framework.RecentFileList
An action event is fired when the user selects one of the files from a menu.
fireChanged() - Method in class org.virion.jam.components.RealNumberField
 
fireChanged() - Method in class org.virion.jam.components.WholeNumberField
 
fireControllerChanged() - Method in class org.virion.jam.controlpalettes.AbstractController
 
fireControlsChanged() - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
fireControlsChanged() - Method in interface org.virion.jam.controlpalettes.ControlPalette
tell listeners that the palette has changed
fireControlsChanged() - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
fireControlsChanged() - Method in interface org.virion.jam.controlpanels.ControlPalette
 
fireEditingStopped() - Method in class org.virion.jam.table.RealNumberCellEditor
 
fireEditingStopped() - Method in class org.virion.jam.table.WholeNumberCellEditor
 
fireNodeClickedEvent(Node) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Tells tree listeners that a node has been clicked.
firePainterChanged() - Method in class jebl.gui.trees.treeviewer.painters.AbstractPainter
 
firePainterChanged() - Method in class jebl.gui.trees.treeviewer_dev.painters.AbstractPainter
 
firePainterSettingsChanged() - Method in class jebl.gui.trees.treeviewer_dev.painters.AbstractPainter
 
fireSearchTextChanged() - Method in class org.virion.jam.panels.SearchPanel
 
fireSetProgress(double) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
fireSetProgress(double) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
 
fireStatusButtonPressed() - Method in interface org.virion.jam.panels.StatusProvider
 
fireStatusButtonPressed() - Method in class org.virion.jam.panels.StatusProvider.Helper
 
fireStatusChanged(int, String) - Method in interface org.virion.jam.panels.StatusProvider
 
fireStatusChanged(int, String) - Method in class org.virion.jam.panels.StatusProvider.Helper
 
fireTreeChanged() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
fireTreeLayoutChanged() - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
fireTreeLayoutChanged() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
fireTreePaneSettingsChanged() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
FIRST - Static variable in class org.virion.jam.demo.menus.DemoMenuFactory
 
firstDerivative(UnivariateFunction, double) - Static method in class jebl.math.NumericalDerivative
determine first derivative
FitchParsimony - Class in jebl.evolution.parsimony
Class for reconstructing characters using Fitch parsimony.
FitchParsimony(List<Pattern>, boolean) - Constructor for class jebl.evolution.parsimony.FitchParsimony
 
FitchParsimony(Patterns, boolean) - Constructor for class jebl.evolution.parsimony.FitchParsimony
 
FixedBitSet - Class in jebl.util
A bit-set of fixed size.
FixedBitSet(int) - Constructor for class jebl.util.FixedBitSet
 
FixedBitSet(FixedBitSet) - Constructor for class jebl.util.FixedBitSet
 
FLATWORM_MT - Static variable in class jebl.evolution.sequences.GeneticCode
 
fminx - Variable in class jebl.math.UnivariateMinimum
function value at minimum
focusGained(FocusEvent) - Method in class org.virion.jam.components.RealNumberField
 
focusGained(FocusEvent) - Method in class org.virion.jam.components.WholeNumberField
 
focusLost(FocusEvent) - Method in class org.virion.jam.components.RealNumberField
 
focusLost(FocusEvent) - Method in class org.virion.jam.components.WholeNumberField
 
forFiles(ProgressListener, List<File>) - Static method in class jebl.util.CompositeProgressListener
 
formatScore(float) - Method in class jebl.evolution.align.Align
 
freqR - Static variable in class jebl.evolution.distances.ModelBasedDistanceMatrix
 
freqY - Static variable in class jebl.evolution.distances.ModelBasedDistanceMatrix
 

G

G_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
G_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
GammaFunction - Class in jebl.math
gamma function
GammaFunction() - Constructor for class jebl.math.GammaFunction
 
GAP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
GAP_STATE - Static variable in class jebl.evolution.sequences.Codons
 
GAP_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
gapFraction() - Method in class jebl.evolution.align.ProfileCharacter
 
GaplessSequence - Class in jebl.evolution.sequences
 
GaplessSequence(Sequence) - Constructor for class jebl.evolution.sequences.GaplessSequence
 
generateFactory(boolean) - Static method in class jebl.math.OrthogonalSearch
Generate a MultivariateMinimum.Factory for an OrthogonalSearch
generateNewMinimiser() - Method in interface jebl.math.MultivariateMinimum.Factory
Generate a new Multivariate Minimum
generateOrthogonalRoundOptimiser(MultivariateFunction) - Method in class jebl.math.OrthogonalSearch
 
generateScores(String) - Static method in class jebl.evolution.align.scores.ScoresFactory
For any matrix.
generateScores(String, int) - Static method in class jebl.evolution.align.scores.ScoresFactory
For Blosum and Pam matrices
generateScores(String, float) - Static method in class jebl.evolution.align.scores.ScoresFactory
For calculated nucleotide matrices.
generateUnivariateMinimum() - Method in class jebl.math.OrthogonalSearch
 
GenericToolbarItem - Class in org.virion.jam.toolbar
 
GenericToolbarItem(String, String, JComponent) - Constructor for class org.virion.jam.toolbar.GenericToolbarItem
 
GENETIC_CODES - Static variable in class jebl.evolution.sequences.GeneticCode
 
GeneticCode - Class in jebl.evolution.sequences
A set of standard genetic codes.
get() - Method in class org.virion.jam.util.SwingWorker
Return the value created by the construct method.
getAboutAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getAboutAction() - Method in class org.virion.jam.framework.Application
 
getAboutString() - Static method in class org.virion.jam.framework.Application
 
getAction() - Method in interface org.virion.jam.framework.Command
Returns the swing Action for this command
getAdjacencies(Node) - Method in interface jebl.evolution.graphs.Graph
Returns a list of nodes connected to this node by an edge
getAdjacencies(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getAdjacencies(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getAdjacencies(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getAdjacencies(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getAdjacencies(Node) - Method in class jebl.evolution.trees.SimpleTree
 
getAdjusted(OrderEnumerator, int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getAdjusted(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
 
getAdjustedFactory(OrderEnumerator.OEFactory, int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getAlignments() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
The indices for these correspond to those for the getScoreMatrix() matrix.
getAllTaxa() - Static method in class jebl.evolution.taxa.Taxon
 
getAlphabet() - Method in class jebl.evolution.align.scores.AminoAcidScores
 
getAlphabet() - Method in class jebl.evolution.align.scores.NucleotideScores
 
getAlphabet() - Method in interface jebl.evolution.align.scores.ScoreMatrix
 
getAlphabet() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
 
getAlphabet(SequenceType) - Static method in class jebl.evolution.sequences.SequenceType.Utils
 
getAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
 
getAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
 
getAngularRange() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getAnswer() - Method in class org.virion.jam.util.LongTask
 
getApplication() - Static method in class org.virion.jam.framework.Application
 
getArgmax(int[]) - Static method in class jebl.util.Utils
Find the maximum "argument".
getArgmax(double[]) - Static method in class jebl.util.Utils
Find the maximum "argument" (of a double array).
getArgument(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getArgument(int) - Method in class jebl.evolution.coalescent.ConstExponential
 
getArgument(int) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getArgument(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns the value of the nth argument of this function.
getArgument(int) - Method in class jebl.evolution.coalescent.Expansion
 
getArgument(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getArgumentCount() - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getArgumentCount() - Method in class jebl.evolution.coalescent.ConstExponential
 
getArgumentCount() - Method in class jebl.evolution.coalescent.ConstLogistic
 
getArgumentCount() - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns the number of arguments for this function.
getArgumentCount() - Method in class jebl.evolution.coalescent.Expansion
 
getArgumentCount() - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstExponential
 
getArgumentName(int) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getArgumentName(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns the name of the nth argument of this function.
getArgumentName(int) - Method in class jebl.evolution.coalescent.Expansion
 
getArgumentName(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getAttribute(String) - Method in class jebl.evolution.alignments.ConsensusSequence
 
getAttribute(String) - Method in class jebl.evolution.sequences.BasicSequence
 
getAttribute(String) - Method in class jebl.evolution.sequences.FilteredSequence
 
getAttribute(String) - Method in class jebl.evolution.taxa.Taxon
 
getAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
 
getAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
 
getAttribute(String) - Method in interface jebl.util.Attributable
 
getAttribute(String) - Method in class jebl.util.AttributableHelper
 
getAttributeMap() - Method in class jebl.evolution.sequences.BasicSequence
 
getAttributeMap() - Method in class jebl.evolution.sequences.FilteredSequence
 
getAttributeMap() - Method in class jebl.evolution.taxa.Taxon
 
getAttributeMap() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getAttributeMap() - Method in class jebl.evolution.trees.MutableRootedTree
 
getAttributeMap() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getAttributeMap() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getAttributeMap() - Method in class jebl.evolution.trees.SimpleTree
 
getAttributeMap() - Method in interface jebl.util.Attributable
Gets the entire attribute map.
getAttributeMap() - Method in class jebl.util.AttributableHelper
 
getAttributeName() - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
getAttributeNames() - Method in class jebl.evolution.alignments.ConsensusSequence
 
getAttributeNames() - Method in class jebl.evolution.sequences.BasicSequence
 
getAttributeNames() - Method in class jebl.evolution.sequences.FilteredSequence
 
getAttributeNames() - Method in class jebl.evolution.taxa.Taxon
 
getAttributeNames() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getAttributeNames() - Method in class jebl.evolution.trees.MutableRootedTree
 
getAttributeNames() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getAttributeNames() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getAttributeNames() - Method in class jebl.evolution.trees.SimpleTree
 
getAttributeNames() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
getAttributeNames() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
getAttributeNames() - Method in interface jebl.util.Attributable
 
getAttributeNames() - Method in class jebl.util.AttributableHelper
 
getAttributes() - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getAttributes() - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getAttributes() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getAttributes() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
getAvailableAminoAcidScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
 
getAvailableNucleotideScores() - Static method in class jebl.evolution.align.scores.ScoresFactory
 
getBackground() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getBackground() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
getBiasAlternating(OrderEnumerator, OrderEnumerator) - Static method in class jebl.math.OrderEnumerator.Utils
 
getBiasAlternatingFactory(OrderEnumerator.OEFactory, OrderEnumerator.OEFactory) - Static method in class jebl.math.OrderEnumerator.Utils
 
getBorderDecorator() - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getBorderPaint() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getBorderPaint() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
getBorderStroke() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getBorderStroke() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
getBranchColouringAttribute() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getBranchColouringAttribute() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getBranchLabelPainter() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getBranchLabelPainter() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getBranchLabelPath(Node) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
getBranchLabelPath(Node) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
 
getBranchLabelPath(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getBranchLabelPath(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getBranchLabelPathMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getBranchLabelPathMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getBranchOrdering() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getBranchPaint(Tree, Node) - Method in class jebl.gui.trees.treeviewer.decorators.AttributeBranchDecorator
 
getBranchPaint(Tree, Node) - Method in interface jebl.gui.trees.treeviewer.decorators.BranchDecorator
 
getBranchPath(Node) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
getBranchPath(Node) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return the shape that represents the given branch
getBranchPath(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getBranchPath(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return the shape that represents the given branch
getBranchPathMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getBranchPathMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getBranchStroke() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getBranchTransform() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getBufferedImage(String) - Static method in class org.virion.jam.util.IconUtils
 
getBufferedImage(Class, String) - Static method in class org.virion.jam.util.IconUtils
 
getBufferedImageFromIcon(Icon) - Static method in class org.virion.jam.util.IconUtils
Creates a buffered image from an icon.
getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.ClusteringTreeBuilder
A factory method to create a ClusteringTreeBuilder
getBuilder(TreeBuilderFactory.Method, DistanceMatrix) - Static method in class jebl.evolution.trees.TreeBuilderFactory
 
getCalloutPath(Node) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
getCalloutPath(Node) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
 
getCalloutPath(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getCalloutPath(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getCalloutPathMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getCalloutPathMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getCalloutStroke() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getCanonicalStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
 
getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Codons
 
getCanonicalStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
 
getCanonicalStateCount() - Method in interface jebl.evolution.sequences.SequenceType
Get number of canonical states
getCanonicalStates() - Static method in class jebl.evolution.sequences.AminoAcids
 
getCanonicalStates() - Static method in class jebl.evolution.sequences.Codons
 
getCanonicalStates() - Static method in class jebl.evolution.sequences.Nucleotides
 
getCanonicalStates() - Method in interface jebl.evolution.sequences.SequenceType
Get a list of canonical states ordered by their indices.
getCanonicalStates() - Method in class jebl.evolution.sequences.State
 
getCataclysmTime() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
 
getCellEditorValue() - Method in class org.virion.jam.table.ColorEditor
 
getCellEditorValue() - Method in class org.virion.jam.table.RealNumberCellEditor
 
getCellEditorValue() - Method in class org.virion.jam.table.WholeNumberCellEditor
 
getChildren(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getChildren(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getChildren(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getChildren(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getChildren(Node) - Method in interface jebl.evolution.trees.RootedTree
 
getChildren(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getChildren(Node) - Method in class jebl.evolution.trees.SortedRootedTree
 
getClade(int) - Method in class jebl.evolution.trees.CladeSystem
 
getCladeCount() - Method in class jebl.evolution.trees.CladeSystem
get number of unique clades
getCladeFrequency(int) - Method in class jebl.evolution.trees.CladeSystem
get clade frequency
getCladeString(int) - Method in class jebl.evolution.trees.CladeSystem
 
getCleanString() - Method in class jebl.evolution.sequences.BasicSequence
 
getCloseWindowAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getCoalescentEvents(int) - Method in interface jebl.evolution.coalescent.IntervalList
Returns the number coalescent events in an interval
getCoalescentEvents(int) - Method in class jebl.evolution.coalescent.Intervals
 
getCode() - Method in class jebl.evolution.sequences.State
 
getCodeLength() - Method in interface jebl.evolution.sequences.SequenceType
 
getCodeTable() - Method in class jebl.evolution.sequences.GeneticCode
Returns the description of the genetic code
getCodonsForAminoAcid(AminoAcidState) - Method in class jebl.evolution.sequences.GeneticCode
 
getCollapseAttributeName() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getCollapsedShape(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getCollapsedShape(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return the shape that represents this node when collapsed
getCollapsedShapeMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getCollapsedShapeMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getColumn(double[][], int) - Static method in class jebl.math.MatrixCalc
takes a matrix and gets a column, then returns it as a vector
getCombined(OrthogonalHints, int, OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
 
getComboBox() - Method in class org.virion.jam.panels.SearchPanel
 
getCommonAncestorNode(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
getCondition() - Method in interface org.virion.jam.panels.RulesPanel.Rule
 
getConditions(Object) - Method in interface org.virion.jam.panels.RuleModel
Returns an array of strings to be presented as a combo box which are possible rule conditions for the specified field.
getConstant(int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getConstantFactory(int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getContentsPanel() - Method in class org.virion.jam.disclosure.DisclosurePanel
 
getControllerCount() - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
getControlPalette() - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
getControlPalette() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerPanel
 
getControls(boolean) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getControls(boolean) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
getControls(boolean) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getControls(boolean) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getControls(boolean) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getControls(boolean) - Method in class jebl.gui.trees.treeviewer.TreePane
 
getControls(boolean) - Method in interface org.virion.jam.controlpanels.ControlsProvider
Get a list of Controls handled by this provider.
getCopy(double[]) - Static method in class jebl.util.Utils
Clones an array of doubles
getCopy(double[], int, int) - Static method in class jebl.util.Utils
Clones an array of doubles from index start (inclusive) to index end (exclusive)
getCopy(double[], int) - Static method in class jebl.util.Utils
Clones an array of doubles from index start (inclusive) to end
getCopy(byte[]) - Static method in class jebl.util.Utils
Clones an array of bytes
getCopy(String[]) - Static method in class jebl.util.Utils
Clones an array of Strings
getCopy(double[][]) - Static method in class jebl.util.Utils
Clones an array of doubles
getCopy(int[][]) - Static method in class jebl.util.Utils
Clones a matrix of ints
getCopy(double[][][]) - Static method in class jebl.util.Utils
Clones an array of doubles
getCopy(byte[][]) - Static method in class jebl.util.Utils
Clones an array of bytes
getCopy(boolean[][]) - Static method in class jebl.util.Utils
Clones an array of booleans
getCopy(int[]) - Static method in class jebl.util.Utils
Clones an array of ints
getCopy(int[], int) - Static method in class jebl.util.Utils
Clones an array of ints
getCopyAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getCurrent() - Method in class org.virion.jam.util.LongTask
Called to find out how much has been done.
getCurrent() - Method in class org.virion.jam.util.SimpleLongTask
Called to find out how much has been done.
getCurrentTreeIndex() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
getCurvature() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getCutAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getDecimalPlaces() - Method in class jebl.util.NumberFormatter
Get the number of decimal places to display when formatted.
getDeclineRate() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
returns the positive-valued decline rate
getDefaultFrame() - Method in class org.virion.jam.console.ConsoleApplication
 
getDefaultFrame() - Method in class org.virion.jam.framework.Application
 
getDefaultFrame() - Method in class org.virion.jam.framework.MultiDocApplication
 
getDefaultFrame() - Method in class org.virion.jam.framework.SingleDocApplication
 
getDefaultTreeLayoutType() - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
getDegree(Graph, Node) - Static method in class jebl.evolution.graphs.Graph.Utils
 
getDegree() - Method in interface jebl.evolution.graphs.Node
 
getDeleteAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getDemographic(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
 
getDemographic(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getDemographic(double) - Method in class jebl.evolution.coalescent.ConstExponential
 
getDemographic(double) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getDemographic(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
Gets the value of the demographic function N(t) at time t.
getDemographic(double) - Method in class jebl.evolution.coalescent.Expansion
 
getDemographic(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getDemographic(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
Gets the value of the demographic function N(t) at time t.
getDesc() - Method in interface jebl.evolution.characters.Character
return the description of the character
getDesc() - Method in class jebl.evolution.characters.ContinuousCharacter
 
getDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
 
getDescendantTips(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
Gets a set of tip nodes descended from the given node.
getDescription() - Method in class jebl.evolution.sequences.GeneticCode
Returns the description of the genetic code
getDescription() - Method in class org.virion.jam.util.LongTask
Called to get the description of this task.
getDescription() - Method in class org.virion.jam.util.SimpleLongTask
 
getDimension() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getDimension() - Method in class jebl.evolution.substmodel.MatrixExponential
 
getDimension() - Method in interface jebl.evolution.substmodel.RateMatrix
 
getDisabledIcon() - Method in class org.virion.jam.toolbar.ToolbarAction
 
getDisclosureButton() - Method in class org.virion.jam.disclosure.DisclosurePanel
 
getDisplay() - Method in class org.virion.jam.toolbar.ToolbarOptions
 
getDisplayAttributeName() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
getDist(int, int) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
getDistance(int, int) - Method in class jebl.evolution.distances.BasicDistanceMatrix
Gets the distance at a particular row and column
getDistance(Taxon, Taxon) - Method in class jebl.evolution.distances.BasicDistanceMatrix
Gets the distance between 2 taxa
getDistance(int, int) - Method in interface jebl.evolution.distances.DistanceMatrix
Gets the distance at a particular row and column
getDistance(Taxon, Taxon) - Method in interface jebl.evolution.distances.DistanceMatrix
Gets the distance between 2 taxa
getDistances() - Method in class jebl.evolution.distances.BasicDistanceMatrix
Gets a 2-dimensional array containing the distances
getDistances() - Method in interface jebl.evolution.distances.DistanceMatrix
Gets a 2-dimensional array containing the distances
getDocumentExtension() - Method in class org.virion.jam.framework.SingleDocApplication
 
getDocumentFrame() - Method in class org.virion.jam.framework.AuxilaryFrame
 
getDocumentFrame(File) - Method in class org.virion.jam.framework.MultiDocApplication
 
getDoubleFromTextField(JTextField, double) - Static method in class org.virion.jam.util.Utils
 
getDragMode() - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
getDragRectangle() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getDragRectangle() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getEdge(Node, Node) - Method in interface jebl.evolution.graphs.Graph
Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getEdge(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getEdge(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
Returns the Edge that connects these two nodes
getEdge(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
Returns the Edge that connects these two nodes
getEdgeLength(Node, Node) - Method in interface jebl.evolution.graphs.Graph
Returns the length of the edge that connects these two nodes
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getEdgeLength(Node, Node) - Method in class jebl.evolution.trees.SimpleTree
 
getEdges(Node) - Method in interface jebl.evolution.graphs.Graph
Returns a list of edges connected to this node
getEdges() - Method in interface jebl.evolution.graphs.Graph
 
getEdges(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getEdges() - Method in class jebl.evolution.trees.CompactRootedTree
 
getEdges(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getEdges(Node) - Method in class jebl.evolution.trees.MutableRootedTree
Returns a list of edges connected to this node
getEdges() - Method in class jebl.evolution.trees.MutableRootedTree
 
getEdges(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
Returns a list of edges connected to this node
getEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getEdges(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
Returns a list of edges connected to this node
getEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getEdges(Node) - Method in class jebl.evolution.trees.SimpleTree
Returns a list of edges connected to this node
getEdges() - Method in class jebl.evolution.trees.SimpleTree
 
getEnv(String) - Static method in class org.virion.jam.util.Utils
 
getEquilibriumFrequencies() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getEquilibriumFrequencies() - Method in interface jebl.evolution.substmodel.RateMatrix
 
getEquilibriumFrequency(int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getEquilibriumFrequency(int) - Method in interface jebl.evolution.substmodel.RateMatrix
 
getEstimatedScores() - Method in class jebl.evolution.align.BartonSternberg
 
getExitAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getExitAction() - Method in class org.virion.jam.framework.Application
 
getExportableComponent() - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
getExportableComponent() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
getExportableComponent() - Method in class org.virion.jam.console.ConsoleFrame
 
getExportableComponent() - Method in class org.virion.jam.demo.DemoFrame
 
getExportableComponent() - Method in class org.virion.jam.framework.AboutBox
 
getExportableComponent() - Method in class org.virion.jam.framework.AuxilaryFrame
 
getExportableComponent() - Method in interface org.virion.jam.framework.Exportable
 
getExportAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getExternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
 
getExternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getExternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
The set of external edges.
getExternalEdges() - Method in class jebl.evolution.trees.SimpleTree
The set of external edges.
getExternalEdges() - Method in interface jebl.evolution.trees.Tree
 
getExternalNodeCount(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
Return the number of external nodes under this node.
getExternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
 
getExternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getExternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
 
getExternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getExternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getExternalNodes() - Method in class jebl.evolution.trees.SimpleTree
 
getExternalNodes() - Method in interface jebl.evolution.trees.Tree
 
getExtraResidues() - Method in class jebl.evolution.align.scores.Scores
 
getField() - Method in interface org.virion.jam.panels.RulesPanel.Rule
 
getFields() - Method in interface org.virion.jam.panels.RuleModel
Returns an array of strings to be presented as a combo box which are available fields to define rules on.
getFile() - Method in class org.virion.jam.framework.DocumentFrame
 
getFillPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getFillPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator
 
getFillPaint(Paint) - Method in interface jebl.gui.trees.treeviewer_dev.decorators.Decorator
 
getFillPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
getFindAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getFirstAction() - Method in class org.virion.jam.demo.DemoFrame
 
getFirstAction() - Method in interface org.virion.jam.demo.menus.DemoMenuHandler
 
getFont(Font) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getFont(Font) - Method in class jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator
 
getFont(Font) - Method in interface jebl.gui.trees.treeviewer_dev.decorators.Decorator
 
getFont(Font) - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
getFont() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getFontAttributeName() - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getForeground() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getForeground() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
getFormattedValue(double) - Method in class jebl.util.NumberFormatter
Returns a string containing the current value for this column with appropriate formatting.
getFrequencies(List<Sequence>) - Static method in class jebl.evolution.distances.ModelBasedDistanceMatrix
As a side effect, this method sets freqR and freqY if called on nucleotide sequences.
getFrequencies(Alignment) - Static method in class jebl.evolution.distances.ModelBasedDistanceMatrix
 
getFrequencies() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getFrequenciesSafe(List<Sequence>) - Static method in class jebl.evolution.distances.ModelBasedDistanceMatrix
As a side effect, this method sets freqR and freqY if called on nucleotide sequences.
getFrequenciesSafe(Alignment) - Static method in class jebl.evolution.distances.ModelBasedDistanceMatrix
 
getGaplessLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
Gets the site location index for this sequence excluding any gaps.
getGappedLocation(Sequence, int) - Static method in class jebl.evolution.sequences.Utils
Gets the site location index for this sequence that corresponds to a location given excluding all gaps.
getGapState() - Static method in class jebl.evolution.sequences.AminoAcids
 
getGapState() - Static method in class jebl.evolution.sequences.Codons
 
getGapState() - Static method in class jebl.evolution.sequences.Nucleotides
 
getGapState() - Method in interface jebl.evolution.sequences.SequenceType
Get state corresponding to a gap
getGrowthRate() - Method in class jebl.evolution.coalescent.ExponentialGrowth
returns growth rate.
getHeight(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getHeight(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getHeight(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getHeight(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getHeight(Node) - Method in interface jebl.evolution.trees.RootedTree
 
getHeight(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getHeight(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
 
getHeightArea(double, double) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getHeightArea(double, double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getHeightArea(double, double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getHeightArea(double, double) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return a shape that defines a particular height interval.
getHeightArea(double, double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getHeightArea(double, double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
getHeightArea(double, double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getHeightArea(double, double) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return a shape that defines a particular height interval.
getHeightAt(Graphics2D, Point2D) - Method in class jebl.gui.trees.treeviewer.TreePane
 
getHeightAt(Graphics2D, Point2D) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getHeightBound() - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getHeightBound() - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
getHeightBound() - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
getHeightBound() - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getHeightBound() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
getHeightBound() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
getHeightBound() - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
 
getHeightBound() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
getHeightLine(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getHeightLine(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getHeightLine(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getHeightLine(double) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return a line that defines a particular height.
getHeightLine(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getHeightLine(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
getHeightLine(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getHeightLine(double) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return a line that defines a particular height.
getHeightOfPoint(Point2D) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getHeightOfPoint(Point2D) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getHeightOfPoint(Point2D) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getHeightOfPoint(Point2D) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return the height (from the youngest tip) for the given 2d point.
getHeightOfPoint(Point2D) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getHeightOfPoint(Point2D) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
getHeightOfPoint(Point2D) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getHeightOfPoint(Point2D) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getHelpAction() - Method in class org.virion.jam.framework.AbstractFrame
override this to provide a document specific help menu item
getHelpAction() - Method in class org.virion.jam.framework.Application
 
getHelpURLString() - Static method in class org.virion.jam.framework.Application
 
getHgap() - Method in class org.virion.jam.layouts.CompassLayout
Returns the horizontal gap between components.
getIcon() - Static method in class org.virion.jam.framework.Application
 
getIcon() - Method in interface org.virion.jam.preferences.PreferencesSection
 
getIcon() - Method in class org.virion.jam.toolbar.ToolbarAction
 
getIcon(String) - Static method in class org.virion.jam.util.IconUtils
 
getIcon(Class, String) - Static method in class org.virion.jam.util.IconUtils
 
getImage(Object, String) - Static method in class org.virion.jam.app.Utils
 
getImage(String) - Static method in class org.virion.jam.util.IconUtils
 
getImage(Class, String) - Static method in class org.virion.jam.util.IconUtils
 
getImageFromIcon(Icon) - Static method in class org.virion.jam.util.IconUtils
Creates an image from an icon.
getImportAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getIndex() - Method in class jebl.evolution.sequences.State
 
getIntegerArrayOption(String) - Method in class org.virion.jam.app.Arguments
Return the value of an integer array option
getIntegerOption(String) - Method in class org.virion.jam.app.Arguments
Return the value of an integer option
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
Calculates the integral 1/N(x) dx between start and finish.
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstExponential
 
getIntegral(double, double) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getIntegral(double, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
Calculates the integral 1/N(x) dx between start and finish
getIntegral(double, double) - Method in class jebl.evolution.coalescent.Expansion
 
getIntegral(double, double) - Method in class jebl.evolution.coalescent.LogisticGrowth
 
getIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
 
getIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
 
getIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
 
getIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getInternalEdges() - Method in class jebl.evolution.trees.CompactRootedTree
 
getInternalEdges() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getInternalEdges() - Method in class jebl.evolution.trees.MutableRootedTree
The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.RootedFromUnrooted
The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.SimpleRootedTree
The set of internal edges.
getInternalEdges() - Method in class jebl.evolution.trees.SimpleTree
The set of internal edges.
getInternalEdges() - Method in interface jebl.evolution.trees.Tree
 
getInternalNodes() - Method in class jebl.evolution.trees.CompactRootedTree
 
getInternalNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getInternalNodes() - Method in class jebl.evolution.trees.MutableRootedTree
 
getInternalNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getInternalNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getInternalNodes() - Method in class jebl.evolution.trees.SimpleTree
 
getInternalNodes() - Method in interface jebl.evolution.trees.Tree
 
getInternalParameterBoundaries(int, double[]) - Method in interface jebl.math.OrthogonalHints
A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)
getInternalParameterBoundaries(OrthogonalHints, int) - Static method in class jebl.math.OrthogonalHints.Utils
 
getInterval(double, int, double) - Method in class jebl.evolution.coalescent.CoalescentIntervalGenerator
 
getInterval(int) - Method in interface jebl.evolution.coalescent.IntervalList
Gets an interval.
getInterval(int) - Method in class jebl.evolution.coalescent.Intervals
 
getInterval(double, int, double) - Method in interface jebl.evolution.trees.IntervalGenerator
 
getIntervalCount() - Method in interface jebl.evolution.coalescent.IntervalList
get number of intervals
getIntervalCount() - Method in class jebl.evolution.coalescent.Intervals
 
getIntervalType(int) - Method in interface jebl.evolution.coalescent.IntervalList
Returns the type of interval observed.
getIntervalType(int) - Method in class jebl.evolution.coalescent.Intervals
 
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
 
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstExponential
 
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getInverseIntensity(double) - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns value of inverse demographic intensity function (returns time, needed for simulation of coalescent intervals).
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.Expansion
 
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getInverseIntensity(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
Returns value of demographic intensity function at time t (= integral 1/N(x) dx from 0 to t).
getLabel(Node) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getLabel(Tree, Node) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getLabel() - Method in class org.virion.jam.toolbar.ToolbarAction
 
getLabelCount() - Method in class jebl.evolution.trees.SplitSystem
get number of labels
getLastDelimiter() - Method in class jebl.evolution.io.ImportHelper
 
getLastMetaComment() - Method in class jebl.evolution.io.ImportHelper
 
getLayoutAlignmentX(Container) - Method in class org.virion.jam.layouts.CompassLayout
Returns the alignment along the x axis.
getLayoutAlignmentY(Container) - Method in class org.virion.jam.layouts.CompassLayout
Returns the alignment along the y axis.
getLeftoverArguments() - Method in class org.virion.jam.app.Arguments
Return any arguments leftover after the options
getLength() - Method in class jebl.evolution.alignments.ConsensusSequence
Returns the length of the sequence
getLength() - Method in interface jebl.evolution.alignments.Pattern
 
getLength() - Method in interface jebl.evolution.graphs.Edge
 
getLength() - Method in class jebl.evolution.sequences.BasicSequence
Returns the length of the sequence
getLength() - Method in class jebl.evolution.sequences.FilteredSequence
Returns the length of the sequence
getLength() - Method in interface jebl.evolution.sequences.Sequence
Get the length of the sequence
getLength(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getLength(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getLength(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getLength(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getLength(Node) - Method in interface jebl.evolution.trees.RootedTree
 
getLength(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getLength(Node) - Method in class jebl.evolution.trees.TransformedRootedTree
 
getLengthOfTask() - Method in class org.virion.jam.util.LongTask
Called to find out how much work needs to be done.
getLengthOfTask() - Method in class org.virion.jam.util.SimpleLongTask
Called to find out how much work needs to be done.
getLineageCount(int) - Method in interface jebl.evolution.coalescent.IntervalList
Returns the number of uncoalesced lineages within this interval.
getLineageCount(IntervalList, double) - Static method in class jebl.evolution.coalescent.IntervalList.Utils
 
getLineageCount(int) - Method in class jebl.evolution.coalescent.Intervals
 
getLineNumber() - Method in class jebl.evolution.io.ImportHelper
 
getLoadFile(String) - Static method in class org.virion.jam.app.Utils
 
getLoadFileName(String) - Static method in class org.virion.jam.app.Utils
 
getLowerBound(int) - Method in class jebl.evolution.coalescent.Coalescent
 
getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
 
getLowerBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getLowerBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns the lower bound of the nth argument of this function.
getLowerBound(int) - Method in class jebl.evolution.coalescent.Expansion
 
getLowerBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getLowerBound(int) - Method in interface jebl.math.MultivariateFunction
get lower bound of argument n
getLowerBound() - Method in class jebl.math.OrthogonalLineFunction
 
getLowerBound() - Method in interface jebl.math.UnivariateFunction
get lower bound of argument
getMatch() - Method in class jebl.evolution.align.Align
 
getMatch() - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
getMatch(char[], char[]) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
 
getMatch() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
getMatch() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
 
getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
 
getMatch() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
 
getMatchScores(int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
 
getMax() - Method in class jebl.evolution.align.SequenceShuffler
 
getMax(double[]) - Static method in class jebl.util.Utils
Calculate the max of an array
getMax(double[], int, int) - Static method in class jebl.util.Utils
Calculate the max of an array
getMaxTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
 
getMean() - Method in class jebl.evolution.align.SequenceShuffler
 
getMean(double[]) - Static method in class jebl.util.Utils
Calculate the mean value of an array
getMenuBarFactory() - Static method in class org.virion.jam.framework.Application
 
getMenuName() - Method in class org.virion.jam.demo.menus.DemoMenuFactory
 
getMenuName() - Method in class org.virion.jam.framework.DefaultEditMenuFactory
 
getMenuName() - Method in class org.virion.jam.framework.DefaultFileMenuFactory
 
getMenuName() - Method in class org.virion.jam.framework.DefaultHelpMenuFactory
 
getMenuName() - Method in interface org.virion.jam.framework.MenuFactory
Give the name of this menu.
getMenuName() - Method in class org.virion.jam.mac.MacFileMenuFactory
 
getMenuName() - Method in class org.virion.jam.mac.MacHelpMenuFactory
 
getMenuName() - Method in class org.virion.jam.mac.MacWindowMenuFactory
 
getMessage() - Method in class org.virion.jam.util.LongTask
Called to get the current message of the task.
getMessage() - Method in class org.virion.jam.util.SimpleLongTask
 
getMin() - Method in class jebl.evolution.align.SequenceShuffler
 
getMin(double[]) - Static method in class jebl.util.Utils
Calculate the min of an array
getMinimizeWindowAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getMinNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
 
getMinTipHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
 
getMostFrequentState() - Method in interface jebl.evolution.alignments.Pattern
Returns the most frequent state in this pattern
getN0() - Method in class jebl.evolution.coalescent.ConstantPopulation
returns initial population size.
getN1() - Method in class jebl.evolution.coalescent.ConstExponential
 
getN1() - Method in class jebl.evolution.coalescent.ConstLogistic
 
getN1() - Method in class jebl.evolution.coalescent.Expansion
 
getName() - Method in class jebl.evolution.align.scores.AminoAcidScores
 
getName() - Method in class jebl.evolution.align.scores.Blosum45
 
getName() - Method in class jebl.evolution.align.scores.Blosum50
 
getName() - Method in class jebl.evolution.align.scores.NucleotideScores
 
getName() - Method in interface jebl.evolution.align.scores.ScoreMatrix
 
getName() - Method in class jebl.evolution.align.scores.SubstScoreMatrix
 
getName() - Method in interface jebl.evolution.characters.Character
return the name of the character
getName() - Method in interface jebl.evolution.characters.CharacterType
 
getName() - Method in class jebl.evolution.characters.ContinuousCharacter
 
getName() - Method in class jebl.evolution.characters.DiscreteCharacter
 
getName() - Method in class jebl.evolution.sequences.GeneticCode
Returns the name of the genetic code
getName() - Method in class jebl.evolution.sequences.Nucleotides
 
getName() - Method in interface jebl.evolution.sequences.SequenceType
name of data type
getName() - Method in class jebl.evolution.sequences.State
 
getName() - Method in class jebl.evolution.sequences.StateClassification.Default
 
getName() - Method in interface jebl.evolution.sequences.StateClassification
 
getName() - Method in class jebl.evolution.taxa.Taxon
get the name of the taxon
getName() - Method in class jebl.evolution.taxa.TaxonomicLevel
get the name of the taxonomic level
getName() - Method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
 
getName() - Method in enum jebl.evolution.trees.TreeBuilderFactory.Method
 
getName() - Method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapeController.NodePainterType
 
getName() - Method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter.NodeShape
 
getNameString() - Static method in class org.virion.jam.framework.Application
 
getNewAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getNewAction() - Method in class org.virion.jam.framework.Application
 
getNext() - Method in interface jebl.math.OrderEnumerator
The next value in the enumeration
getNextBlockName() - Method in class jebl.evolution.io.NexusImporter
 
getNexusDataType() - Method in interface jebl.evolution.sequences.SequenceType
 
getNode(Taxon) - Method in class jebl.evolution.trees.CompactRootedTree
 
getNode(Taxon) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getNode(Taxon) - Method in class jebl.evolution.trees.MutableRootedTree
 
getNode(Taxon) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getNode(Taxon) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getNode(Taxon) - Method in class jebl.evolution.trees.SimpleTree
 
getNode(Taxon) - Method in interface jebl.evolution.trees.Tree
 
getNodeAt(Graphics2D, Point) - Method in class jebl.gui.trees.treeviewer.TreePane
 
getNodeAt(Graphics2D, Point) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getNodeBar() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
getNodeBarPainter() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getNodeBarPath(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getNodeBarPath(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getNodeBarPathMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getNodeBarPathMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getNodeLabelPainter() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getNodeLabelPainter() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getNodeLabelPath(Node) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
getNodeLabelPath(Node) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
 
getNodeLabelPath(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getNodeLabelPath(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getNodeLabelPathMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getNodeLabelPathMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getNodePoint(Node) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
getNodePoint(Node) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return the point in 2d space of the given node
getNodePoint(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getNodePoint(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return the point in 2d space of the given node
getNodes(Edge) - Method in interface jebl.evolution.graphs.Graph
Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes() - Method in interface jebl.evolution.graphs.Graph
 
getNodes(int) - Method in interface jebl.evolution.graphs.Graph
 
getNodes(Edge) - Method in class jebl.evolution.trees.CompactRootedTree
 
getNodes() - Method in class jebl.evolution.trees.CompactRootedTree
 
getNodes(int) - Method in class jebl.evolution.trees.CompactRootedTree
 
getNodes(Edge) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getNodes() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getNodes(int) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getNodes(Edge) - Method in class jebl.evolution.trees.MutableRootedTree
Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes() - Method in class jebl.evolution.trees.MutableRootedTree
 
getNodes(int) - Method in class jebl.evolution.trees.MutableRootedTree
 
getNodes(Edge) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getNodes() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getNodes(int) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getNodes(Edge) - Method in class jebl.evolution.trees.SimpleRootedTree
Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getNodes(int) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getNodes(Edge) - Method in class jebl.evolution.trees.SimpleTree
Returns an array of 2 nodes which are the nodes at either end of the edge.
getNodes() - Method in class jebl.evolution.trees.SimpleTree
 
getNodes(int) - Method in class jebl.evolution.trees.SimpleTree
 
getNodesAt(Graphics2D, Rectangle) - Method in class jebl.gui.trees.treeviewer.TreePane
 
getNodesAt(Graphics2D, Rectangle) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getNormalized(double[]) - Static method in class jebl.math.Random
 
getNull() - Static method in class jebl.math.OrthogonalHints.Utils
 
getNumArguments() - Method in class jebl.evolution.coalescent.Coalescent
 
getNumArguments() - Method in interface jebl.math.MultivariateFunction
get number of arguments
getNumberFormat() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
getNumOfStates() - Method in class jebl.evolution.characters.DiscreteCharacter
 
getOpenAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getOpenAction() - Method in class org.virion.jam.framework.Application
 
getOrdered(int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getOrderedFactory() - Static method in class jebl.math.OrderEnumerator.Utils
 
getOriginalFrequencies(double[]) - Static method in class jebl.evolution.substmodel.WAG
get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
getOriginalFrequencies() - Static method in class jebl.evolution.substmodel.WAG
 
getOriginalTree() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getOrthogonalHints() - Method in class jebl.evolution.coalescent.Coalescent
 
getOrthogonalHints() - Method in interface jebl.math.MultivariateFunction
 
getPageSetupAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getPageSetupAction() - Method in class org.virion.jam.framework.Application
 
getPaint(Object) - Method in class jebl.gui.trees.treeviewer.decorators.AttributeBranchDecorator
 
getPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator
 
getPaint(Paint) - Method in interface jebl.gui.trees.treeviewer_dev.decorators.Decorator
 
getPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
getPaintAttributeName() - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.TreePaneController
 
getPanel() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
getPanel() - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
getPanel() - Method in interface org.virion.jam.controlpalettes.Controller
Get a JPanel which is the main section for the palette.
getPanel() - Method in interface org.virion.jam.controlpalettes.ControlPalette
get the panel that encloses the control palette
getPanel() - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
getPanel() - Method in interface org.virion.jam.controlpanels.ControlPalette
 
getPanel() - Method in class org.virion.jam.controlpanels.Controls
 
getPanel() - Method in interface org.virion.jam.preferences.PreferencesSection
 
getPanels() - Method in class org.virion.jam.panels.AddRemovePanel
 
getParent(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getParent(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getParent(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getParent(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getParent(Node) - Method in interface jebl.evolution.trees.RootedTree
 
getParent(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getPasteAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getPathLength(Tree, Node, Node) - Static method in class jebl.evolution.trees.Utils
 
getPatternCount() - Method in class jebl.evolution.alignments.BasicAlignment
 
getPatternCount() - Method in interface jebl.evolution.alignments.Patterns
 
getPatternCount() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getPatternLength() - Method in class jebl.evolution.alignments.BasicAlignment
 
getPatternLength() - Method in interface jebl.evolution.alignments.Patterns
 
getPatternLength() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getPatterns() - Method in class jebl.evolution.alignments.BasicAlignment
 
getPatterns() - Method in interface jebl.evolution.alignments.Patterns
Get a list of all the patterns
getPatterns() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getPhenotypes() - Method in class jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
 
getPhenotypesSE() - Method in class jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
 
getPreferencesAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getPreferencesAction() - Method in class org.virion.jam.framework.Application
 
getPreferredAlignment() - Method in class org.virion.jam.demo.menus.DemoMenuFactory
 
getPreferredAlignment() - Method in class org.virion.jam.framework.DefaultEditMenuFactory
 
getPreferredAlignment() - Method in class org.virion.jam.framework.DefaultFileMenuFactory
 
getPreferredAlignment() - Method in class org.virion.jam.framework.DefaultHelpMenuFactory
 
getPreferredAlignment() - Method in interface org.virion.jam.framework.MenuFactory
Returns the preferred alignment of the menu in the menu bar.
getPreferredAlignment() - Method in class org.virion.jam.mac.MacFileMenuFactory
 
getPreferredAlignment() - Method in class org.virion.jam.mac.MacHelpMenuFactory
 
getPreferredAlignment() - Method in class org.virion.jam.mac.MacWindowMenuFactory
 
getPreferredHeight() - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getPreferredHeight() - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
getPreferredHeight() - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
getPreferredHeight() - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getPreferredHeight() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
getPreferredHeight() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
getPreferredHeight() - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
 
getPreferredHeight() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
getPreferredMenu() - Method in interface org.virion.jam.framework.Command
 
getPreferredPosition() - Method in interface org.virion.jam.framework.Command
 
getPreferredSize() - Method in class org.virion.jam.components.JVerticalLabel
 
getPreferredSize() - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
getPreferredSize() - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
getPreferredWidth() - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getPreferredWidth() - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
getPreferredWidth() - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
getPreferredWidth() - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getPreferredWidth() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
getPreferredWidth() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
getPreferredWidth() - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
 
getPreferredWidth() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
getPressedIcon() - Method in class org.virion.jam.toolbar.ToolbarAction
 
getPrimaryCheckbox() - Method in class org.virion.jam.controlpanels.Controls
 
getPrintAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getProgress() - Method in class jebl.evolution.io.ImportHelper
 
getRealArrayOption(String) - Method in class org.virion.jam.app.Arguments
Return the value of an real array option
getRealOption(String) - Method in class org.virion.jam.app.Arguments
Return the value of an real number option
getRecentFileMenu() - Method in class org.virion.jam.framework.Application
 
getRelativeRates() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getRelativeRates() - Method in interface jebl.evolution.substmodel.RateMatrix
 
getRestricted(OrderEnumerator, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getRestrictedFactory(OrderEnumerator.OEFactory, int, int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getRootAngle() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getRootLength() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getRootLength() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getRootNode() - Method in class jebl.evolution.trees.CompactRootedTree
 
getRootNode() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getRootNode() - Method in class jebl.evolution.trees.MutableRootedTree
The root of the tree has the largest node height of all nodes in the tree.
getRootNode() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getRootNode() - Method in interface jebl.evolution.trees.RootedTree
The root of the tree has the largest node height of all nodes in the tree.
getRootNode() - Method in class jebl.evolution.trees.SimpleRootedTree
The root of the tree has the largest node height of all nodes in the tree.
getRules() - Method in class org.virion.jam.panels.RulesPanel
 
getSampleCount() - Method in interface jebl.evolution.coalescent.IntervalList
get the total number of sampling events.
getSampleCount() - Method in class jebl.evolution.coalescent.Intervals
 
getSaveAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getSaveAction() - Method in class org.virion.jam.framework.AuxilaryFrame
 
getSaveAction() - Method in class org.virion.jam.framework.DocumentFrame
 
getSaveAsAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getSaveAsAction() - Method in class org.virion.jam.framework.AuxilaryFrame
 
getSaveAsAction() - Method in class org.virion.jam.framework.DocumentFrame
 
getSaveFile(String) - Static method in class org.virion.jam.app.Utils
 
getSaveFileName(String) - Static method in class org.virion.jam.app.Utils
 
getScaleBarPainter() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getScaleBarPainter() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getScaleBarStroke() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
getScaleRange() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
getScore() - Method in class jebl.evolution.align.Align
 
getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
 
getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
 
getScore() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
getScore(Sequence, Sequence) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
getScore() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
 
getScore(Sequence, Sequence) - Method in interface jebl.evolution.align.PairwiseAligner
 
getScore(char, char) - Method in interface jebl.evolution.align.scores.ScoreMatrix
 
getScore(char, char) - Method in class jebl.evolution.align.scores.Scores
 
getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpace
 
getScore() - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
 
getScore(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
 
getScore(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
getScores() - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
The indices for these correspond to those for the getAlignments() matrix.
getSE(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
 
getSecondAction() - Method in class org.virion.jam.demo.DemoFrame
 
getSecondAction() - Method in interface org.virion.jam.demo.menus.DemoMenuHandler
 
getSelectAllAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getSelectedNodes() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getSelectedNodes() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getSelectedTaxa() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getSelectedTips() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getSelectionMode() - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
getSelectionPaint() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getSequence(Taxon) - Method in class jebl.evolution.alignments.BasicAlignment
 
getSequence(Taxon) - Method in class jebl.evolution.alignments.ResampledAlignment
 
getSequence(Taxon) - Method in interface jebl.evolution.sequences.Sequences
 
getSequenceList() - Method in interface jebl.evolution.alignments.Alignment
 
getSequenceList() - Method in class jebl.evolution.alignments.BasicAlignment
 
getSequenceList() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getSequences() - Method in class jebl.evolution.alignments.BasicAlignment
 
getSequences() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getSequences() - Method in interface jebl.evolution.sequences.Sequences
 
getSequenceType() - Method in class jebl.evolution.alignments.BasicAlignment
 
getSequenceType() - Method in class jebl.evolution.alignments.ConsensusSequence
 
getSequenceType() - Method in interface jebl.evolution.alignments.Pattern
 
getSequenceType() - Method in interface jebl.evolution.alignments.Patterns
 
getSequenceType() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getSequenceType() - Method in class jebl.evolution.sequences.BasicSequence
 
getSequenceType() - Method in class jebl.evolution.sequences.FilteredSequence
 
getSequenceType() - Method in interface jebl.evolution.sequences.Sequence
 
getSequenceType() - Method in class jebl.evolution.sequences.TranslatedSequence
 
getSequenceType() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getSequenceType() - Method in interface jebl.evolution.substmodel.RateMatrix
Get the data type of this rate matrix
getSetName(State) - Method in class jebl.evolution.sequences.StateClassification.Default
 
getSetName(State) - Method in interface jebl.evolution.sequences.StateClassification
 
getSetNames() - Method in class jebl.evolution.sequences.StateClassification.Default
 
getSetNames() - Method in interface jebl.evolution.sequences.StateClassification
 
getSetting(String) - Method in interface org.virion.jam.controlpanels.ControlsSettings
 
getSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
getSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.TreePane
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneController
 
getSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
getSettings(Map<String, Object>) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
getSettings(Map<String, Object>) - Method in interface org.virion.jam.controlpalettes.Controller
Collect the settings for this controller.
getSettings(Map<String, Object>) - Method in interface org.virion.jam.controlpalettes.ControlPalette
Gather up all the settings from all the controls in the palette.
getSettings(ControlsSettings) - Method in interface org.virion.jam.controlpanels.ControlsProvider
Get the settings for a given Controls object.
getShape() - Method in class jebl.evolution.coalescent.LogisticGrowth
 
getShuffled(int) - Static method in class jebl.math.OrderEnumerator.Utils
 
getShuffledFactory() - Static method in class jebl.math.OrderEnumerator.Utils
 
getSignificantFigures() - Method in class jebl.util.NumberFormatter
Get the number of significant figures to display when formatted.
getSiteCount() - Method in interface jebl.evolution.alignments.Alignment
 
getSiteCount() - Method in class jebl.evolution.alignments.BasicAlignment
 
getSiteCount() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getSiteScores(Tree) - Method in class jebl.evolution.parsimony.FitchParsimony
Calculates the minimum number of siteScores for the parsimony reconstruction of a a set of character patterns on a tree.
getSiteScores(Tree) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
Calculates the minimum number of steps for the parsimony reconstruction for the given tree.
getSize() - Method in class jebl.evolution.distances.BasicDistanceMatrix
Gets the size of the matrix (which is square), i.e., number of rows or columns.
getSize() - Method in interface jebl.evolution.distances.DistanceMatrix
Gets the size of the matrix (which is square), i.e., number of rows or columns.
getSmallSize() - Method in class org.virion.jam.toolbar.ToolbarOptions
 
getSource() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getSplit(int) - Method in class jebl.evolution.trees.SplitSystem
get split
getSplit(List<Taxon>, Tree, Edge, boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
get split for branch associated with internal node
getSplitCount() - Method in class jebl.evolution.trees.SplitSystem
get number of splits
getSplits(Tree) - Static method in class jebl.evolution.trees.SplitUtils
creates a split system from a tree (using tree-induced order of sequences)
getSplits(List<Taxon>, Tree) - Static method in class jebl.evolution.trees.SplitUtils
creates a split system from a tree (using a pre-specified order of sequences)
getSplitVector() - Method in class jebl.evolution.trees.SplitSystem
get split vector
getSpread() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
getState(int) - Method in class jebl.evolution.alignments.ConsensusSequence
 
getState(int) - Method in interface jebl.evolution.alignments.Pattern
Get the state for the ith taxon
getState(char) - Static method in class jebl.evolution.sequences.AminoAcids
 
getState(String) - Static method in class jebl.evolution.sequences.AminoAcids
 
getState(int) - Static method in class jebl.evolution.sequences.AminoAcids
 
getState(int) - Method in class jebl.evolution.sequences.BasicSequence
 
getState(NucleotideState, NucleotideState, NucleotideState) - Static method in class jebl.evolution.sequences.Codons
 
getState(String) - Static method in class jebl.evolution.sequences.Codons
Gets the state object for the given code.
getState(int) - Static method in class jebl.evolution.sequences.Codons
 
getState(int) - Method in class jebl.evolution.sequences.FilteredSequence
 
getState(char) - Static method in class jebl.evolution.sequences.Nucleotides
 
getState(String) - Static method in class jebl.evolution.sequences.Nucleotides
 
getState(int) - Static method in class jebl.evolution.sequences.Nucleotides
 
getState(int) - Method in interface jebl.evolution.sequences.Sequence
 
getState(String) - Method in interface jebl.evolution.sequences.SequenceType
Get state corresponding to a string code
getState(char) - Method in interface jebl.evolution.sequences.SequenceType
 
getState(int) - Method in interface jebl.evolution.sequences.SequenceType
Get state corresponding to a state index
getStateCount() - Static method in class jebl.evolution.sequences.AminoAcids
 
getStateCount() - Static method in class jebl.evolution.sequences.Codons
 
getStateCount() - Static method in class jebl.evolution.sequences.Nucleotides
 
getStateCount() - Method in interface jebl.evolution.sequences.SequenceType
Get number of states including ambiguous states
getStateDesc() - Method in class jebl.evolution.characters.DiscreteCharacter
 
getStateDesc(int) - Method in class jebl.evolution.characters.DiscreteCharacter
 
getStateFrequency(State) - Method in interface jebl.evolution.alignments.Pattern
Returns the frequent of the given state in this pattern
getStateIndices() - Method in class jebl.evolution.alignments.ConsensusSequence
 
getStateIndices() - Method in class jebl.evolution.sequences.BasicSequence
 
getStateIndices() - Method in class jebl.evolution.sequences.FilteredSequence
 
getStateIndices() - Method in interface jebl.evolution.sequences.Sequence
 
getStateIndices(State[]) - Static method in class jebl.evolution.sequences.Utils
 
getStates() - Method in class jebl.evolution.alignments.ConsensusSequence
 
getStates() - Method in interface jebl.evolution.alignments.Pattern
 
getStates(Tree, Node) - Method in class jebl.evolution.parsimony.FitchParsimony
Returns the reconstructed character states for a given node in the tree.
getStates(Tree, Node) - Method in interface jebl.evolution.parsimony.ParsimonyCriterion
Returns the reconstructed character states for a given node in the tree.
getStates() - Static method in class jebl.evolution.sequences.AminoAcids
 
getStates() - Method in class jebl.evolution.sequences.BasicSequence
 
getStates() - Static method in class jebl.evolution.sequences.Codons
 
getStates() - Method in class jebl.evolution.sequences.FilteredSequence
 
getStates() - Static method in class jebl.evolution.sequences.Nucleotides
 
getStates() - Method in interface jebl.evolution.sequences.Sequence
 
getStates() - Method in interface jebl.evolution.sequences.SequenceType
Get a list of states ordered by their indices.
getStateSet() - Method in interface jebl.evolution.alignments.Pattern
 
getStateSet(String) - Method in class jebl.evolution.sequences.StateClassification.Default
 
getStateSet(String) - Method in interface jebl.evolution.sequences.StateClassification
 
getStatus() - Method in interface org.virion.jam.panels.StatusProvider
 
getStatus() - Method in class org.virion.jam.panels.StatusProvider.Helper
 
getStatusText() - Method in interface org.virion.jam.panels.StatusProvider
 
getStatusText() - Method in class org.virion.jam.panels.StatusProvider.Helper
 
getStdev() - Method in class jebl.evolution.align.SequenceShuffler
 
getStopCodonCount() - Method in class jebl.evolution.sequences.GeneticCode
Returns the number of terminator amino acids.
getStopCodons() - Method in class jebl.evolution.sequences.GeneticCode
 
getString() - Method in class jebl.evolution.alignments.ConsensusSequence
 
getString() - Method in class jebl.evolution.sequences.BasicSequence
 
getString() - Method in class jebl.evolution.sequences.FilteredSequence
 
getString() - Method in interface jebl.evolution.sequences.Sequence
 
getStringOption(String) - Method in class org.virion.jam.app.Arguments
Return the value of an string option
getStroke(Stroke) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getStroke(Stroke) - Method in class jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator
 
getStroke(Stroke) - Method in interface jebl.gui.trees.treeviewer_dev.decorators.Decorator
 
getStroke(Stroke) - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
getStroke() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
getStrokeAttributeName() - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
getSubmatrix(Collection<Taxon>) - Method in class jebl.evolution.distances.BasicDistanceMatrix
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
getSubmatrix(Collection<Taxon>) - Method in interface jebl.evolution.distances.DistanceMatrix
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
getSuggestedOrdering(OrderEnumerator) - Method in interface jebl.math.OrthogonalHints
If there is a "best" ordering to use it can be specified here, if not should return null
getSum(double[]) - Static method in class jebl.util.Utils
Calculate the total of an array
getSupportAttributeName() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.virion.jam.table.ColorEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.virion.jam.table.RealNumberCellEditor
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.virion.jam.table.WholeNumberCellEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.virion.jam.table.ColorRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.virion.jam.table.HeaderRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.virion.jam.table.TableRenderer
 
getTaxa() - Method in class jebl.evolution.alignments.BasicAlignment
 
getTaxa() - Method in interface jebl.evolution.alignments.Pattern
 
getTaxa() - Method in interface jebl.evolution.alignments.Patterns
 
getTaxa() - Method in class jebl.evolution.alignments.ResampledAlignment
 
getTaxa() - Method in interface jebl.evolution.characters.Character
get a Set of all the taxa for this character
getTaxa() - Method in class jebl.evolution.characters.ContinuousCharacter
 
getTaxa() - Method in class jebl.evolution.characters.DiscreteCharacter
 
getTaxa() - Method in class jebl.evolution.distances.BasicDistanceMatrix
 
getTaxa() - Method in interface jebl.evolution.distances.DistanceMatrix
 
getTaxa() - Method in class jebl.evolution.trees.CompactRootedTree
 
getTaxa() - Method in class jebl.evolution.trees.FilteredRootedTree
 
getTaxa() - Method in class jebl.evolution.trees.MutableRootedTree
 
getTaxa() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getTaxa() - Method in class jebl.evolution.trees.SimpleRootedTree
 
getTaxa() - Method in class jebl.evolution.trees.SimpleTree
 
getTaxa() - Method in class jebl.evolution.trees.SplitSystem
get taxon list
getTaxa() - Method in interface jebl.evolution.trees.Tree
 
getTaxon() - Method in class jebl.evolution.alignments.ConsensusSequence
 
getTaxon() - Method in class jebl.evolution.sequences.BasicSequence
 
getTaxon() - Method in class jebl.evolution.sequences.FilteredSequence
 
getTaxon() - Method in interface jebl.evolution.sequences.Sequence
 
getTaxon(String) - Static method in class jebl.evolution.taxa.Taxon
A static method that returns a Taxon object with the given name.
getTaxon(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
getTaxon(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
getTaxon(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
getTaxon(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
getTaxon(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
getTaxon(Node) - Method in class jebl.evolution.trees.SimpleTree
 
getTaxon(Node) - Method in interface jebl.evolution.trees.Tree
 
getTaxonFont(Taxon, Font) - Method in interface jebl.gui.trees.treeviewer.decorators.TaxonDecorator
 
getTaxonLabelPainter() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getTaxonLabelPath(Node) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
getTaxonLabelPath(Node) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
 
getTaxonomicLevel() - Method in class jebl.evolution.taxa.Taxon
get the taxonomic level of the taxon
getTaxonomicLevel(String) - Static method in class jebl.evolution.taxa.TaxonomicLevel
A static method that returns a TaxonomicLevel object with the given name.
getTaxonomicLevels() - Static method in class jebl.evolution.taxa.TaxonomicLevel
Returns a Set containing all the currently created taxonomic levels.
getTaxonPaint(Taxon) - Method in interface jebl.gui.trees.treeviewer.decorators.TaxonDecorator
 
getTestSequence1() - Static method in class jebl.evolution.sequences.SequenceTester
 
getTestSequence1(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
 
getTestSequence2() - Static method in class jebl.evolution.sequences.SequenceTester
 
getTestSequence2(String[]) - Static method in class jebl.evolution.sequences.SequenceTester
 
getTextDecorator() - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
getTipCount(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
Return the number of leaves under this node.
getTipLabelPainter() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getTipLabelPath(Node) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getTipLabelPath(Node) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getTipLabelPathMap() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
getTipLabelPathMap() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
getTipLabelPosition() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getTipsForTaxa(RootedTree, Collection<Taxon>) - Static method in class jebl.evolution.trees.RootedTreeUtils
Gets a set of external nodes that correspond to the given taxa.
getTitle() - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
getTitle() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
getTitle() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
getTitle() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
getTitle() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
getTitle() - Method in class org.virion.jam.controlpanels.Controls
 
getTitle() - Method in interface org.virion.jam.preferences.PreferencesSection
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.TreePaneController
 
getTitleComponent() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
getTitleComponent() - Method in interface org.virion.jam.controlpalettes.Controller
Get a component that will be put in the title bar of the palette section.
getTitleComponent() - Method in class org.virion.jam.disclosure.DisclosurePanel
 
getToolTipText() - Method in class org.virion.jam.toolbar.ToolbarAction
 
getTotal(double[], int, int) - Static method in class jebl.math.Random
 
getTotal(double[]) - Static method in class jebl.math.Random
 
getTotalDuration() - Method in interface jebl.evolution.coalescent.IntervalList
get the total duration of these intervals.
getTotalDuration() - Method in class jebl.evolution.coalescent.Intervals
 
getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
A utility method for speed, transfers trans prob information quickly into store
getTransitionProbabilities(double[][]) - Method in class jebl.evolution.substmodel.MatrixExponential
A utility method for speed, transfers trans prob information quickly into store
getTransitionProbabilities(double[][]) - Method in interface jebl.evolution.substmodel.RateMatrix
A utility method for speed, transfers trans prob information quickly into store.
getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
getTransitionProbability(int, int) - Method in class jebl.evolution.substmodel.MatrixExponential
 
getTransitionProbability(int, int) - Method in interface jebl.evolution.substmodel.RateMatrix
 
getTranslation(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
Returns the state associated with AminoAcid represented by codonState.
getTree() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
getTree() - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
 
getTree() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getTree() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getTree() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
getTreeBounds() - Method in class jebl.gui.trees.treeviewer.TreePane
 
getTreeBounds() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getTreeCount() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
getTreeLayout() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
getTreePane() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
getTrees() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
getTreeScale() - Method in class jebl.gui.trees.treeviewer.TreePane
This returns the scaling factor between the graphical image and the branch lengths of the tree
getTreeScale() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
This returns the scaling factor between the graphical image and the branch lengths of the tree
getTreeViewer() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerPanel
 
getTripletCode(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
 
getType() - Method in interface jebl.evolution.characters.Character
return the CharacterType of the character
getType() - Method in class jebl.evolution.characters.ContinuousCharacter
 
getType() - Method in class jebl.evolution.characters.DiscreteCharacter
 
getUniqueName() - Method in interface jebl.evolution.substmodel.RateMatrix
 
getUniqueName() - Method in class jebl.evolution.substmodel.WAG
 
getUnknownState() - Static method in class jebl.evolution.sequences.AminoAcids
 
getUnknownState() - Static method in class jebl.evolution.sequences.Codons
 
getUnknownState() - Static method in class jebl.evolution.sequences.Nucleotides
 
getUnknownState() - Method in interface jebl.evolution.sequences.SequenceType
Get state corresponding to an unknown
getUpperBound(int) - Method in class jebl.evolution.coalescent.Coalescent
 
getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstExponential
 
getUpperBound(int) - Method in class jebl.evolution.coalescent.ConstLogistic
 
getUpperBound(int) - Method in interface jebl.evolution.coalescent.DemographicFunction
Returns the upper bound of the nth argument of this function.
getUpperBound(int) - Method in class jebl.evolution.coalescent.Expansion
 
getUpperBound(int) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
getUpperBound(int) - Method in interface jebl.math.MultivariateFunction
get upper bound of argument n
getUpperBound() - Method in class jebl.math.OrthogonalLineFunction
 
getUpperBound() - Method in interface jebl.math.UnivariateFunction
get upper bound of argument
getUpperDocumentFrame() - Method in class org.virion.jam.framework.MultiDocApplication
 
getV() - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
 
getValue(Taxon) - Method in interface jebl.evolution.characters.Character
get a value for a taxon containing the character
getValue(Taxon) - Method in class jebl.evolution.characters.ContinuousCharacter
 
getValue(Taxon) - Method in class jebl.evolution.characters.DiscreteCharacter
 
getValue() - Method in class org.virion.jam.components.RealNumberField
 
getValue(double) - Method in class org.virion.jam.components.RealNumberField
 
getValue() - Method in class org.virion.jam.components.WholeNumberField
 
getValue(int) - Method in class org.virion.jam.components.WholeNumberField
 
getValue() - Method in interface org.virion.jam.panels.RulesPanel.Rule
 
getValue() - Method in class org.virion.jam.util.SwingWorker
Get the value produced by the worker thread, or null if it hasn't been constructed yet.
getValues(Object, Object) - Method in interface org.virion.jam.panels.RuleModel
Returns an array of strings to be presented as a combo box which are possible values for the field.
getVgap() - Method in class org.virion.jam.layouts.CompassLayout
Returns the vertical gap between components.
getWebsiteAction() - Method in class org.virion.jam.framework.AbstractFrame
 
getWebsiteAction() - Method in class org.virion.jam.framework.Application
 
getWebsiteURLString() - Static method in class org.virion.jam.framework.Application
 
getWeight() - Method in interface jebl.evolution.alignments.Pattern
Get the weight of this pattern
getX() - Method in class jebl.evolution.align.Traceback
 
getXAxisType() - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getXAxisType() - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getXAxisType() - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getXAxisType() - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return whether the x axis is continuous or discrete
getXAxisType() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getXAxisType() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
getXAxisType() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getXAxisType() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return whether the x axis is continuous or discrete
getY() - Method in class jebl.evolution.align.Traceback
 
getYAxisType() - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
getYAxisType() - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
getYAxisType() - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
getYAxisType() - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return whether the y axis is continuous or discrete
getYAxisType() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
getYAxisType() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
getYAxisType() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
getYAxisType() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return whether the y axis is continuous or discrete
getZero() - Static method in class jebl.math.OrderEnumerator.Utils
 
getZeroFactory() - Static method in class jebl.math.OrderEnumerator.Utils
 
getZoomWindowAction() - Method in class org.virion.jam.framework.AbstractFrame
 
go() - Method in class org.virion.jam.util.LongTask
Called to start the task.
gradient(MultivariateFunction, double[]) - Static method in class jebl.math.NumericalDerivative
determine gradient
gradient(MultivariateFunction, double[], double[]) - Static method in class jebl.math.NumericalDerivative
determine gradient
Graph - Interface in jebl.evolution.graphs
 
Graph.NoEdgeException - Exception in jebl.evolution.graphs
This class is thrown by getEdgeLength(node1, node2) if node1 and node2 are not directly connected by an edge.
Graph.NoEdgeException() - Constructor for exception jebl.evolution.graphs.Graph.NoEdgeException
 
Graph.Utils - Class in jebl.evolution.graphs
 
Graph.Utils() - Constructor for class jebl.evolution.graphs.Graph.Utils
 
gray(Icon) - Static method in class org.virion.jam.util.IconUtils
Returns a grayed version of the icon.
GreedyRootedConsensusTreeBuilder - Class in jebl.evolution.trees
Date: 5/03/2006 Time: 09:40:18
GreedyRootedConsensusTreeBuilder(RootedTree[], double) - Constructor for class jebl.evolution.trees.GreedyRootedConsensusTreeBuilder
 
GreedyRootedConsensusTreeBuilder(RootedTree[], double, String, boolean) - Constructor for class jebl.evolution.trees.GreedyRootedConsensusTreeBuilder
 
GreedyUnrootedConsensusTreeBuilder - Class in jebl.evolution.trees
Builds greedy consensus tree given a set of unrooted trees.
gridbag - Variable in class org.virion.jam.panels.OptionsPanel
 
guessSequenceType(CharSequence) - Static method in class jebl.evolution.sequences.Utils
Guess type of sequence from contents

H

H_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
H_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
Hamming - Class in jebl.evolution.align.scores
 
Hamming() - Constructor for class jebl.evolution.align.scores.Hamming
 
handleAbout(ApplicationEvent) - Method in class org.virion.jam.maconly.OSXAdapter
 
handleOpenFile(ApplicationEvent) - Method in class org.virion.jam.maconly.OSXAdapter
 
handlePreferences(ApplicationEvent) - Method in class org.virion.jam.maconly.OSXAdapter
 
handleQuit(ApplicationEvent) - Method in class org.virion.jam.maconly.OSXAdapter
 
hasFile() - Method in class org.virion.jam.framework.DocumentFrame
 
hashCode() - Method in class jebl.evolution.sequences.AminoAcidState
 
hashCode() - Method in class jebl.evolution.sequences.NucleotideState
 
hashCode() - Method in class jebl.evolution.sequences.State
 
hashCode() - Method in class jebl.evolution.taxa.Taxon
 
hashCode() - Method in class jebl.util.FixedBitSet
 
hasHeights() - Method in class jebl.evolution.trees.CompactRootedTree
 
hasHeights() - Method in class jebl.evolution.trees.FilteredRootedTree
 
hasHeights() - Method in class jebl.evolution.trees.MutableRootedTree
 
hasHeights() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
hasHeights() - Method in interface jebl.evolution.trees.RootedTree
 
hasHeights() - Method in class jebl.evolution.trees.SimpleRootedTree
 
hasHeights() - Method in class jebl.evolution.trees.TransformedRootedTree
 
hasIntegral() - Method in class jebl.evolution.coalescent.CataclysmicDemographic
 
hasIntegral() - Method in class jebl.evolution.coalescent.ConstantPopulation
 
hasIntegral() - Method in class jebl.evolution.coalescent.ConstExponential
 
hasIntegral() - Method in class jebl.evolution.coalescent.ConstLogistic
 
hasIntegral() - Method in interface jebl.evolution.coalescent.DemographicFunction
returns whether an analytical expression for the integral is implemented
hasIntegral() - Method in class jebl.evolution.coalescent.Expansion
 
hasIntegral() - Method in class jebl.evolution.coalescent.LogisticGrowth
 
hasLengths() - Method in class jebl.evolution.trees.CompactRootedTree
 
hasLengths() - Method in class jebl.evolution.trees.FilteredRootedTree
 
hasLengths() - Method in class jebl.evolution.trees.MutableRootedTree
 
hasLengths() - Method in class jebl.evolution.trees.RootedFromUnrooted
 
hasLengths() - Method in interface jebl.evolution.trees.RootedTree
 
hasLengths() - Method in class jebl.evolution.trees.SimpleRootedTree
 
hasLengths() - Method in class jebl.evolution.trees.TransformedRootedTree
 
hasMore() - Method in interface jebl.math.OrderEnumerator
If hasMore returns false reset should be called
hasNextSubtask() - Method in class jebl.util.CompositeProgressListener
 
hasOption(String) - Method in class org.virion.jam.app.Arguments
Does an argument with label exist?
hasSelection() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
hasSplit(boolean[]) - Method in class jebl.evolution.trees.SplitSystem
+ test whether a split is contained in this split system (assuming the same leaf order)
hasTree() - Method in class jebl.evolution.io.NewickImporter
 
hasTree() - Method in class jebl.evolution.io.NexusImporter
return whether another tree is available.
hasTree() - Method in interface jebl.evolution.io.TreeImporter
This can be used to read one tree at a time in a loop: List trees = new ArrayList(); while (hasTree()) { trees.add(importNextTree()); } return whether another tree is available.
HeaderRenderer - Class in org.virion.jam.table
 
HeaderRenderer(int, Insets) - Constructor for class org.virion.jam.table.HeaderRenderer
 
HEIGHT_ATTRIBUTE - Static variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
helpAction - Variable in class org.virion.jam.framework.Application
 
helper - Variable in class jebl.evolution.io.NexusImporter
 
hilightLabelFont - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
hilightLabelPaint - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
hilightPaint - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
hilightStroke - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
HKYDistanceMatrix - Class in jebl.evolution.distances
Compute HKY corrected distance matrix
HKYDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.HKYDistanceMatrix
 
HTMLViewer - Class in org.virion.jam.html
General-purpose class to display HTML in a standalone frame.
HTMLViewer(String, String) - Constructor for class org.virion.jam.html.HTMLViewer
 
HYDROPATHY_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.virion.jam.html.SimpleLinkListener
 

I

I_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
ICON_AND_TEXT - Static variable in class org.virion.jam.toolbar.ToolbarOptions
 
ICON_ONLY - Static variable in class org.virion.jam.toolbar.ToolbarOptions
 
IconUtils - Class in org.virion.jam.util
 
IconUtils() - Constructor for class org.virion.jam.util.IconUtils
 
ImmediateSequenceImporter - Interface in jebl.evolution.io
A sequence importer sending the sequences back one by one, which makes it possible to import larger documents if handled wisely on the other side.
ImmediateSequenceImporter.Callback - Interface in jebl.evolution.io
 
importAlignments() - Method in interface jebl.evolution.io.AlignmentImporter
importAlignment.
importAlignments() - Method in class jebl.evolution.io.NexusImporter
importAlignment.
importDistanceMatrices() - Method in interface jebl.evolution.io.DistanceMatrixImporter
importDistances.
importDistanceMatrices() - Method in class jebl.evolution.io.NexusImporter
importDistances.
importDistanceMatrices() - Method in class jebl.evolution.io.TabDelimitedImporter
importDistances.
ImportException - Exception in jebl.evolution.io
 
ImportException() - Constructor for exception jebl.evolution.io.ImportException
 
ImportException(String) - Constructor for exception jebl.evolution.io.ImportException
 
ImportException.BadFormatException - Exception in jebl.evolution.io
 
ImportException.BadFormatException() - Constructor for exception jebl.evolution.io.ImportException.BadFormatException
 
ImportException.BadFormatException(String) - Constructor for exception jebl.evolution.io.ImportException.BadFormatException
 
ImportException.DuplicateFieldException - Exception in jebl.evolution.io
 
ImportException.DuplicateFieldException() - Constructor for exception jebl.evolution.io.ImportException.DuplicateFieldException
 
ImportException.DuplicateFieldException(String) - Constructor for exception jebl.evolution.io.ImportException.DuplicateFieldException
 
ImportException.DuplicateTaxaException - Exception in jebl.evolution.io
 
ImportException.DuplicateTaxaException() - Constructor for exception jebl.evolution.io.ImportException.DuplicateTaxaException
 
ImportException.DuplicateTaxaException(String) - Constructor for exception jebl.evolution.io.ImportException.DuplicateTaxaException
 
ImportException.MissingFieldException - Exception in jebl.evolution.io
 
ImportException.MissingFieldException() - Constructor for exception jebl.evolution.io.ImportException.MissingFieldException
 
ImportException.MissingFieldException(String) - Constructor for exception jebl.evolution.io.ImportException.MissingFieldException
 
ImportException.ShortSequenceException - Exception in jebl.evolution.io
 
ImportException.ShortSequenceException() - Constructor for exception jebl.evolution.io.ImportException.ShortSequenceException
 
ImportException.ShortSequenceException(String) - Constructor for exception jebl.evolution.io.ImportException.ShortSequenceException
 
ImportException.TooFewTaxaException - Exception in jebl.evolution.io
 
ImportException.TooFewTaxaException() - Constructor for exception jebl.evolution.io.ImportException.TooFewTaxaException
 
ImportException.TooFewTaxaException(String) - Constructor for exception jebl.evolution.io.ImportException.TooFewTaxaException
 
ImportException.UnknownTaxonException - Exception in jebl.evolution.io
 
ImportException.UnknownTaxonException() - Constructor for exception jebl.evolution.io.ImportException.UnknownTaxonException
 
ImportException.UnknownTaxonException(String) - Constructor for exception jebl.evolution.io.ImportException.UnknownTaxonException
 
ImportException.UnparsableDataException - Exception in jebl.evolution.io
 
ImportException.UnparsableDataException() - Constructor for exception jebl.evolution.io.ImportException.UnparsableDataException
 
ImportException.UnparsableDataException(String) - Constructor for exception jebl.evolution.io.ImportException.UnparsableDataException
 
ImportHelper - Class in jebl.evolution.io
A helper class for phylogenetic file format importers
ImportHelper(Reader) - Constructor for class jebl.evolution.io.ImportHelper
ATTENTION: The ImportHelper never closes the reader passed to the constructor.
ImportHelper(Reader, Writer) - Constructor for class jebl.evolution.io.ImportHelper
 
importNextTree() - Method in class jebl.evolution.io.NewickImporter
 
importNextTree() - Method in class jebl.evolution.io.NexusImporter
import the next tree.
importNextTree() - Method in interface jebl.evolution.io.TreeImporter
Import a single tree
importSequences() - Method in class jebl.evolution.io.FastaImporter
 
importSequences(ImmediateSequenceImporter.Callback, ProgressListener) - Method in class jebl.evolution.io.FastaImporter
 
importSequences(ImmediateSequenceImporter.Callback, ProgressListener) - Method in interface jebl.evolution.io.ImmediateSequenceImporter
 
importSequences() - Method in class jebl.evolution.io.NexusImporter
importSequences.
importSequences() - Method in class jebl.evolution.io.PhylipSequentialImporter
importSequences.
importSequences() - Method in interface jebl.evolution.io.SequenceImporter
importSequences.
importTrees() - Method in class jebl.evolution.io.NewickImporter
 
importTrees() - Method in class jebl.evolution.io.NexusImporter
 
importTrees() - Method in interface jebl.evolution.io.TreeImporter
Import all the trees
includeAdditionalCharacters(Scores, String) - Static method in class jebl.evolution.align.scores.Scores
includes additional characters in the score matrix which will all have scored zero when compared to other characters.
includeGaps(Scores, float, float) - Static method in class jebl.evolution.align.scores.Scores
 
incompleteGammaP(double, double) - Static method in class jebl.math.GammaFunction
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
incompleteGammaP(double, double, double) - Static method in class jebl.math.GammaFunction
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
incompleteGammaQ(double, double) - Static method in class jebl.math.GammaFunction
Incomplete Gamma function Q(a,x) (a cleanroom implementation of Numerical Recipes gammq(a,x); in Mathematica this function is called GammaRegularized)
init(Alignment, int[]) - Method in class jebl.evolution.alignments.ResampledAlignment
Setup resampled alignment.
init(DistanceMatrix) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.TreePaneController
 
initialize() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
initialize() - Method in class org.virion.jam.console.ConsoleApplication
 
initialize() - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
initialize() - Method in interface org.virion.jam.controlpalettes.Controller
Initialize this controller when a new document is created.
initialize() - Method in interface org.virion.jam.controlpalettes.ControlPalette
Initialize all controllers when a new document is created.
initialize() - Method in class org.virion.jam.framework.AbstractFrame
 
initialize() - Method in class org.virion.jam.framework.Application
 
initialize() - Method in class org.virion.jam.framework.MultiDocApplication
 
initialize() - Method in class org.virion.jam.framework.SingleDocApplication
 
initializeComponents() - Method in class org.virion.jam.console.ConsoleFrame
 
initializeComponents() - Method in class org.virion.jam.demo.DemoFrame
 
initializeComponents() - Method in class org.virion.jam.framework.AboutBox
 
initializeComponents() - Method in class org.virion.jam.framework.AbstractFrame
 
initializeComponents() - Method in class org.virion.jam.framework.AuxilaryFrame
 
initializeComponents() - Method in class org.virion.jam.framework.DocumentFrame
 
innerProduct(double[], double[], int) - Static method in class jebl.math.MatrixCalc
innerProdect calculates inner product of two vectors from i down
insertUpdate(DocumentEvent) - Method in class org.virion.jam.components.RealNumberField
 
insertUpdate(DocumentEvent) - Method in class org.virion.jam.components.WholeNumberField
 
installUI(JComponent) - Method in class org.virion.jam.table.AdvancedTableUI
 
internalNodes - Variable in class jebl.evolution.trees.MutableRootedTree
 
internalNodes - Variable in class jebl.evolution.trees.SimpleRootedTree
 
interrupt() - Method in class org.virion.jam.util.SwingWorker
A new method that interrupts the worker thread.
intersect(FixedBitSet) - Method in class jebl.util.FixedBitSet
 
intersectCardinality(FixedBitSet) - Method in class jebl.util.FixedBitSet
 
IntervalGenerator - Interface in jebl.evolution.trees
 
IntervalList - Interface in jebl.evolution.coalescent
An interface for a set of coalescent intevals.
IntervalList.IntervalType - Enum in jebl.evolution.coalescent
 
IntervalList.Utils - Class in jebl.evolution.coalescent
 
IntervalList.Utils() - Constructor for class jebl.evolution.coalescent.IntervalList.Utils
 
Intervals - Class in jebl.evolution.coalescent
A concrete class for a set of coalescent intevals.
Intervals(RootedTree) - Constructor for class jebl.evolution.coalescent.Intervals
 
Intervals(int) - Constructor for class jebl.evolution.coalescent.Intervals
 
invalidate() - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
invalidate() - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Force the layout to re-layout all its components
invalidate() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
invalidate() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Force the layout to re-layout all its components
invalidateLayout(Container) - Method in class org.virion.jam.layouts.CompassLayout
Invalidates the layout, indicating that if the layout manager has cached information it should be discarded.
INVERTEBRATE_MT - Static variable in class jebl.evolution.sequences.GeneticCode
 
isAcyclical(Graph) - Method in class jebl.evolution.graphs.Utils
 
isAlignTipLabels() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
isAllGaps() - Method in class jebl.evolution.align.ProfileCharacter
 
isAmbiguous() - Method in class jebl.evolution.sequences.State
 
isATstate(State) - Static method in class jebl.evolution.sequences.Nucleotides
 
isBinary(RootedTree) - Static method in class jebl.evolution.trees.RootedTreeUtils
 
isBinary(RootedTree) - Static method in class jebl.evolution.trees.Utils
 
isBinaryCoalescent() - Method in interface jebl.evolution.coalescent.IntervalList
Checks whether this set of coalescent intervals is fully resolved (i.e.
isBinaryCoalescent() - Method in class jebl.evolution.coalescent.Intervals
 
isCanceled() - Method in class jebl.util.CompositeProgressListener
 
isCanceled() - Method in class jebl.util.ProgressListener
This method must be implemented by all subclasses.
isCoalescentOnly() - Method in interface jebl.evolution.coalescent.IntervalList
Checks whether this set of coalescent intervals coalescent only (i.e.
isCoalescentOnly() - Method in class jebl.evolution.coalescent.Intervals
 
isConnected(Graph) - Method in class jebl.evolution.graphs.Utils
 
isContains(String[], String) - Static method in class jebl.util.Utils
Test if a string occurs within a set
isDebug() - Method in class jebl.math.OrthogonalSearch
 
isDirty() - Method in class org.virion.jam.framework.AbstractFrame
 
isExternal(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
isExternal(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
isExternal(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
isExternal(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
isExternal(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
isExternal(Node) - Method in class jebl.evolution.trees.SimpleTree
 
isExternal(Edge) - Method in class jebl.evolution.trees.SimpleTree
 
isExternal(Node) - Method in interface jebl.evolution.trees.Tree
 
isFrequentMonitoring() - Method in class jebl.math.OrthogonalSearch
 
isGap(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
 
isGap() - Method in class jebl.evolution.sequences.AminoAcidState
 
isGap(CodonState) - Static method in class jebl.evolution.sequences.Codons
 
isGap() - Method in class jebl.evolution.sequences.CodonState
 
isGap(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
 
isGap() - Method in class jebl.evolution.sequences.NucleotideState
 
isGap(State) - Method in interface jebl.evolution.sequences.SequenceType
 
isGap() - Method in class jebl.evolution.sequences.State
 
isGCstate(State) - Static method in class jebl.evolution.sequences.Nucleotides
 
isGeneratedTreeName(String) - Static method in class jebl.evolution.io.NexusExporter
 
isIgnoreNonMinimalUnivariateMinimisations() - Method in class jebl.math.OrthogonalSearch
Should we ignore new minisations that are not as minimal as the current one?
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.TreePaneController
 
isInitiallyVisible() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
isInitiallyVisible() - Method in interface org.virion.jam.controlpalettes.Controller
 
isMacOSX() - Static method in class org.virion.jam.mac.Utils
 
isMonophyletic(RootedTree, Set<Node>) - Static method in class jebl.evolution.trees.RootedTreeUtils
Performs the a monophyly test on a set of tip nodes.
isOrderBranchesOn() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
isOrdered() - Method in class jebl.evolution.characters.DiscreteCharacter
 
isPinned() - Method in class org.virion.jam.controlpanels.Controls
 
isPurine(State) - Static method in class jebl.evolution.sequences.Nucleotides
 
isPyrimidine(State) - Static method in class jebl.evolution.sequences.Nucleotides
 
isRoot(Node) - Method in class jebl.evolution.trees.CompactRootedTree
 
isRoot(Node) - Method in class jebl.evolution.trees.FilteredRootedTree
 
isRoot(Node) - Method in class jebl.evolution.trees.MutableRootedTree
 
isRoot(Node) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
isRoot(Node) - Method in interface jebl.evolution.trees.RootedTree
 
isRoot(Node) - Method in class jebl.evolution.trees.SimpleRootedTree
 
isRootedMethod(TreeBuilderFactory.Method) - Static method in class jebl.evolution.trees.TreeBuilderFactory
 
isSame(boolean[], boolean[]) - Static method in class jebl.evolution.trees.SplitUtils
checks whether two splits are identical (assuming they are of the same length and use the same leaf order)
isShowingCollapsedTipLabels() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
isShowingColouring() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
isShowingColouring() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return whether this layout is showing a branch colouring
isShowingRootBranch() - Method in class jebl.gui.trees.treeviewer.TreePane
 
isShowingRootBranch() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
isShowingRootBranch() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
isShowingRootBranch() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
isShowingRootBranch() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return whether this layout displays a root branch
isShowingTaxonCallouts() - Method in class jebl.gui.trees.treeviewer.TreePane
 
isShowingTipCallouts() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
isStop() - Method in class jebl.evolution.sequences.AminoAcidState
 
isStopCodon(CodonState) - Method in class jebl.evolution.sequences.GeneticCode
Note that the state is the canonical state (generated combinatorially)
isSupportAsPercent() - Method in class jebl.evolution.trees.ConsensusTreeBuilder
 
isTransformBranchesOn() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
isTransition(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
 
isTransversion(State, State) - Static method in class jebl.evolution.sequences.Nucleotides
 
isTree(Graph) - Method in class jebl.evolution.graphs.Utils
 
isUltrametric(RootedTree, double) - Static method in class jebl.evolution.trees.RootedTreeUtils
 
isUltrametric(RootedTree) - Static method in class jebl.evolution.trees.Utils
 
isUnknown(AminoAcidState) - Static method in class jebl.evolution.sequences.AminoAcids
 
isUnknown(CodonState) - Static method in class jebl.evolution.sequences.Codons
 
isUnknown(NucleotideState) - Static method in class jebl.evolution.sequences.Nucleotides
 
isUnknown(State) - Method in interface jebl.evolution.sequences.SequenceType
 
isUseCurrentInUnivariateMinimisation() - Method in class jebl.math.OrthogonalSearch
 
isVisible() - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
isVisible() - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
isVisible() - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
isVisible() - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
isVisible() - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
isVisible() - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
If this is false then the painter should not be displayed.
isVisible() - Method in class org.virion.jam.controlpanels.Controls
 
iterator() - Method in class jebl.evolution.io.NewickImporter
Returns an iterator over a set of elements of type T.
iterator() - Method in class jebl.evolution.io.NexusImporter
Returns an iterator over a set of elements of type T.
IUB - Static variable in class jebl.evolution.align.scores.NucleotideScores
 

J

JackknifedAlignment - Class in jebl.evolution.alignments
Date: 17/01/2006 Time: 08:18:32
JackknifedAlignment(Alignment, double) - Constructor for class jebl.evolution.alignments.JackknifedAlignment
 
jebl.evolution.align - package jebl.evolution.align
Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.align.scores - package jebl.evolution.align.scores
 
jebl.evolution.aligners - package jebl.evolution.aligners
 
jebl.evolution.alignments - package jebl.evolution.alignments
 
jebl.evolution.characterReconstruction - package jebl.evolution.characterReconstruction
 
jebl.evolution.characters - package jebl.evolution.characters
 
jebl.evolution.coalescent - package jebl.evolution.coalescent
 
jebl.evolution.distances - package jebl.evolution.distances
 
jebl.evolution.graphs - package jebl.evolution.graphs
 
jebl.evolution.io - package jebl.evolution.io
 
jebl.evolution.parsimony - package jebl.evolution.parsimony
 
jebl.evolution.sequences - package jebl.evolution.sequences
 
jebl.evolution.substmodel - package jebl.evolution.substmodel
 
jebl.evolution.taxa - package jebl.evolution.taxa
 
jebl.evolution.trees - package jebl.evolution.trees
 
jebl.gui.trees.treecomponent - package jebl.gui.trees.treecomponent
 
jebl.gui.trees.treeviewer - package jebl.gui.trees.treeviewer
 
jebl.gui.trees.treeviewer.decorators - package jebl.gui.trees.treeviewer.decorators
 
jebl.gui.trees.treeviewer.painters - package jebl.gui.trees.treeviewer.painters
 
jebl.gui.trees.treeviewer.treelayouts - package jebl.gui.trees.treeviewer.treelayouts
 
jebl.gui.trees.treeviewer_dev - package jebl.gui.trees.treeviewer_dev
 
jebl.gui.trees.treeviewer_dev.decorators - package jebl.gui.trees.treeviewer_dev.decorators
 
jebl.gui.trees.treeviewer_dev.painters - package jebl.gui.trees.treeviewer_dev.painters
 
jebl.gui.trees.treeviewer_dev.treelayouts - package jebl.gui.trees.treeviewer_dev.treelayouts
 
jebl.math - package jebl.math
 
jebl.util - package jebl.util
 
JExceptionDialog - Class in org.virion.jam.util
 
JExceptionDialog(Frame, boolean, String, String) - Constructor for class org.virion.jam.util.JExceptionDialog
Creates new form JExceptionDialog
joinClusters() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
Inform derived class that clusters besti,bestj are being joinded into a new cluster.
joinClusters() - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
 
JukesCantor - Class in jebl.evolution.align.scores
Jukes Cantor assumes equal substitution frequencies and equal nucleotide equilibrium frequencies.
JukesCantor(float) - Constructor for class jebl.evolution.align.scores.JukesCantor
 
JukesCantorDistanceMatrix - Class in jebl.evolution.distances
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
JukesCantorDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.JukesCantorDistanceMatrix
 
JVerticalLabel - Class in org.virion.jam.components
 
JVerticalLabel(boolean) - Constructor for class org.virion.jam.components.JVerticalLabel
 
JVerticalLabel(Icon, boolean) - Constructor for class org.virion.jam.components.JVerticalLabel
 
JVerticalLabel(Icon, int, boolean) - Constructor for class org.virion.jam.components.JVerticalLabel
 
JVerticalLabel(String, boolean) - Constructor for class org.virion.jam.components.JVerticalLabel
 
JVerticalLabel(String, Icon, int, boolean) - Constructor for class org.virion.jam.components.JVerticalLabel
 
JVerticalLabel(String, int, boolean) - Constructor for class org.virion.jam.components.JVerticalLabel
 

K

K_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
K_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 

L

L_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
labelFont - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
labelPaint - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
LabelPainter<T> - Class in jebl.gui.trees.treeviewer_dev.painters
 
LabelPainter() - Constructor for class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
LabelPainterController - Class in jebl.gui.trees.treeviewer_dev.painters
 
LabelPainterController(String, String, LabelPainter) - Constructor for class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
layoutContainer(Container) - Method in class org.virion.jam.layouts.CompassLayout
Lays out the specified container.
layoutControls() - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
LEFT - Static variable in interface org.virion.jam.framework.MenuFactory
 
length() - Method in class jebl.evolution.io.ByteBuilder
 
length - Variable in class org.virion.jam.util.SimpleLongTask
 
linePaint - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
lineStroke - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
listener - Variable in class jebl.util.CompositeProgressListener
 
ListItemView - Interface in org.virion.jam.util
 
lnGamma(double) - Static method in class jebl.math.GammaFunction
log Gamma function: ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places
load(Properties) - Method in class org.virion.jam.framework.RecentFileList
Load the recent file list from a Properties set
LogisticGrowth - Class in jebl.evolution.coalescent
This class models logistic growth.
LogisticGrowth() - Constructor for class jebl.evolution.coalescent.LogisticGrowth
Construct demographic model with default settings
LogisticGrowth(double, double, double) - Constructor for class jebl.evolution.coalescent.LogisticGrowth
Construct demographic model with given settings
LongTask - Class in org.virion.jam.util
 
LongTask() - Constructor for class org.virion.jam.util.LongTask
 
LongTaskMonitor - Class in org.virion.jam.util
 
LongTaskMonitor(LongTask, JComponent, TaskListener) - Constructor for class org.virion.jam.util.LongTaskMonitor
 
LOWER_ATTRIBUTE - Static variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
lowerSolve(double[][], double[], double) - Static method in class jebl.math.MatrixCalc
lower Solve forward elimination with (optional) default diagonal value

M

M_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
M_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
MAC_OS_X - Static variable in class org.virion.jam.mac.Utils
 
MAC_OS_X_VERSION - Static variable in class org.virion.jam.mac.Utils
 
MacFileMenuFactory - Class in org.virion.jam.mac
 
MacFileMenuFactory(boolean) - Constructor for class org.virion.jam.mac.MacFileMenuFactory
 
MacHelpMenuFactory - Class in org.virion.jam.mac
 
MacHelpMenuFactory() - Constructor for class org.virion.jam.mac.MacHelpMenuFactory
 
MachineAccuracy - Class in jebl.math
determines machine accuracy
MachineAccuracy() - Constructor for class jebl.math.MachineAccuracy
 
macOSXRegistration(Application) - Static method in class org.virion.jam.mac.Utils
 
MacWindowMenuFactory - Class in org.virion.jam.mac
 
MacWindowMenuFactory() - Constructor for class org.virion.jam.mac.MacWindowMenuFactory
 
main(String[]) - Static method in class jebl.evolution.align.AlignCommand
 
main(String[]) - Static method in class jebl.evolution.align.BartonSternberg
 
main(String[]) - Static method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
main(String[]) - Static method in class jebl.evolution.trees.TreeSimulator
A main() to test the tree simulation classes.
main(String[]) - Static method in class jebl.gui.trees.treeviewer.TreeViewer
 
main(String[]) - Static method in class jebl.gui.trees.treeviewer_dev.TreeViewerPanel
 
main(String[]) - Static method in class org.virion.jam.demo.DemoApplication
 
main(String[]) - Static method in class org.virion.jam.util.JExceptionDialog
 
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
maintainAspectRatio() - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Return whether the two axis scales should be maintained relative to each other
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer.TreePane
Return whether the two axis scales should be maintained relative to each other
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
maintainAspectRatio() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Return whether the two axis scales should be maintained relative to each other
maintainAspectRatio() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
Return whether the two axis scales should be maintained relative to each other
MatrixCalc - Class in jebl.math
 
MatrixCalc() - Constructor for class jebl.math.MatrixCalc
 
MatrixCalcException - Exception in jebl.math
 
MatrixCalcException() - Constructor for exception jebl.math.MatrixCalcException
 
MatrixCalcException(String) - Constructor for exception jebl.math.MatrixCalcException
 
MatrixCalcException.NotSquareMatrixException - Exception in jebl.math
 
MatrixCalcException.NotSquareMatrixException() - Constructor for exception jebl.math.MatrixCalcException.NotSquareMatrixException
 
MatrixCalcException.NotSquareMatrixException(String) - Constructor for exception jebl.math.MatrixCalcException.NotSquareMatrixException
 
MatrixCalcException.PositiveDefiniteException - Exception in jebl.math
 
MatrixCalcException.PositiveDefiniteException() - Constructor for exception jebl.math.MatrixCalcException.PositiveDefiniteException
 
MatrixCalcException.PositiveDefiniteException(String) - Constructor for exception jebl.math.MatrixCalcException.PositiveDefiniteException
 
MatrixExponential - Class in jebl.evolution.substmodel
compute matrix exponential and, subsequently, transition probabilities for a given rate matrix
MatrixExponential(int) - Constructor for class jebl.evolution.substmodel.MatrixExponential
 
MatrixExponential(RateMatrix) - Constructor for class jebl.evolution.substmodel.MatrixExponential
create module
max - Variable in class org.virion.jam.components.RealNumberField
 
max - Variable in class org.virion.jam.components.WholeNumberField
 
MAX_DISTANCE - Static variable in class jebl.evolution.distances.ModelBasedDistanceMatrix
 
maxFontSize - Variable in class jebl.gui.trees.treecomponent.SquareTreePainter
 
maxFun - Variable in class jebl.math.MultivariateMinimum
maxFun is the maximum number of calls to fun allowed.
maxFun - Variable in class jebl.math.UnivariateMinimum
maximum number of function evaluations (default 0 indicates no limit on calls)
MaximalSegmentPair - Class in jebl.evolution.align
 
MaximalSegmentPair(Scores) - Constructor for class jebl.evolution.align.MaximalSegmentPair
 
maximumLayoutSize(Container) - Method in class org.virion.jam.layouts.CompassLayout
Returns the maximum dimensions for this layout given the components in the specified target container.
maxLevels(RootedTree) - Static method in class jebl.evolution.trees.Utils
 
MEGAExporter - Class in jebl.evolution.io
* Export to MEGA.
MEGAExporter(Writer, String) - Constructor for class jebl.evolution.io.MEGAExporter
 
MENU_MASK - Static variable in interface org.virion.jam.framework.MenuBarFactory
 
MenuBarFactory - Interface in org.virion.jam.framework
 
MenuFactory - Interface in org.virion.jam.framework
 
message - Variable in class org.virion.jam.util.SimpleLongTask
 
min - Variable in class org.virion.jam.components.RealNumberField
 
min - Variable in class org.virion.jam.components.WholeNumberField
 
MinimiserMonitor - Interface in jebl.math
interface for a classes that wish to monitor the progress of a Minimiser
MinimiserMonitor.Utils - Class in jebl.math
 
MinimiserMonitor.Utils() - Constructor for class jebl.math.MinimiserMonitor.Utils
 
minimumLayoutSize(Container) - Method in class org.virion.jam.layouts.CompassLayout
Returns the minimum dimensions needed to layout the components contained in the specified target container.
minimumTaxa - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
MINUS - Static variable in class org.virion.jam.components.RealNumberField
 
MINUS_CHAR - Static variable in class org.virion.jam.components.WholeNumberField
 
minx - Variable in class jebl.math.UnivariateMinimum
last minimum
MissingTaxonException - Class in jebl.evolution.taxa
 
MissingTaxonException(Taxon) - Constructor for class jebl.evolution.taxa.MissingTaxonException
 
MLContinuousCharacterReconstructor - Class in jebl.evolution.characterReconstruction
This is the main class that controls the ancestral calculations by the Schluter ML method The theoretical foundations are found in Schulter et al.
MLContinuousCharacterReconstructor(ContinuousCharacter, SimpleRootedTree) - Constructor for class jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
a basic constructor which just defines the tree and character
ModelBasedDistanceMatrix - Class in jebl.evolution.distances
 
ModelBasedDistanceMatrix() - Constructor for class jebl.evolution.distances.ModelBasedDistanceMatrix
 
MOLD_PROTOZOAN_MT - Static variable in class jebl.evolution.sequences.GeneticCode
 
mouseClicked(MouseEvent) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent.MListener
 
mouseClicked(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mouseClicked(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mouseClicked(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mouseClicked(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
mouseDragged(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mouseDragged(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mouseDragged(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mouseDragged(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
mouseEntered(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mouseEntered(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mouseEntered(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mouseEntered(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
mouseExited(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mouseExited(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mouseExited(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mouseExited(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
mouseMoved(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mouseMoved(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mouseMoved(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mouseMoved(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
mousePressed(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mousePressed(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mousePressed(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mousePressed(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
mouseReleased(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneRuler
 
mouseReleased(MouseEvent) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
mouseReleased(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
mouseReleased(MouseEvent) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
MRCACConsensusTreeBuilder - Class in jebl.evolution.trees
Construct a consensus tree for a set of rooted trees.
MRCACConsensusTreeBuilder(Tree[], double) - Constructor for class jebl.evolution.trees.MRCACConsensusTreeBuilder
 
MRCACConsensusTreeBuilder(Tree[], double, String, boolean) - Constructor for class jebl.evolution.trees.MRCACConsensusTreeBuilder
 
MultiDocApplication - Class in org.virion.jam.framework
 
MultiDocApplication(String, String, Icon) - Constructor for class org.virion.jam.framework.MultiDocApplication
 
MultiDocApplication(String, String, Icon, String, String) - Constructor for class org.virion.jam.framework.MultiDocApplication
 
MultiDocApplication(MenuBarFactory, String, String, Icon) - Constructor for class org.virion.jam.framework.MultiDocApplication
 
MultiDocApplication(MenuBarFactory, String, String, Icon, String, String) - Constructor for class org.virion.jam.framework.MultiDocApplication
 
MultiDocMenuBarFactory - Class in org.virion.jam.framework
 
MultiDocMenuBarFactory() - Constructor for class org.virion.jam.framework.MultiDocMenuBarFactory
 
MultipleAligner - Interface in jebl.evolution.align
 
MultipleTreeViewer - Class in jebl.gui.trees.treeviewer
 
MultipleTreeViewer() - Constructor for class jebl.gui.trees.treeviewer.MultipleTreeViewer
 
MultipleTreeViewer(int, BasicControlPalette.DisplayMode) - Constructor for class jebl.gui.trees.treeviewer.MultipleTreeViewer
 
MultipleTreeViewer(ControlPalette, int) - Constructor for class jebl.gui.trees.treeviewer.MultipleTreeViewer
 
MultipleTreeViewer - Class in jebl.gui.trees.treeviewer_dev
 
MultipleTreeViewer() - Constructor for class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
MultipleTreeViewer(TreePane) - Constructor for class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
MultipleTreeViewerController - Class in jebl.gui.trees.treeviewer_dev
 
MultipleTreeViewerController(MultipleTreeViewer) - Constructor for class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
MultivariateFunction - Interface in jebl.math
interface for a function of several variables
MultivariateMinimum - Class in jebl.math
abstract base class for minimisation of a multivariate function
MultivariateMinimum() - Constructor for class jebl.math.MultivariateMinimum
 
MultivariateMinimum.Factory - Interface in jebl.math
A factory interface for MultivariateMinimums (because they aren't statefree)
MutableRootedTree - Class in jebl.evolution.trees
A simple rooted tree providing some ability to manipulate the tree.
MutableRootedTree(Tree, Node) - Constructor for class jebl.evolution.trees.MutableRootedTree
Construct a rooted tree from unrooted.
MYCOPLASMA - Static variable in class jebl.evolution.sequences.GeneticCode
 

N

N_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
N_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
NAME - Static variable in class jebl.evolution.sequences.AminoAcids
 
NAME - Static variable in class jebl.evolution.sequences.Codons
 
NAME - Static variable in class jebl.evolution.sequences.Nucleotides
 
NeedlemanWunsch - Class in jebl.evolution.align
 
NeedlemanWunsch(Scores, float) - Constructor for class jebl.evolution.align.NeedlemanWunsch
 
NeedlemanWunschAffine - Class in jebl.evolution.align
 
NeedlemanWunschAffine(Scores, float, float) - Constructor for class jebl.evolution.align.NeedlemanWunschAffine
 
NeedlemanWunschLinearSpace - Class in jebl.evolution.align
 
NeedlemanWunschLinearSpace(Scores, float) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpace
 
NeedlemanWunschLinearSpaceAffine - Class in jebl.evolution.align
 
NeedlemanWunschLinearSpaceAffine(Scores, float, float) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
NeedlemanWunschLinearSpaceAffine(Scores, float, float, boolean) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
NeedlemanWunschLinearSpaceAffine(Scores, float, float, boolean, boolean) - Constructor for class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
NeighborJoiningTreeBuilder - Class in jebl.evolution.trees
Constructs an unrooted tree by neighbor-joining using pairwise distances.
NeighborJoiningTreeBuilder(DistanceMatrix) - Constructor for class jebl.evolution.trees.NeighborJoiningTreeBuilder
construct NJ tree
newAction - Variable in class org.virion.jam.framework.Application
 
newCluster - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
newCluster() - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
NewickExporter - Class in jebl.evolution.io
 
NewickExporter(Writer) - Constructor for class jebl.evolution.io.NewickExporter
 
NewickImporter - Class in jebl.evolution.io
 
NewickImporter(Reader, boolean) - Constructor for class jebl.evolution.io.NewickImporter
Constructor
newMinimum(double, double[], MultivariateFunction) - Method in interface jebl.math.MinimiserMonitor
Inform monitor of a new minimum, along with the current arguments.
newTraceBack(String, String) - Method in interface jebl.evolution.align.TracebackPlotter
 
next(Traceback) - Method in class jebl.evolution.align.Align
Get the next state in the traceback
next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair
 
next() - Method in class jebl.evolution.io.ImportHelper
 
nextBoolean() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextByte() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextBytes(byte[]) - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextChar() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextCharacter() - Method in class jebl.evolution.io.ImportHelper
 
nextDouble() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nExternalNodes - Variable in class jebl.evolution.trees.ConsensusTreeBuilder
Number of external nodes/taxa
nextFloat() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextGaussian() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextInt() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextInt(int) - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextLong() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
nextOnBit(int) - Method in class jebl.util.FixedBitSet
Iteration helper.
nextShort() - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
NexusExporter - Class in jebl.evolution.io
Export sequences and trees to Nexus format.
NexusExporter(Writer) - Constructor for class jebl.evolution.io.NexusExporter
 
NexusImporter - Class in jebl.evolution.io
Class for importing NEXUS file format
NexusImporter(Reader) - Constructor for class jebl.evolution.io.NexusImporter
Constructor
NexusImporter(Reader, boolean) - Constructor for class jebl.evolution.io.NexusImporter
 
NexusImporter.MissingBlockException - Exception in jebl.evolution.io
 
NexusImporter.MissingBlockException() - Constructor for exception jebl.evolution.io.NexusImporter.MissingBlockException
 
NexusImporter.MissingBlockException(String) - Constructor for exception jebl.evolution.io.NexusImporter.MissingBlockException
 
NexusImporter.NexusBlock - Enum in jebl.evolution.io
 
Node - Interface in jebl.evolution.graphs
Represents a node in a graph or tree.
NODE_HEIGHTS - Static variable in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
NODE_HEIGHTS - Static variable in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
NodeBarController - Class in jebl.gui.trees.treeviewer_dev.painters
 
NodeBarController(String, NodeBarPainter) - Constructor for class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
NodeBarPainter - Class in jebl.gui.trees.treeviewer_dev.painters
 
NodeBarPainter() - Constructor for class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
nodeBarPaths - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
nodeClicked(RootedTree, Node) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent.Adaptor
 
nodeClicked(RootedTree, Node) - Method in interface jebl.gui.trees.treecomponent.RootedTreeComponent.Listener
 
nodeLabelPaths - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
nodeLabelPaths - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
NodePainter - Class in jebl.gui.trees.treeviewer_dev.painters
 
NodePainter() - Constructor for class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
nodePoints - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
nodePoints - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
NodeShapeController - Class in jebl.gui.trees.treeviewer_dev.painters
 
NodeShapeController(String, NodeShapePainter) - Constructor for class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
NodeShapeController.NodePainterType - Enum in jebl.gui.trees.treeviewer_dev.painters
 
NodeShapePainter - Class in jebl.gui.trees.treeviewer_dev.painters
 
NodeShapePainter() - Constructor for class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
NodeShapePainter.NodeShape - Enum in jebl.gui.trees.treeviewer_dev.painters
 
NonOverlapMultipleLocalAffine - Class in jebl.evolution.align
Performs recursive local alignments.
NonOverlapMultipleLocalAffine(Scores, float, float, int) - Constructor for class jebl.evolution.align.NonOverlapMultipleLocalAffine
 
NORMAL - Static variable in class org.virion.jam.panels.StatusPanel
 
NUCLEOTIDE - Static variable in interface jebl.evolution.sequences.SequenceType
 
Nucleotides - Class in jebl.evolution.sequences
 
Nucleotides() - Constructor for class jebl.evolution.sequences.Nucleotides
 
NucleotideScores - Class in jebl.evolution.align.scores
 
NucleotideScores() - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(NucleotideScores) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(float, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(String, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(String, float, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(String, float, float, float, float) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideScores(Scores, double) - Constructor for class jebl.evolution.align.scores.NucleotideScores
 
NucleotideState - Class in jebl.evolution.sequences
 
NumberFormatter - Class in jebl.util
An interface for a numerical column in a log.
NumberFormatter(int) - Constructor for class jebl.util.NumberFormatter
 
numberOfUniqueCharacters - Variable in class jebl.evolution.align.ProfileCharacter
 
numClusters - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
NumericalDerivative - Class in jebl.math
approximates numerically the first and second derivatives of a function of a single variable and approximates gradient and diagonal of Hessian for multivariate functions
NumericalDerivative() - Constructor for class jebl.math.NumericalDerivative
 
numFun - Variable in class jebl.math.MultivariateMinimum
total number of function evaluations necessary
numFun - Variable in class jebl.math.UnivariateMinimum
total number of function evaluations neccessary
numFuncStops - Variable in class jebl.math.MultivariateMinimum
numFuncStops is the number of consecutive positive evaluations of the stop criterion based on function evaluation necessary to cause the abortion of the optimization (default is 4)
numOperations - Variable in class jebl.util.CompositeProgressListener
 

O

objectChanged() - Method in interface org.virion.jam.util.SimpleListener
 
OldNeedlemanWunschAffine - Class in jebl.evolution.align
 
OldNeedlemanWunschAffine(Scores, float, float) - Constructor for class jebl.evolution.align.OldNeedlemanWunschAffine
 
ONE_SECOND - Static variable in class org.virion.jam.util.LongTaskMonitor
 
openAction - Variable in class org.virion.jam.framework.Application
 
opened(Component) - Method in interface org.virion.jam.disclosure.DisclosureListener
 
openFile(File) - Method in class org.virion.jam.framework.DocumentFrame
 
opening(Component) - Method in interface org.virion.jam.disclosure.DisclosureListener
 
openURL(String) - Static method in class org.virion.jam.util.BrowserLauncher
Attempts to open the default web browser to the given URL.
optimize(MultivariateFunction, double[], double, double) - Method in class jebl.math.MultivariateMinimum
The actual optimization routine (needs to be implemented in a subclass of MultivariateMinimum).
optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class jebl.math.MultivariateMinimum
The actual optimization routine It finds a minimum close to vector x when the absolute tolerance for each parameter is specified.
optimize(MultivariateFunction, double[], double, double) - Method in class jebl.math.OrthogonalSearch
 
optimize(MultivariateFunction, double[], double, double, MinimiserMonitor) - Method in class jebl.math.OrthogonalSearch
 
optimize(UnivariateFunction, double, double, double) - Method in class jebl.math.UnivariateMinimum
The actual optimization routine (Brent's golden section method)
optimize(UnivariateFunction, double) - Method in class jebl.math.UnivariateMinimum
The actual optimization routine (Brent's golden section method)
optimize(double, UnivariateFunction, double, double, double) - Method in class jebl.math.UnivariateMinimum
The actual optimization routine (Brent's golden section method)
optimize(double, UnivariateFunction, double) - Method in class jebl.math.UnivariateMinimum
The actual optimization routine (Brent's golden section method)
OptionsPanel - Class in org.virion.jam.panels
OptionsPanel.
OptionsPanel() - Constructor for class org.virion.jam.panels.OptionsPanel
 
OptionsPanel(int, int) - Constructor for class org.virion.jam.panels.OptionsPanel
 
OrderEnumerator - Interface in jebl.math
A means for describing odering information, and Utilities for creating such Orderings
OrderEnumerator.OEFactory - Interface in jebl.math
 
OrderEnumerator.Utils - Class in jebl.math
 
OrderEnumerator.Utils() - Constructor for class jebl.math.OrderEnumerator.Utils
 
org.virion.jam.app - package org.virion.jam.app
 
org.virion.jam.components - package org.virion.jam.components
 
org.virion.jam.console - package org.virion.jam.console
 
org.virion.jam.controlpalettes - package org.virion.jam.controlpalettes
 
org.virion.jam.controlpanels - package org.virion.jam.controlpanels
 
org.virion.jam.demo - package org.virion.jam.demo
 
org.virion.jam.demo.menus - package org.virion.jam.demo.menus
 
org.virion.jam.disclosure - package org.virion.jam.disclosure
 
org.virion.jam.framework - package org.virion.jam.framework
 
org.virion.jam.html - package org.virion.jam.html
 
org.virion.jam.layouts - package org.virion.jam.layouts
 
org.virion.jam.mac - package org.virion.jam.mac
 
org.virion.jam.maconly - package org.virion.jam.maconly
 
org.virion.jam.panels - package org.virion.jam.panels
 
org.virion.jam.preferences - package org.virion.jam.preferences
 
org.virion.jam.table - package org.virion.jam.table
 
org.virion.jam.toolbar - package org.virion.jam.toolbar
 
org.virion.jam.util - package org.virion.jam.util
 
OrthogonalHints - Interface in jebl.math
Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
OrthogonalHints.Utils - Class in jebl.math
 
OrthogonalHints.Utils() - Constructor for class jebl.math.OrthogonalHints.Utils
 
OrthogonalLineFunction - Class in jebl.math
converts a multivariate function into a univariate function by keeping all but one argument constant
OrthogonalLineFunction(MultivariateFunction) - Constructor for class jebl.math.OrthogonalLineFunction
construct univariate function from multivariate function
OrthogonalLineFunction(MultivariateFunction, int, double[]) - Constructor for class jebl.math.OrthogonalLineFunction
construct univariate function from multivariate function
OrthogonalSearch - Class in jebl.math
minimization of a real-valued function of several variables without using derivatives, using the simple strategy of optimizing variables one by one.
OrthogonalSearch() - Constructor for class jebl.math.OrthogonalSearch
Initialization
OrthogonalSearch(boolean) - Constructor for class jebl.math.OrthogonalSearch
Initialization
OrthogonalSearch(OrderEnumerator.OEFactory) - Constructor for class jebl.math.OrthogonalSearch
Initialization
OrthogonalSearch.RoundOptimiser - Interface in jebl.math
 
OSXAdapter - Class in org.virion.jam.maconly
 
Output - Class in jebl.evolution.align
 
Output() - Constructor for class jebl.evolution.align.Output
 
OverlapAlign - Class in jebl.evolution.align
 
OverlapAlign(Scores, float) - Constructor for class jebl.evolution.align.OverlapAlign
 

P

P_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
pageSetupAction - Variable in class org.virion.jam.framework.Application
 
paint(Graphics2D, Node, Painter.Justification, Rectangle2D) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
paint(Graphics2D, T, Painter.Justification, Rectangle2D) - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
paint(Graphics2D, TreePane, Painter.Justification, Rectangle2D) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
paint(Graphics) - Method in class jebl.gui.trees.treeviewer.TreePane
 
paint(Graphics) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
paint(Graphics2D, Node, Painter.Justification, Rectangle2D) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
paint(Graphics2D, Node, Painter.Justification, Shape) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
The bounds define the shape of the nodeBar so just draw it
paint(Graphics2D, Node, Painter.Justification, Rectangle2D) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
The bounds define the shape of the nodeBar so just draw it
paint(Graphics2D, Node, Painter.Justification, Rectangle2D) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
The bounds define the shape of the bar so just draw it
paint(Graphics2D, T, Painter.Justification, Rectangle2D) - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
Called to actually paint into the current graphics context.
paint(Graphics2D, TreePane, Painter.Justification, Rectangle2D) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
paint(Graphics) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
paint(Graphics) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
paint(Graphics) - Method in class org.virion.jam.components.JVerticalLabel
 
paintComponent(Graphics) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
 
paintComponent(Graphics) - Method in class org.virion.jam.panels.StatusBar
 
Painter<T> - Interface in jebl.gui.trees.treeviewer.painters
A painter draws a particular decoration onto the tree within a rectangle.
Painter<T> - Interface in jebl.gui.trees.treeviewer_dev.painters
A painter draws a particular decoration onto the tree within a rectangle.
Painter.Justification - Enum in jebl.gui.trees.treeviewer.painters
 
Painter.Justification - Enum in jebl.gui.trees.treeviewer_dev.painters
 
Painter.Orientation - Enum in jebl.gui.trees.treeviewer.painters
 
Painter.Orientation - Enum in jebl.gui.trees.treeviewer_dev.painters
 
painterChanged() - Method in interface jebl.gui.trees.treeviewer.painters.PainterListener
 
painterChanged() - Method in class jebl.gui.trees.treeviewer.TreePane
 
painterChanged() - Method in interface jebl.gui.trees.treeviewer_dev.painters.PainterListener
 
painterChanged() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
PainterListener - Interface in jebl.gui.trees.treeviewer.painters
 
PainterListener - Interface in jebl.gui.trees.treeviewer_dev.painters
 
painterSettingsChanged() - Method in interface jebl.gui.trees.treeviewer_dev.painters.PainterListener
 
painterSettingsChanged() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
paintMap - Variable in class jebl.gui.trees.treeviewer.decorators.AttributeBranchDecorator
 
paintTree(Graphics2D, Dimension, RootedTree) - Method in interface jebl.gui.trees.treecomponent.RootedTreePainter
Do the actual painting.
paintTree(Graphics2D, Dimension, RootedTree) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Do the actual painting.
PairwiseAligner - Interface in jebl.evolution.align
 
PairwiseAligner.Result - Class in jebl.evolution.align
 
Pam100 - Class in jebl.evolution.align.scores
 
Pam100() - Constructor for class jebl.evolution.align.scores.Pam100
 
Pam110 - Class in jebl.evolution.align.scores
 
Pam110() - Constructor for class jebl.evolution.align.scores.Pam110
 
Pam120 - Class in jebl.evolution.align.scores
 
Pam120() - Constructor for class jebl.evolution.align.scores.Pam120
 
Pam130 - Class in jebl.evolution.align.scores
 
Pam130() - Constructor for class jebl.evolution.align.scores.Pam130
 
Pam140 - Class in jebl.evolution.align.scores
 
Pam140() - Constructor for class jebl.evolution.align.scores.Pam140
 
Pam150 - Class in jebl.evolution.align.scores
 
Pam150() - Constructor for class jebl.evolution.align.scores.Pam150
 
Pam160 - Class in jebl.evolution.align.scores
 
Pam160() - Constructor for class jebl.evolution.align.scores.Pam160
 
Pam170 - Class in jebl.evolution.align.scores
 
Pam170() - Constructor for class jebl.evolution.align.scores.Pam170
 
Pam180 - Class in jebl.evolution.align.scores
 
Pam180() - Constructor for class jebl.evolution.align.scores.Pam180
 
Pam190 - Class in jebl.evolution.align.scores
 
Pam190() - Constructor for class jebl.evolution.align.scores.Pam190
 
Pam200 - Class in jebl.evolution.align.scores
 
Pam200() - Constructor for class jebl.evolution.align.scores.Pam200
 
Pam210 - Class in jebl.evolution.align.scores
 
Pam210() - Constructor for class jebl.evolution.align.scores.Pam210
 
Pam220 - Class in jebl.evolution.align.scores
 
Pam220() - Constructor for class jebl.evolution.align.scores.Pam220
 
Pam230 - Class in jebl.evolution.align.scores
 
Pam230() - Constructor for class jebl.evolution.align.scores.Pam230
 
Pam240 - Class in jebl.evolution.align.scores
 
Pam240() - Constructor for class jebl.evolution.align.scores.Pam240
 
Pam250 - Class in jebl.evolution.align.scores
 
Pam250() - Constructor for class jebl.evolution.align.scores.Pam250
 
parseArguments(String[]) - Method in class org.virion.jam.app.Arguments
Parse a list of arguments ready for accessing
parseCharactersBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
Parses a 'CHARACTERS' block.
parseDataBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
Parses a 'DATA' block.
parseDistancesBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
 
parseTaxaBlock() - Method in class jebl.evolution.io.NexusImporter
Parses a 'TAXA' block.
parseTreesBlock(List<Taxon>) - Method in class jebl.evolution.io.NexusImporter
Parses a 'TREES' block.
ParsimonyCriterion - Interface in jebl.evolution.parsimony
 
Pattern - Interface in jebl.evolution.alignments
An interface representing a list of states for a list of taxa.
Patterns - Interface in jebl.evolution.alignments
An interface representing a set of site patterns.
PERIOD - Static variable in class org.virion.jam.components.RealNumberField
 
PHYLIPExporter - Class in jebl.evolution.io
Export alignment to Phylip format.
PHYLIPExporter(Writer) - Constructor for class jebl.evolution.io.PHYLIPExporter
 
PhylipSequentialImporter - Class in jebl.evolution.io
Class for importing PHYLIP sequential file format
PhylipSequentialImporter(Reader, SequenceType, int) - Constructor for class jebl.evolution.io.PhylipSequentialImporter
Constructor
PinnedButton - Class in org.virion.jam.controlpalettes
 
PinnedButton() - Constructor for class org.virion.jam.controlpalettes.PinnedButton
 
pleaseStop - Variable in class org.virion.jam.util.SimpleLongTask
 
PolarTreeLayout - Class in jebl.gui.trees.treeviewer.treelayouts
 
PolarTreeLayout() - Constructor for class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
PolarTreeLayout - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
PolarTreeLayout() - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
PolarTreeLayout.TaxonLabelPosition - Enum in jebl.gui.trees.treeviewer.treelayouts
 
PolarTreeLayout.TipLabelPosition - Enum in jebl.gui.trees.treeviewer_dev.treelayouts
 
PolarTreeLayoutController - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
PolarTreeLayoutController(PolarTreeLayout) - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.demo.menus.DemoMenuFactory
 
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.framework.DefaultEditMenuFactory
 
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.framework.DefaultFileMenuFactory
 
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.framework.DefaultHelpMenuFactory
 
populateMenu(JMenu, AbstractFrame) - Method in interface org.virion.jam.framework.MenuFactory
This method should populate the menu with menu items.
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.mac.MacFileMenuFactory
 
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.mac.MacHelpMenuFactory
 
populateMenu(JMenu, AbstractFrame) - Method in class org.virion.jam.mac.MacWindowMenuFactory
 
populateMenuBar(JMenuBar, AbstractFrame) - Method in class org.virion.jam.framework.DefaultMenuBarFactory
 
populateMenuBar(JMenuBar, AbstractFrame) - Method in interface org.virion.jam.framework.MenuBarFactory
 
possiblyEqual(State) - Method in class jebl.evolution.sequences.State
 
preferencesAction - Variable in class org.virion.jam.framework.Application
 
PreferencesDialog - Class in org.virion.jam.preferences
DemographicDialog.java Title: Tracer Description: An application for analysing MCMC trace files.
PreferencesDialog(JFrame) - Constructor for class org.virion.jam.preferences.PreferencesDialog
 
PreferencesSection - Interface in org.virion.jam.preferences
 
preferredLayoutSize(Container) - Method in class org.virion.jam.layouts.CompassLayout
Returns the preferred dimensions for this layout given the components in the specified target container.
prepareAlignment(String, String) - Method in class jebl.evolution.align.Align
Initialises the matrices for the alignment.
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschAffine
 
print(String) - Method in class jebl.evolution.align.Output
 
print() - Method in class jebl.evolution.align.ProfileCharacter
 
print(Graphics, PageFormat, int) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
 
print(Graphics, PageFormat, int) - Method in class jebl.gui.trees.treeviewer.TreePane
 
print(Graphics, PageFormat, int) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
print(Graphics, PageFormat, int) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
print(Graphics, PageFormat, int) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
print() - Method in class org.virion.jam.util.PrintUtilities
 
print(Graphics, PageFormat, int) - Method in class org.virion.jam.util.PrintUtilities
 
printComponent(Component) - Static method in class org.virion.jam.util.PrintUtilities
 
printComponentScaled(Component) - Static method in class org.virion.jam.util.PrintUtilities
 
printf(Output) - Method in class jebl.evolution.align.Align
Print the matrix (matrices) used to compute the alignment
printf(Output) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
Print matrix used to calculate this alignment.
println(String) - Method in class jebl.evolution.align.Output
 
println() - Method in class jebl.evolution.align.Output
 
printScaled(Graphics, PageFormat, int) - Method in class org.virion.jam.util.PrintUtilities
 
printScaled(Component, Graphics, PageFormat, int) - Static method in class org.virion.jam.util.PrintUtilities
 
printUsage(String, String) - Method in class org.virion.jam.app.Arguments
 
PrintUtilities - Class in org.virion.jam.util
A simple utility class that lets you very simply print an arbitrary component.
PrintUtilities(Component) - Constructor for class org.virion.jam.util.PrintUtilities
 
PrintUtilities(Component, boolean) - Constructor for class org.virion.jam.util.PrintUtilities
 
ProfileCharacter - Class in jebl.evolution.align
 
ProfileCharacter(int) - Constructor for class jebl.evolution.align.ProfileCharacter
 
ProgressListener - Class in jebl.util
 
ProgressListener() - Constructor for class jebl.util.ProgressListener
 
putSetting(String, Object) - Method in interface org.virion.jam.controlpanels.ControlsSettings
 

Q

Q_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 

R

R_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
R_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
RadialTreeLayout - Class in jebl.gui.trees.treeviewer.treelayouts
 
RadialTreeLayout() - Constructor for class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
RadialTreeLayout - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
RadialTreeLayout() - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
RadialTreeLayoutController - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
RadialTreeLayoutController(RadialTreeLayout) - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
RADIUS_ATTRIBUTE - Static variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
Random - Class in jebl.math
Random number generation.
randomChoice(double[]) - Static method in class jebl.math.Random
 
range_check - Variable in class org.virion.jam.components.RealNumberField
 
range_check - Variable in class org.virion.jam.components.WholeNumberField
 
range_checked - Variable in class org.virion.jam.components.RealNumberField
 
range_checked - Variable in class org.virion.jam.components.WholeNumberField
 
RateMatrix - Interface in jebl.evolution.substmodel
abstract base class for all rate matrices
read() - Method in class jebl.evolution.io.ImportHelper
All read attempts pass through this function.
readCharacter() - Method in class jebl.evolution.io.ImportHelper
 
readDouble() - Method in class jebl.evolution.io.ImportHelper
Attempts to read and parse a double delimited by whitespace.
readDouble(String) - Method in class jebl.evolution.io.ImportHelper
Attempts to read and parse a double delimited by whitespace or by any character in delimiters.
readFromFile(File) - Method in class org.virion.jam.console.ConsoleFrame
 
readFromFile(File) - Method in class org.virion.jam.demo.DemoFrame
 
readFromFile(File) - Method in class org.virion.jam.framework.DocumentFrame
 
readInteger() - Method in class jebl.evolution.io.ImportHelper
Attempts to read and parse an integer delimited by whitespace.
readInteger(String) - Method in class jebl.evolution.io.ImportHelper
Attempts to read and parse an integer delimited by whitespace or by any character in delimiters.
readLine() - Method in class jebl.evolution.io.ImportHelper
Reads a line, skipping over any comments.
readSequence(StringBuilder, SequenceType, String, int, String, String, String, String) - Method in class jebl.evolution.io.ImportHelper
 
readSequence(StringBuilder, SequenceType, String, int, String, String, String, String, ProgressListener) - Method in class jebl.evolution.io.ImportHelper
Reads sequence, skipping over any comments and filtering using sequenceType.
readSequence(String) - Static method in class jebl.evolution.sequences.SequenceTester
 
readSequenceLine(StringBuffer, SequenceType, String, String, String, String, String) - Method in class jebl.evolution.io.ImportHelper
Reads a line of sequence, skipping over any comments and filtering using sequenceType.
readToken() - Method in class jebl.evolution.io.ImportHelper
Reads a token stopping when any whitespace or a comment is found.
readToken(String) - Method in class jebl.evolution.io.ImportHelper
Reads a token stopping when any whitespace, a comment or when any character in delimiters is found.
RealNumberCellEditor - Class in org.virion.jam.table
 
RealNumberCellEditor(double, double) - Constructor for class org.virion.jam.table.RealNumberCellEditor
 
RealNumberField - Class in org.virion.jam.components
 
RealNumberField() - Constructor for class org.virion.jam.components.RealNumberField
 
RealNumberField(double, double) - Constructor for class org.virion.jam.components.RealNumberField
 
rebuild() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
rebuildRateMatrix(double[][], double[]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
rebuildRateMatrix(double[][], double[]) - Method in class jebl.evolution.substmodel.WAG
 
RecentFileList - Class in org.virion.jam.framework
A class for maintaining a "Recent File List".
RecentFileList() - Constructor for class org.virion.jam.framework.RecentFileList
Create a RecentFileList
RecentFileList(int) - Constructor for class org.virion.jam.framework.RecentFileList
Create a RecentFileList with a given maximum length
RecentFileList(String) - Constructor for class org.virion.jam.framework.RecentFileList
Create a recent file list.
RecentFileList(String, int) - Constructor for class org.virion.jam.framework.RecentFileList
Create a recent file list with a given type and size
reconstruct() - Method in class jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
initiates the analysis
RectilinearTreeLayout - Class in jebl.gui.trees.treeviewer.treelayouts
 
RectilinearTreeLayout() - Constructor for class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
RectilinearTreeLayout - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
RectilinearTreeLayout() - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
RectilinearTreeLayoutController - Class in jebl.gui.trees.treeviewer_dev.treelayouts
 
RectilinearTreeLayoutController(RectilinearTreeLayout) - Constructor for class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
recurseAlignment(String, int) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
 
refineNode(Node, int[]) - Method in class jebl.evolution.trees.MutableRootedTree
 
registerMacOSXApplication(Application) - Static method in class org.virion.jam.maconly.OSXAdapter
 
registerMenuFactory(MenuFactory) - Method in class org.virion.jam.framework.DefaultMenuBarFactory
 
registerMenuFactory(MenuFactory) - Method in interface org.virion.jam.framework.MenuBarFactory
 
registerPermanentMenuFactory(MenuFactory) - Method in class org.virion.jam.framework.DefaultMenuBarFactory
 
registerPermanentMenuFactory(MenuFactory) - Method in interface org.virion.jam.framework.MenuBarFactory
 
remove(File) - Method in class org.virion.jam.framework.RecentFileList
Remove a file from the list
remove(String) - Method in class org.virion.jam.framework.RecentFileList
Remove a file from the list
remove(SimpleListener) - Method in class org.virion.jam.util.SimpleListenerManager
 
removeActionListener(ActionListener) - Method in class org.virion.jam.framework.RecentFileList
 
removeAllDataSourceListeners() - Method in class org.virion.jam.panels.SearchPanel
 
removeAttribute(String) - Method in class jebl.evolution.sequences.BasicSequence
 
removeAttribute(String) - Method in class jebl.evolution.sequences.FilteredSequence
 
removeAttribute(String) - Method in class jebl.evolution.taxa.Taxon
 
removeAttribute(String) - Method in class jebl.evolution.trees.FilteredRootedTree
 
removeAttribute(String) - Method in class jebl.evolution.trees.MutableRootedTree
 
removeAttribute(String) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
removeAttribute(String) - Method in class jebl.evolution.trees.SimpleRootedTree
 
removeAttribute(String) - Method in class jebl.evolution.trees.SimpleTree
 
removeAttribute(String) - Method in interface jebl.util.Attributable
 
removeAttribute(String) - Method in class jebl.util.AttributableHelper
 
removeChangeListener(ChangeListener) - Method in class org.virion.jam.components.RealNumberField
 
removeChangeListener(ChangeListener) - Method in class org.virion.jam.components.WholeNumberField
 
removeCharacter(char, int) - Method in class jebl.evolution.align.ProfileCharacter
 
removeController(Controller) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
removeControllerListener(ControllerListener) - Method in class org.virion.jam.controlpalettes.AbstractController
Remove a listener
removeControllerListener(ControllerListener) - Method in interface org.virion.jam.controlpalettes.Controller
Remove a listener
removeControlPaletteListener(ControlPaletteListener) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
removeControlPaletteListener(ControlPaletteListener) - Method in interface org.virion.jam.controlpalettes.ControlPalette
Remove a listener fromm this palette
removeControlPanelListener(ControlPaletteListener) - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
removeControlPanelListener(ControlPaletteListener) - Method in interface org.virion.jam.controlpanels.ControlPalette
 
removeDataSourceListener(SearchPanelListener) - Method in class org.virion.jam.panels.SearchPanel
 
removeDisclosureListener(DisclosureListener) - Method in class org.virion.jam.disclosure.DisclosureButton
 
removeDisclosureListener(DisclosureListener) - Method in class org.virion.jam.disclosure.DisclosurePanel
 
removeInternalNode(Node) - Method in class jebl.evolution.trees.MutableRootedTree
Remove internal node.
removeLayoutComponent(Component) - Method in class org.virion.jam.layouts.CompassLayout
Removes the specified component from the layout.
removeOverrideProvider(StatusProvider) - Method in class org.virion.jam.panels.StatusProvider.Helper
 
removeOverrideProvider(StatusProvider) - Method in interface org.virion.jam.panels.StatusProvider
 
removePainterListener(PainterListener) - Method in class jebl.gui.trees.treeviewer.painters.AbstractPainter
 
removePainterListener(PainterListener) - Method in interface jebl.gui.trees.treeviewer.painters.Painter
 
removePainterListener(PainterListener) - Method in class jebl.gui.trees.treeviewer_dev.painters.AbstractPainter
 
removePainterListener(PainterListener) - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
 
removeProfileCharacter(ProfileCharacter) - Method in class jebl.evolution.align.ProfileCharacter
 
removeProgressListener(ProgressListener) - Method in interface jebl.evolution.aligners.Aligner
 
removeProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
 
removeProgressListener(ProgressListener) - Method in class jebl.evolution.trees.ConsensusTreeBuilder
 
removeProgressListener(ProgressListener) - Method in interface jebl.evolution.trees.TreeBuilder
 
removeStatusListener(StatusListener) - Method in class org.virion.jam.panels.StatusProvider.Helper
 
removeStatusListener(StatusListener) - Method in interface org.virion.jam.panels.StatusProvider
Remove the given StatusListener from the provider's list.
removeTreeLayoutListener(TreeLayoutListener) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
removeTreeLayoutListener(TreeLayoutListener) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Remove a listener from this layout
removeTreeLayoutListener(TreeLayoutListener) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
removeTreeLayoutListener(TreeLayoutListener) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Remove a listener from this layout
removeTreePaneListener(TreePaneListener) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
removeTreeSelectionListener(TreeSelectionListener) - Method in class jebl.gui.trees.treeviewer.TreePane
 
removeTreeSelectionListener(TreeSelectionListener) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
removeTreeViewerListener(TreeViewerListener) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
removeUpdate(DocumentEvent) - Method in class org.virion.jam.components.RealNumberField
 
removeUpdate(DocumentEvent) - Method in class org.virion.jam.components.WholeNumberField
 
requestClose() - Method in class org.virion.jam.framework.AboutBox
 
requestClose() - Method in class org.virion.jam.framework.AbstractFrame
 
requestClose() - Method in class org.virion.jam.framework.AuxilaryFrame
 
requestClose() - Method in class org.virion.jam.framework.DocumentFrame
 
requestFocusInWindow() - Method in class org.virion.jam.panels.SearchPanel
 
reRootWithOutgroup(Node, Set<String>) - Method in class jebl.evolution.trees.MutableRootedTree
Re-root tree using an outgroup.
ResampledAlignment - Class in jebl.evolution.alignments
Date: 17/01/2006 Time: 08:08:44
ResampledAlignment() - Constructor for class jebl.evolution.alignments.ResampledAlignment
 
reset() - Method in interface jebl.math.OrderEnumerator
Reset back to starting state, may have a differnet number of values, and a different ordering after a reset!
resetEvents() - Method in class jebl.evolution.coalescent.Intervals
 
resize(Icon, int, int) - Static method in class org.virion.jam.util.IconUtils
Resizes an icon.
retrievePreferences() - Method in interface org.virion.jam.preferences.PreferencesSection
 
reverse(State[]) - Static method in class jebl.evolution.sequences.Utils
 
reverseComplement(String) - Static method in class jebl.evolution.sequences.Utils
 
reverseComplement(NucleotideState[]) - Static method in class jebl.evolution.sequences.Utils
 
reverseComplementWithGaps(String) - Static method in class jebl.evolution.sequences.Utils
 
reverseMatrix(double[][]) - Static method in class jebl.math.MatrixCalc
reverse a matrix
reverseVector(double[]) - Static method in class jebl.math.MatrixCalc
reverse a vector
RIGHT - Static variable in interface org.virion.jam.framework.MenuFactory
 
RootedFromUnrooted - Class in jebl.evolution.trees
Root an unrooted tree.
RootedFromUnrooted(Tree, Node, boolean) - Constructor for class jebl.evolution.trees.RootedFromUnrooted
Root tree source at root.
RootedFromUnrooted(Tree, Node, Node, double) - Constructor for class jebl.evolution.trees.RootedFromUnrooted
Root source by creating a new internal node whose children are (the adjacent) left and right.
RootedTree - Interface in jebl.evolution.trees
A tree with a root (node with maximum height).
RootedTreeComponent - Class in jebl.gui.trees.treecomponent
 
RootedTreeComponent(RootedTreePainter) - Constructor for class jebl.gui.trees.treecomponent.RootedTreeComponent
 
RootedTreeComponent(RootedTreePainter, RootedTree) - Constructor for class jebl.gui.trees.treecomponent.RootedTreeComponent
 
RootedTreeComponent.Adaptor - Class in jebl.gui.trees.treecomponent
 
RootedTreeComponent.Adaptor() - Constructor for class jebl.gui.trees.treecomponent.RootedTreeComponent.Adaptor
 
RootedTreeComponent.Listener - Interface in jebl.gui.trees.treecomponent
 
RootedTreeComponent.MListener - Class in jebl.gui.trees.treecomponent
 
RootedTreeComponent.MListener() - Constructor for class jebl.gui.trees.treecomponent.RootedTreeComponent.MListener
 
RootedTreePainter - Interface in jebl.gui.trees.treecomponent
 
RootedTreeUtils - Class in jebl.evolution.trees
Static utility functions for rooted trees.
RootedTreeUtils() - Constructor for class jebl.evolution.trees.RootedTreeUtils
 
rootNode - Variable in class jebl.evolution.trees.MutableRootedTree
 
rootNode - Variable in class jebl.evolution.trees.SimpleRootedTree
 
rootTheTree(Tree) - Static method in class jebl.evolution.trees.Utils
Return a rooted tree from any tree.
rootTreeAtCenter(Tree) - Static method in class jebl.evolution.trees.Utils
 
RuleModel - Interface in org.virion.jam.panels
RuleModel.
RulesPanel - Class in org.virion.jam.panels
OptionsPanel.
RulesPanel(RuleModel) - Constructor for class org.virion.jam.panels.RulesPanel
 
RulesPanel.Rule - Interface in org.virion.jam.panels
 

S

S_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
S_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
safeNodeHeight(RootedTree, Node) - Static method in class jebl.evolution.trees.Utils
 
same(double, double) - Static method in class jebl.math.MachineAccuracy
 
save(Properties) - Method in class org.virion.jam.framework.RecentFileList
Save the recent file list in a Properties set
scale(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
ScaleBarPainter - Class in jebl.gui.trees.treeviewer.painters
 
ScaleBarPainter() - Constructor for class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
ScaleBarPainter(double) - Constructor for class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
ScaleBarPainter(int) - Constructor for class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
ScaleBarPainter(double, int) - Constructor for class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
ScaleBarPainter - Class in jebl.gui.trees.treeviewer_dev.painters
 
ScaleBarPainter() - Constructor for class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
ScaleBarPainter(double) - Constructor for class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
ScaleBarPainterController - Class in jebl.gui.trees.treeviewer_dev.painters
 
ScaleBarPainterController(ScaleBarPainter) - Constructor for class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
score - Variable in class jebl.evolution.align.PairwiseAligner.Result
 
score(ProfileCharacter, ProfileCharacter, Scores) - Static method in class jebl.evolution.align.ProfileCharacter
 
score - Variable in class jebl.evolution.align.scores.Scores
 
ScoreMatrix - Interface in jebl.evolution.align.scores
 
Scores - Class in jebl.evolution.align.scores
Base class for all score matrices in the package.
Scores() - Constructor for class jebl.evolution.align.scores.Scores
 
scoreSelf(ProfileCharacter, Scores) - Static method in class jebl.evolution.align.ProfileCharacter
 
ScoresFactory - Class in jebl.evolution.align.scores
 
ScoresFactory() - Constructor for class jebl.evolution.align.scores.ScoresFactory
 
scrollPointToVisible(Point) - Method in class jebl.gui.trees.treeviewer.TreePane
 
scrollPointToVisible(Point) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
SearchPanel - Class in org.virion.jam.panels
 
SearchPanel(String, boolean) - Constructor for class org.virion.jam.panels.SearchPanel
 
SearchPanel(String, JPopupMenu, boolean) - Constructor for class org.virion.jam.panels.SearchPanel
 
SearchPanelListener - Interface in org.virion.jam.panels
An interface for listeners to the SearchPanel class.
searchStarted(String) - Method in interface org.virion.jam.panels.SearchPanelListener
Called when the user requests a search by pressing return having typed a search string into the text field.
searchStopped() - Method in interface org.virion.jam.panels.SearchPanelListener
Called when the user presses the cancel search button or presses escape while the search is in focus.
SECOND - Static variable in class org.virion.jam.demo.menus.DemoMenuFactory
 
secondDerivative(UnivariateFunction, double) - Static method in class jebl.math.NumericalDerivative
determine second derivative
selectAll() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
selectAllNodes() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
selectAllTaxa() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
selectArgument(int) - Method in class jebl.math.OrthogonalLineFunction
use only the specified argument in the constructed univariate function and keep all others constant
selectCladesFromSelectedNodes() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
selectionChanged() - Method in interface jebl.gui.trees.treeviewer.TreeSelectionListener
 
selectionChanged() - Method in interface jebl.gui.trees.treeviewer_dev.TreeSelectionListener
 
selectNodes(String, TreeViewer.SearchType, String, boolean) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
selectNodes(String, TreeViewer.SearchType, String, boolean) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
selectNodesFromSelectedTips() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
selectTaxa(TreeViewer.SearchType, String, boolean) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
selectTaxa(TreeViewer.SearchType, String, boolean) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
selectTipsFromSelectedNodes() - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
Sequence - Interface in jebl.evolution.sequences
A biomolecular sequence.
SequenceAlignmentsDistanceMatrix - Class in jebl.evolution.align
 
SequenceAlignmentsDistanceMatrix(List<Sequence>, PairwiseAligner, ProgressListener) - Constructor for class jebl.evolution.align.SequenceAlignmentsDistanceMatrix
 
SequenceExporter - Interface in jebl.evolution.io
 
SequenceImporter - Interface in jebl.evolution.io
Interface for importers that do sequences
Sequences - Interface in jebl.evolution.sequences
A set of sequence objects.
SequenceShuffler - Class in jebl.evolution.align
Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences.
SequenceShuffler() - Constructor for class jebl.evolution.align.SequenceShuffler
 
SequenceStateException - Exception in jebl.evolution.sequences
 
SequenceStateException(String) - Constructor for exception jebl.evolution.sequences.SequenceStateException
 
SequenceTester - Class in jebl.evolution.sequences
 
SequenceTester() - Constructor for class jebl.evolution.sequences.SequenceTester
 
SequenceType - Interface in jebl.evolution.sequences
Interface for sequences data types.
SequenceType.Utils - Class in jebl.evolution.sequences
 
SequenceType.Utils() - Constructor for class jebl.evolution.sequences.SequenceType.Utils
 
set(int) - Method in class jebl.util.FixedBitSet
 
setAction(Action) - Method in class org.virion.jam.toolbar.GenericToolbarItem
 
setAction(Action) - Method in class org.virion.jam.toolbar.ToolbarButton
 
setActionAction(Action) - Method in class org.virion.jam.panels.ActionPanel
 
setActionToolTipText(String) - Method in class org.virion.jam.panels.ActionPanel
 
setAddAction(Action) - Method in class org.virion.jam.panels.ActionPanel
 
setAddToolTipText(String) - Method in class org.virion.jam.panels.ActionPanel
 
setAlignTaxonLabels(boolean) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
setAlignTipLabels(boolean) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
setAllArguments(double[]) - Method in class jebl.math.OrthogonalLineFunction
set (change) values of all arguments (start values)
setAndStoreTreeLayoutType(TreeViewer.TreeLayoutType) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setAngularRange(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
setAngularRange(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstantPopulation
 
setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstExponential
 
setArgument(int, double) - Method in class jebl.evolution.coalescent.ConstLogistic
 
setArgument(int, double) - Method in interface jebl.evolution.coalescent.DemographicFunction
Sets the value of the nth argument of this function.
setArgument(int, double) - Method in class jebl.evolution.coalescent.Expansion
 
setArgument(int, double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
 
setArgument(double) - Method in class jebl.math.OrthogonalLineFunction
set (change) value of a single argument (the one currently active)
setAttribute(String, Object) - Method in class jebl.evolution.alignments.ConsensusSequence
 
setAttribute(String, Object) - Method in class jebl.evolution.sequences.BasicSequence
 
setAttribute(String, Object) - Method in class jebl.evolution.sequences.FilteredSequence
 
setAttribute(String, Object) - Method in class jebl.evolution.taxa.Taxon
 
setAttribute(String, Object) - Method in class jebl.evolution.trees.FilteredRootedTree
 
setAttribute(String, Object) - Method in class jebl.evolution.trees.MutableRootedTree
 
setAttribute(String, Object) - Method in class jebl.evolution.trees.RootedFromUnrooted
 
setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleRootedTree
 
setAttribute(String, Object) - Method in class jebl.evolution.trees.SimpleTree
 
setAttribute(String) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setAttribute(String, Object) - Method in interface jebl.util.Attributable
Sets an named attribute for this object.
setAttribute(String, Object) - Method in class jebl.util.AttributableHelper
 
setAutomaticScale(boolean) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setBackground(Paint) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setBackground(Paint) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setBackground(Paint) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setBackground(Paint) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
setBorder(Paint, Stroke) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setBorder(Paint, Stroke) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setBorder(Paint, Stroke) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setBorder(Paint, Stroke) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
setBorderDecorator(Decorator) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
setBounds(int, int, int, int) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBounds(Rectangle) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBounds(int, int, int, int) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBounds(Rectangle) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBranchColouringAttribute(String) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
setBranchColouringAttribute(String) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
setBranchColouringDecorator(String, Decorator) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBranchCurveProportion(double, double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
setBranchDecorator(BranchDecorator) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBranchDecorator(BranchDecorator) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setBranchDecorator(Decorator) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBranchLabelPainter(Painter<Node>) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBranchLabelPainter(LabelPainter<Node>) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBranchLineWeight(float) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBranchOrdering(boolean, SortedRootedTree.BranchOrdering) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBranchOrdering(SortedRootedTree.BranchOrdering) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBranchStroke(BasicStroke) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setBranchTransform(boolean, TransformedRootedTree.Transform) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setBranchTransform(TransformedRootedTree.Transform) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setCalloutStroke(BasicStroke) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setCataclysmTime(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
 
setChar(ContinuousCharacter) - Method in class jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
 
setCollapseAttributeName(String) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
setCollapseAttributeName(String) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
 
setColouringAttributeName(String) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
setComboBox(JComboBox) - Method in class org.virion.jam.panels.SearchPanel
 
setCommentDelimiters(char) - Method in class jebl.evolution.io.ImportHelper
 
setCommentDelimiters(char, char) - Method in class jebl.evolution.io.ImportHelper
 
setCommentDelimiters(char, char, char) - Method in class jebl.evolution.io.ImportHelper
 
setCommentDelimiters(char, char, char, char, char) - Method in class jebl.evolution.io.ImportHelper
 
setCommentWriter(Writer) - Method in class jebl.evolution.io.ImportHelper
 
setComplete() - Method in class jebl.util.CompositeProgressListener
 
setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.MutableRootedTree
 
setConceptuallyUnrooted(boolean) - Method in class jebl.evolution.trees.SimpleRootedTree
 
setContentsPanel(JPanel) - Method in class org.virion.jam.framework.AuxilaryFrame
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setControlPalette(ControlPalette) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setControlPalette(ControlPalette) - Method in interface org.virion.jam.controlpanels.ControlsProvider
Give the controls provider with a handle for the controlPalette object.
setControlPanelVisible(boolean) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setCurvature(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
setDebug(boolean) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
 
setDecimalPlaces(int) - Method in class jebl.util.NumberFormatter
Set the number of decimal places to display when formatted.
setDeclineRate(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
sets the decline rate.
setDefaultTreeLayoutType(TreeViewer.TreeLayoutType) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setDesc(String) - Method in interface jebl.evolution.characters.Character
set the description of the character
setDesc(String) - Method in class jebl.evolution.characters.ContinuousCharacter
 
setDesc(String) - Method in class jebl.evolution.characters.DiscreteCharacter
 
setDirty() - Method in class org.virion.jam.framework.AbstractFrame
 
setDisplayAttribute(String) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
setDisplayAttribute(String) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setDisplayAttribute(String) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
setDisplayAttribute(String, String) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
setDisplayAttribute(String) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setDisplayValues(String, double) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
setDistance(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistance(double) - Method in class jebl.evolution.substmodel.MatrixExponential
compute transition probabilities for a expected distance using the prespecified rate matrix
setDistance(double) - Method in interface jebl.evolution.substmodel.RateMatrix
Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
Sets the distance (such as time/branch length) used when calculating the probabilities.
setDistanceTranspose(double) - Method in class jebl.evolution.substmodel.MatrixExponential
compute transition probabilities for a expected distance using the prespecified rate matrix.
setDocumentFrame(DocumentFrame) - Method in class org.virion.jam.framework.SingleDocApplication
 
setDocumentFrameFactory(DocumentFrameFactory) - Method in class org.virion.jam.framework.MultiDocApplication
 
setDoublingTime(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
An alternative parameterization of this model.
setDragMode(TreePaneSelector.DragMode) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
setDragMode(TreePaneSelector.DragMode) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setDragMode(TreePaneSelector.DragMode) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
setDragMode(TreePaneSelector.DragMode) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
setDragRectangle(Rectangle2D) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setDragRectangle(Rectangle2D) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setEdgeLength(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
Set edge distance between two nodes.
setEnabled(boolean) - Method in class org.virion.jam.panels.SearchPanel
 
setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
 
setExportAction(Action) - Method in class org.virion.jam.framework.AbstractFrame
 
setFindIcon(Icon) - Method in class org.virion.jam.panels.SearchPanel
 
setFont(Font) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setFontAttributeName(String) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
setFontSize(int) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
 
setFontSize(float) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setFontSize(float) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setForeground(Paint) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setForeground(Paint) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setForeground(Paint) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setForeground(Paint) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
setFrameTitle() - Method in class org.virion.jam.framework.DocumentFrame
 
setFrequencies(double[]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
setGapOpen(float) - Method in class jebl.evolution.align.Align
 
setGrowthRate(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
sets growth rate.
setHeight(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
 
setHeight(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
 
setHgap(int) - Method in class org.virion.jam.layouts.CompassLayout
Sets the horizontal gap between components.
setHilightLabelStyle(Font, Paint) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Set hilight label style.
setHilightLabelStyle(Font, Paint) - Method in interface jebl.gui.trees.treecomponent.RootedTreePainter
Set hilight label style.
setHilightLabelStyle(Font, Paint) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Set hilight label style.
setHilightStyle(Stroke, Paint) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Set hilight style
setHilightStyle(Stroke, Paint) - Method in interface jebl.gui.trees.treecomponent.RootedTreePainter
Set hilight style
setHilightStyle(Stroke, Paint) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Set hilight style
setIgnoreNonMinimalUnivariateMinimisations(boolean) - Method in class jebl.math.OrthogonalSearch
Should we ignore new minisations that are not as minimal as the current one?
setImportAction(Action) - Method in class org.virion.jam.framework.AbstractFrame
 
setInclusion(FixedBitSet) - Method in class jebl.util.FixedBitSet
 
setIndeterminateProgress() - Method in class jebl.util.ProgressListener
Sets indefinite progress (i.e.
setIsOrdered(boolean) - Method in class jebl.evolution.characters.DiscreteCharacter
 
setItem(Object) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
setItem(Object) - Method in class jebl.gui.trees.treeviewer_dev.decorators.ContinuousColorDecorator
 
setItem(Object) - Method in interface jebl.gui.trees.treeviewer_dev.decorators.Decorator
 
setItem(Object) - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
setItemToView(Object) - Method in interface org.virion.jam.util.ListItemView
 
setLabelStyle(Font, Paint) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Set label style.
setLabelStyle(Font, Paint) - Method in interface jebl.gui.trees.treecomponent.RootedTreePainter
Set label style.
setLabelStyle(Font, Paint) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Set label style.
setLength(Node, double) - Method in class jebl.evolution.trees.MutableRootedTree
 
setLength(Node, double) - Method in class jebl.evolution.trees.SimpleRootedTree
 
setLinePaint(Paint) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Set line style
setLineStyle(Stroke, Paint) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Set line style
setLineStyle(Stroke, Paint) - Method in interface jebl.gui.trees.treecomponent.RootedTreePainter
Set line style
setLineStyle(Stroke, Paint) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
Set line style
setLineWeight(float) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setMatrix(RateMatrix) - Method in class jebl.evolution.substmodel.MatrixExponential
update rate matrix used in present module
setMessage(String) - Method in class jebl.util.ProgressListener
Set visible user message.
setMinus(FixedBitSet) - Method in class jebl.util.FixedBitSet
 
setN0(double) - Method in class jebl.evolution.coalescent.ConstantPopulation
sets initial population size.
setN1(double) - Method in class jebl.evolution.coalescent.ConstExponential
 
setN1(double) - Method in class jebl.evolution.coalescent.ConstLogistic
 
setN1(double) - Method in class jebl.evolution.coalescent.Expansion
 
setName(String) - Method in interface jebl.evolution.characters.Character
set the name of the character
setName(String) - Method in class jebl.evolution.characters.ContinuousCharacter
 
setName(String) - Method in class jebl.evolution.characters.DiscreteCharacter
 
setNodeBarPainter(NodeBarPainter) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setNodeLabelPainter(Painter<Node>) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setNodeLabelPainter(Painter<Node>) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setNodeLabelPainter(LabelPainter<Node>) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setNumberFormat(NumberFormat) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setNumOfStates(int) - Method in class jebl.evolution.characters.DiscreteCharacter
 
setOpen(boolean) - Method in class org.virion.jam.disclosure.DisclosurePanel
 
setOrderBranchesOn(boolean) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setPaintAttributeName(String) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
setParametersNoScale(double[]) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
setPinned(boolean) - Method in class org.virion.jam.controlpanels.Controls
 
setPreferredSize(Dimension) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setPreferredSize(Dimension) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setPriority(int) - Method in class org.virion.jam.util.SwingWorker
Allows the priority of the worker thread to be set.
setProgress(double) - Method in class jebl.util.ProgressListener
 
setProgressMonitor(ProgressMonitor) - Method in class jebl.evolution.align.SequenceShuffler
 
setProportion(double) - Method in class jebl.evolution.coalescent.ConstExponential
 
setProportion(double) - Method in class jebl.evolution.coalescent.Expansion
 
setRange(double, double) - Method in class org.virion.jam.components.RealNumberField
 
setRemoveAction(Action) - Method in class org.virion.jam.panels.ActionPanel
 
setRemoveToolTipText(String) - Method in class org.virion.jam.panels.ActionPanel
 
setRootAngle(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
setRootAngle(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
setRootAngle(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
setRootLength(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
setRootLength(double) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
setRootLength(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
setRootLength(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
setRuler(double) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setRuler(double) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setScaleBarPainter(Painter<TreePane>) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setScaleBarPainter(Painter<TreePane>) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setScaleBarStroke(BasicStroke) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setScaleRange(double) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setScaleRange(double) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setScores(Scores) - Method in class jebl.evolution.align.Align
 
setSeed(long) - Static method in class jebl.math.Random
Access a default instance of this class, access is synchronized
setSelected(boolean) - Method in class org.virion.jam.controlpalettes.PinnedButton
This overridden because when the button is programmatically selected, we want to skip the animation and jump straight to the final icon.
setSelected(boolean) - Method in class org.virion.jam.disclosure.DisclosureButton
This overridden because when the button is programmatically selected, we want to skip the animation and jump straight to the final icon.
setSelectedClade(Node) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSelectedClade(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSelectedNode(Node) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSelectedNode(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSelectedTaxa(Node) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSelectedTaxon(Taxon) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSelectedTip(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSelectedTips(Node) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSelectionMode(TreePaneSelector.SelectionMode) - Method in class jebl.gui.trees.treeviewer.TreePaneSelector
 
setSelectionMode(TreePaneSelector.SelectionMode) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setSelectionMode(TreePaneSelector.SelectionMode) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
setSelectionMode(TreePaneSelector.SelectionMode) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
setSelectionPaint(Paint) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSequenceType(SequenceType) - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
setSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
setSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
setSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
setSettings(ControlsSettings) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewerController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainterController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapeController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainterController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayoutController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayoutController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayoutController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.TreePaneController
 
setSettings(Map<String, Object>) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
setSettings(Map<String, Object>) - Method in class org.virion.jam.controlpalettes.BasicControlPalette
 
setSettings(Map<String, Object>) - Method in interface org.virion.jam.controlpalettes.Controller
Set the settings for this controller.
setSettings(Map<String, Object>) - Method in interface org.virion.jam.controlpalettes.ControlPalette
Distribute all the settings to all the controls in the palette.
setSettings(ControlsSettings) - Method in interface org.virion.jam.controlpanels.ControlsProvider
Give the provider some settings.
setShape(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
 
setShowingCollapsedTipLabels(boolean) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
setShowingRootBranch(boolean) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setShowingRootBranch(boolean) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
setShowingTaxonCallouts(boolean) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setShowingTipCallouts(boolean) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSignificantFigures(int) - Method in class jebl.util.NumberFormatter
Set the number of significant figures to display when formatted.
setSize(Dimension) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSize(int, int) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setSize(Dimension) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSize(int, int) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setSpikeFactor(double) - Method in class jebl.evolution.coalescent.CataclysmicDemographic
An alternative parameterization of this model.
setSpread(double) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
setStateDesc(Map<Integer, String>) - Method in class jebl.evolution.characters.DiscreteCharacter
 
setStatusProvider(StatusProvider) - Method in class org.virion.jam.panels.StatusPanel
 
setStroke(Stroke) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
setStrokeAttributeName(String) - Method in class jebl.gui.trees.treeviewer_dev.decorators.AttributableDecorator
 
setTaxonLabelPainter(Painter<Node>) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setTaxonLabelPosition(PolarTreeLayout.TaxonLabelPosition) - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
setText(Double) - Method in class org.virion.jam.components.RealNumberField
 
setText(Integer) - Method in class org.virion.jam.components.RealNumberField
 
setText(Long) - Method in class org.virion.jam.components.RealNumberField
 
setText(Integer) - Method in class org.virion.jam.components.WholeNumberField
 
setText(String) - Method in class org.virion.jam.util.JExceptionDialog
 
setTextDecorator(Decorator) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
setTime50(double) - Method in class jebl.evolution.coalescent.LogisticGrowth
An alternative parameterization of this model.
setTipLabelPainter(LabelPainter<Node>) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setTipLabelPosition(PolarTreeLayout.TipLabelPosition) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
setToolbarOptions(ToolbarOptions) - Method in class org.virion.jam.toolbar.GenericToolbarItem
 
setToolbarOptions(ToolbarOptions) - Method in class org.virion.jam.toolbar.ToolbarButton
 
setToolbarOptions(ToolbarOptions) - Method in interface org.virion.jam.toolbar.ToolbarItem
 
setToolTipText(String) - Method in class org.virion.jam.panels.SearchPanel
 
setTransformBranchesOn(boolean) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setTree(SimpleRootedTree) - Method in class jebl.evolution.characterReconstruction.MLContinuousCharacterReconstructor
 
setTree(RootedTree) - Method in class jebl.gui.trees.treecomponent.RootedTreeComponent
Set the tree.
setTree(Tree) - Method in class jebl.gui.trees.treeviewer.MultipleTreeViewer
 
setTree(Tree) - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
setTree(Tree) - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayout
Set the tree for the layout0
setTree(RootedTree) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setTree(Tree, int) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setTree(Tree) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setTree(Tree) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
setTree(Tree) - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
setTree(Tree) - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout
Set the tree for the layout0
setTree(RootedTree) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setTree(Tree) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
setTreeLayout(TreeLayout) - Method in class jebl.gui.trees.treeviewer.TreePane
 
setTreeLayout(TreeLayout) - Method in class jebl.gui.trees.treeviewer_dev.TreePane
 
setTreeLayout(TreeLayout) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
setTreeLayoutType(TreeViewer.TreeLayoutType) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setTreePane(TreePane) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
setTreePane(TreePane) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
setTreePane(TreePane) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
setTreePane(TreePane) - Method in interface jebl.gui.trees.treeviewer_dev.painters.Painter
Called when the painter is installed in a TreePane.
setTreePane(TreePane) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setTrees(Collection<? extends Tree>) - Method in class jebl.gui.trees.treeviewer.MultipleTreeViewer
 
setTrees(Collection<? extends Tree>, int) - Method in class jebl.gui.trees.treeviewer.MultipleTreeViewer
 
setTrees(Collection<? extends Tree>) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
setupAttributes(Tree) - Method in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
setupAttributes(Tree) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setupAttributes(Tree) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeBarPainter
 
setupAttributes(Tree) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
setupAttributes(Tree) - Method in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
setupControls() - Method in class org.virion.jam.controlpanels.BasicControlPalette
 
setupControls() - Method in interface org.virion.jam.controlpanels.ControlPalette
 
setUseCurrentInUnivariateMinimisation(boolean) - Method in class jebl.math.OrthogonalSearch
 
setUserDefinedHeight(double) - Method in class jebl.gui.trees.treecomponent.SquareTreePainter
 
setValue(double) - Method in class org.virion.jam.components.RealNumberField
 
setValue(int) - Method in class org.virion.jam.components.WholeNumberField
 
setValues(Collection<? extends Object>, Color[]) - Method in class jebl.gui.trees.treeviewer_dev.decorators.DiscreteColorDecorator
 
setVerticalExpansion(double) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setVerticalExpansion(double) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
setVgap(int) - Method in class org.virion.jam.layouts.CompassLayout
Sets the vertical gap between components.
setVisible(boolean) - Method in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
setVisible(boolean) - Method in class jebl.gui.trees.treeviewer.painters.ScaleBarPainter
 
setVisible(boolean) - Method in class jebl.gui.trees.treeviewer_dev.painters.LabelPainter
 
setVisible(boolean) - Method in class jebl.gui.trees.treeviewer_dev.painters.NodePainter
 
setVisible(boolean) - Method in class org.virion.jam.controlpanels.Controls
 
setZoom(double) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setZoom(double, double) - Method in class jebl.gui.trees.treeviewer.TreeViewer
 
setZoom(double) - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
showDefaultCursor(Component) - Static method in class org.virion.jam.util.Utils
 
showDialog() - Method in class org.virion.jam.preferences.PreferencesDialog
 
showingCollapsedTipLabels - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
showNextTree() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
showPredefinedCursor(Component, int) - Static method in class org.virion.jam.util.Utils
 
showPreviousTree() - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
showSection(String) - Method in class org.virion.jam.preferences.PreferencesDialog
 
showTree(int) - Method in class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer
 
showWaitCursor(Component) - Static method in class org.virion.jam.util.Utils
 
shuffle(Align, String, String, int) - Method in class jebl.evolution.align.SequenceShuffler
 
shuffle(int[]) - Static method in class jebl.math.Random
Shuffles an array.
shuffle(int[], int) - Static method in class jebl.math.Random
Shuffles an array.
shuffled(int) - Static method in class jebl.math.Random
Returns an array of shuffled indices of length l.
SimpleLinkListener - Class in org.virion.jam.html
iSeek prototype.
SimpleLinkListener() - Constructor for class org.virion.jam.html.SimpleLinkListener
 
SimpleListener - Interface in org.virion.jam.util
 
SimpleListenerManager - Class in org.virion.jam.util
 
SimpleListenerManager(SimpleListenerManager) - Constructor for class org.virion.jam.util.SimpleListenerManager
 
SimpleListenerManager() - Constructor for class org.virion.jam.util.SimpleListenerManager
 
SimpleLongTask - Class in org.virion.jam.util
 
SimpleLongTask() - Constructor for class org.virion.jam.util.SimpleLongTask
 
SimpleRootedTree - Class in jebl.evolution.trees
A simple, and initially immutable rooted tree implementation.
SimpleRootedTree() - Constructor for class jebl.evolution.trees.SimpleRootedTree
 
SimpleRootedTree(RootedTree) - Constructor for class jebl.evolution.trees.SimpleRootedTree
Make a copy of the given rooted tree
SimpleRootedTree(Tree, Node, Node, double) - Constructor for class jebl.evolution.trees.SimpleRootedTree
Make a copy of the given unrooted tree
SimpleTree - Class in jebl.evolution.trees
A basic implementation on an unrooted tree.
SimpleTree() - Constructor for class jebl.evolution.trees.SimpleTree
 
SimpleTree(RootedTree) - Constructor for class jebl.evolution.trees.SimpleTree
Make a copy of the given rooted tree.
simulate() - Method in class jebl.evolution.trees.TreeSimulator
 
simulate(boolean) - Method in class jebl.evolution.trees.TreeSimulator
 
SingleDocApplication - Class in org.virion.jam.framework
 
SingleDocApplication(String, String, Icon) - Constructor for class org.virion.jam.framework.SingleDocApplication
 
SingleDocApplication(String, String, Icon, String, String) - Constructor for class org.virion.jam.framework.SingleDocApplication
 
SingleDocApplication(MenuBarFactory, String, String, Icon) - Constructor for class org.virion.jam.framework.SingleDocApplication
 
SingleDocApplication(MenuBarFactory, String, String, Icon, String, String) - Constructor for class org.virion.jam.framework.SingleDocApplication
 
SingleDocMenuBarFactory - Class in org.virion.jam.framework
 
SingleDocMenuBarFactory() - Constructor for class org.virion.jam.framework.SingleDocMenuBarFactory
 
skipCharacters(String) - Method in class jebl.evolution.io.ImportHelper
Skips over any contiguous characters in skip.
skipComments(char) - Method in class jebl.evolution.io.ImportHelper
Skips over any comments.
skipSpace() - Method in class jebl.evolution.io.ImportHelper
Skips over any space (plus tabs and returns) in the file.
skipToEndOfLine() - Method in class jebl.evolution.io.ImportHelper
Skips to the end of the line.
skipUntil(String) - Method in class jebl.evolution.io.ImportHelper
Skips over the file until a character from delimiters is found.
skipWhile(String) - Method in class jebl.evolution.io.ImportHelper
Skips char any contiguous characters in skip.
SmithWaterman - Class in jebl.evolution.align
 
SmithWaterman(Scores, float) - Constructor for class jebl.evolution.align.SmithWaterman
 
SmithWatermanLinearSpace - Class in jebl.evolution.align
 
SmithWatermanLinearSpace(Scores, float) - Constructor for class jebl.evolution.align.SmithWatermanLinearSpace
 
SmithWatermanLinearSpaceAffine - Class in jebl.evolution.align
 
SmithWatermanLinearSpaceAffine(Scores, float, float) - Constructor for class jebl.evolution.align.SmithWatermanLinearSpaceAffine
 
SortedRootedTree - Class in jebl.evolution.trees
 
SortedRootedTree(RootedTree, SortedRootedTree.BranchOrdering) - Constructor for class jebl.evolution.trees.SortedRootedTree
 
SortedRootedTree(RootedTree, Comparator<Node>) - Constructor for class jebl.evolution.trees.SortedRootedTree
 
SortedRootedTree.BranchOrdering - Enum in jebl.evolution.trees
 
source - Variable in class jebl.evolution.trees.FilteredRootedTree
 
splitPane - Variable in class jebl.gui.trees.treeviewer.TreeViewer
 
SplitSystem - Class in jebl.evolution.trees
data structure for a set of splits
SplitSystem(Collection<Taxon>, int) - Constructor for class jebl.evolution.trees.SplitSystem
 
SplitUtils - Class in jebl.evolution.trees
utilities for split systems
SplitUtils() - Constructor for class jebl.evolution.trees.SplitUtils
 
SQRT_EPSILON - Static variable in class jebl.math.MachineAccuracy
 
SQRT_SQRT_EPSILON - Static variable in class jebl.math.MachineAccuracy
 
SquareTreePainter - Class in jebl.gui.trees.treecomponent
 
SquareTreePainter() - Constructor for class jebl.gui.trees.treecomponent.SquareTreePainter
 
SquareTreePainter(boolean) - Constructor for class jebl.gui.trees.treecomponent.SquareTreePainter
 
start() - Method in class org.virion.jam.util.SwingWorker
Start the worker thread.
startReadingTrees() - Method in class jebl.evolution.io.NexusImporter
 
State - Class in jebl.evolution.sequences
 
STATE_COUNT - Static variable in class jebl.evolution.sequences.AminoAcids
 
STATE_COUNT - Static variable in class jebl.evolution.sequences.Codons
 
STATE_COUNT - Static variable in class jebl.evolution.sequences.Nucleotides
 
StateClassification - Interface in jebl.evolution.sequences
 
StateClassification.Default - Class in jebl.evolution.sequences
 
StateClassification.Default(String, String[], State[][]) - Constructor for class jebl.evolution.sequences.StateClassification.Default
 
STATES - Static variable in class jebl.evolution.sequences.AminoAcids
 
STATES - Static variable in class jebl.evolution.sequences.Codons
 
STATES - Static variable in class jebl.evolution.sequences.Nucleotides
 
StatusBar - Class in org.virion.jam.panels
 
StatusBar(String) - Constructor for class org.virion.jam.panels.StatusBar
 
statusButtonPressed() - Method in class org.virion.jam.panels.StatusProvider.Helper
 
statusButtonPressed() - Method in interface org.virion.jam.panels.StatusProvider
 
statusChanged(int, String) - Method in interface org.virion.jam.panels.StatusListener
Called when the status is to be changed.
statusChanged(int, String) - Method in class org.virion.jam.panels.StatusPanel
 
StatusListener - Interface in org.virion.jam.panels
 
StatusPanel - Class in org.virion.jam.panels
 
StatusPanel() - Constructor for class org.virion.jam.panels.StatusPanel
 
StatusPanel(String) - Constructor for class org.virion.jam.panels.StatusPanel
 
StatusProvider - Interface in org.virion.jam.panels
 
StatusProvider.Helper - Class in org.virion.jam.panels
 
StatusProvider.Helper() - Constructor for class org.virion.jam.panels.StatusProvider.Helper
 
stop() - Method in class org.virion.jam.util.LongTask
Called to stop task.
stop() - Method in class org.virion.jam.util.SimpleLongTask
Called to stop task.
STOP_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
stopCondition(double, double[], double, double, boolean) - Method in class jebl.math.MultivariateMinimum
Checks whether optimization should stop
storePreferences() - Method in interface org.virion.jam.preferences.PreferencesSection
 
striped - Variable in class org.virion.jam.table.TableRenderer
 
stripGaps(State[]) - Static method in class jebl.evolution.sequences.Utils
 
subSequence(int, int) - Method in class jebl.evolution.io.ByteBuilder
 
SubstScoreMatrix - Class in jebl.evolution.align.scores
 
SubstScoreMatrix(RateMatrix) - Constructor for class jebl.evolution.align.scores.SubstScoreMatrix
 
sumVector(double[]) - Static method in class jebl.math.MatrixCalc
sum a vector
SwingWorker - Class in org.virion.jam.util
This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.
SwingWorker() - Constructor for class org.virion.jam.util.SwingWorker
Start a thread that will call the construct method and then exit.

T

T_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
T_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
TabDelimitedImporter - Class in jebl.evolution.io
 
TabDelimitedImporter(Reader, DistanceMatrixImporter.Triangle, boolean, boolean, boolean) - Constructor for class jebl.evolution.io.TabDelimitedImporter
Constructor
TableRenderer - Class in org.virion.jam.table
 
TableRenderer(int, Insets) - Constructor for class org.virion.jam.table.TableRenderer
 
TableRenderer(boolean, int, Insets) - Constructor for class org.virion.jam.table.TableRenderer
 
TamuraNeiDistanceMatrix - Class in jebl.evolution.distances
Date: 22/01/2006 Time: 17:28:59
TamuraNeiDistanceMatrix(Alignment, ProgressListener) - Constructor for class jebl.evolution.distances.TamuraNeiDistanceMatrix
 
taskCanceled() - Method in interface org.virion.jam.util.TaskListener
 
taskFinished() - Method in interface org.virion.jam.util.TaskListener
 
TaskListener - Interface in org.virion.jam.util
 
Taxon - Class in jebl.evolution.taxa
 
TAXON_NAMES - Static variable in class jebl.gui.trees.treeviewer.painters.BasicLabelPainter
 
TAXON_NAMES - Static variable in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
TaxonDecorator - Interface in jebl.gui.trees.treeviewer.decorators
 
taxonLabelPaths - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
TaxonomicLevel - Class in jebl.evolution.taxa
 
taxons - Variable in class jebl.evolution.trees.ConsensusTreeBuilder
List of common taxa in all trees
testConsistency(DemographicFunction, int, double) - Static method in class jebl.evolution.coalescent.DemographicFunction.Utils
This function tests the consistency of the getIntensity and getInverseIntensity methods of this demographic model.
TEXT_ONLY - Static variable in class org.virion.jam.toolbar.ToolbarOptions
 
time - Variable in class jebl.util.CompositeProgressListener
 
tipCount - Variable in class jebl.evolution.trees.ClusteringTreeBuilder
 
tipLabelPaths - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
toNewick(RootedTree) - Static method in class jebl.evolution.trees.Utils
 
toNucleotides(CodonState) - Static method in class jebl.evolution.sequences.Codons
 
Toolbar - Class in org.virion.jam.toolbar
 
Toolbar() - Constructor for class org.virion.jam.toolbar.Toolbar
 
Toolbar(ToolbarOptions) - Constructor for class org.virion.jam.toolbar.Toolbar
 
ToolbarAction - Class in org.virion.jam.toolbar
 
ToolbarAction(String, String, Icon) - Constructor for class org.virion.jam.toolbar.ToolbarAction
 
ToolbarAction(String, String, Icon, Icon, Icon) - Constructor for class org.virion.jam.toolbar.ToolbarAction
 
ToolbarButton - Class in org.virion.jam.toolbar
 
ToolbarButton(ToolbarAction) - Constructor for class org.virion.jam.toolbar.ToolbarButton
 
ToolbarItem - Interface in org.virion.jam.toolbar
 
ToolbarOptions - Class in org.virion.jam.toolbar
 
ToolbarOptions(int, boolean) - Constructor for class org.virion.jam.toolbar.ToolbarOptions
 
toStateArray(String) - Static method in class jebl.evolution.sequences.AminoAcids
 
toStateArray(byte[]) - Static method in class jebl.evolution.sequences.AminoAcids
 
toStateArray(String) - Static method in class jebl.evolution.sequences.Codons
 
toStateArray(byte[]) - Static method in class jebl.evolution.sequences.Codons
 
toStateArray(String) - Static method in class jebl.evolution.sequences.Nucleotides
 
toStateArray(byte[]) - Static method in class jebl.evolution.sequences.Nucleotides
 
toStateArray(String) - Method in interface jebl.evolution.sequences.SequenceType
Converts a string of state codes into an array of State objects for this SequenceType
toStateArray(byte[]) - Method in interface jebl.evolution.sequences.SequenceType
Converts an array of state indices into an array of State objects for this SequenceType
toString() - Method in class jebl.evolution.align.ProfileCharacter
 
toString() - Method in class jebl.evolution.align.scores.Hamming
 
toString() - Method in class jebl.evolution.align.scores.NucleotideScores
 
toString() - Method in class jebl.evolution.align.scores.Scores
 
toString() - Method in class jebl.evolution.align.Traceback
 
toString() - Method in enum jebl.evolution.coalescent.IntervalList.IntervalType
 
toString() - Method in class jebl.evolution.io.ByteBuilder
 
toString() - Method in class jebl.evolution.sequences.GeneticCode
 
toString() - Method in class jebl.evolution.sequences.State
 
toString() - Method in class jebl.evolution.taxa.Taxon
 
toString() - Method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
 
toString() - Method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
 
toString() - Method in class jebl.evolution.trees.SplitSystem
print split system
toString() - Method in enum jebl.evolution.trees.TransformedRootedTree.Transform
 
toString() - Method in enum jebl.evolution.trees.TreeBuilderFactory.Method
 
toString() - Method in enum jebl.gui.trees.treeviewer.TreeViewer.SearchType
 
toString() - Method in enum jebl.gui.trees.treeviewer.TreeViewer.TreeLayoutType
 
toString() - Method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapeController.NodePainterType
 
toString() - Method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter.NodeShape
 
toString() - Method in enum jebl.gui.trees.treeviewer_dev.TreeViewer.SearchType
 
toString() - Method in enum jebl.gui.trees.treeviewer_dev.TreeViewerController.TreeLayoutType
 
toString() - Method in class jebl.util.FixedBitSet
 
toString(double[], int) - Static method in class jebl.util.Utils
A simple toString method for an array of doubles.
toString(Object[], int) - Static method in class jebl.util.Utils
A simple toString method for an array of objects.
toString(Object[], String) - Static method in class jebl.util.Utils
A simple toString method for an array of objects.
toString(Object[], String, int) - Static method in class jebl.util.Utils
A simple toString method for an array of objects.
toString(Object[]) - Static method in class jebl.util.Utils
A simple toString method for an array of doubles.
toString(double[]) - Static method in class jebl.util.Utils
A simple toString method for an array of doubles.
toString(int[]) - Static method in class jebl.util.Utils
A simple toString method for an array of ints.
toString(int[], int) - Static method in class jebl.util.Utils
 
toString(double[][]) - Static method in class jebl.util.Utils
A simple toString method for an array of doubles.
toString(int[][]) - Static method in class jebl.util.Utils
A simple toString method for an array of ints.
toString() - Method in class org.virion.jam.layouts.CompassLayout
Returns the String representation of this CompassLayout's values.
totalCharacters - Variable in class jebl.evolution.align.ProfileCharacter
 
traceback(TracebackPlotter) - Method in class jebl.evolution.align.Align
 
traceback(TracebackPlotter) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
 
traceback(TracebackPlotter, int, int, String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
 
traceback(TracebackPlotter) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
 
traceback(TracebackPlotter) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
 
Traceback - Class in jebl.evolution.align
 
Traceback() - Constructor for class jebl.evolution.align.Traceback
 
traceBack(Traceback) - Method in interface jebl.evolution.align.TracebackPlotter
 
TracebackPlotter - Interface in jebl.evolution.align
 
TransformedRootedTree - Class in jebl.evolution.trees
This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.
TransformedRootedTree(RootedTree, TransformedRootedTree.Transform) - Constructor for class jebl.evolution.trees.TransformedRootedTree
 
TransformedRootedTree.Transform - Enum in jebl.evolution.trees
 
translate(State[], GeneticCode) - Static method in class jebl.evolution.sequences.Utils
 
translate(String, GeneticCode) - Static method in class jebl.evolution.sequences.Utils
 
TranslatedSequence - Class in jebl.evolution.sequences
 
TranslatedSequence(Sequence, GeneticCode) - Constructor for class jebl.evolution.sequences.TranslatedSequence
 
tree - Variable in class jebl.evolution.align.AlignmentTreeBuilderFactory.Result
 
Tree - Interface in jebl.evolution.trees
An unrooted tree.
tree - Variable in class jebl.gui.trees.treecomponent.RootedTreeComponent
the tree
tree - Variable in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
tree - Variable in class jebl.gui.trees.treeviewer.TreeViewer
 
tree - Variable in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
TreeAppearanceController - Class in jebl.gui.trees.treeviewer_dev
 
TreeAppearanceController(TreePane) - Constructor for class jebl.gui.trees.treeviewer_dev.TreeAppearanceController
 
TreeBuilder<T extends Tree> - Interface in jebl.evolution.trees
 
TreeBuilderFactory - Class in jebl.evolution.trees
A meeting point for tree building from sequence data.
TreeBuilderFactory() - Constructor for class jebl.evolution.trees.TreeBuilderFactory
 
TreeBuilderFactory.ConsensusMethod - Enum in jebl.evolution.trees
Supported consensus methods.
TreeBuilderFactory.DistanceModel - Enum in jebl.evolution.trees
Supported pairwise distance methods
TreeBuilderFactory.Method - Enum in jebl.evolution.trees
Supported methods for tree building
treeChanged() - Method in interface jebl.gui.trees.treeviewer_dev.TreeViewerListener
 
TreeExporter - Interface in jebl.evolution.io
 
TreeImporter - Interface in jebl.evolution.io
Interface for importers that do trees
TreeLayout - Interface in jebl.gui.trees.treeviewer.treelayouts
 
TreeLayout - Interface in jebl.gui.trees.treeviewer_dev.treelayouts
 
TreeLayout.AxisType - Enum in jebl.gui.trees.treeviewer.treelayouts
 
TreeLayout.AxisType - Enum in jebl.gui.trees.treeviewer_dev.treelayouts
 
treeLayoutChanged() - Method in interface jebl.gui.trees.treeviewer.treelayouts.TreeLayoutListener
 
treeLayoutChanged() - Method in interface jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayoutListener
 
TreeLayoutListener - Interface in jebl.gui.trees.treeviewer.treelayouts
 
TreeLayoutListener - Interface in jebl.gui.trees.treeviewer_dev.treelayouts
 
treeNameAttributeKey - Static variable in class jebl.evolution.io.NexusExporter
 
TreePane - Class in jebl.gui.trees.treeviewer
 
TreePane() - Constructor for class jebl.gui.trees.treeviewer.TreePane
 
treePane - Variable in class jebl.gui.trees.treeviewer.TreeViewer
 
treePane - Variable in class jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter
 
treePane - Variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
treePane - Variable in class jebl.gui.trees.treeviewer_dev.painters.ScaleBarPainter
 
TreePane - Class in jebl.gui.trees.treeviewer_dev
 
TreePane() - Constructor for class jebl.gui.trees.treeviewer_dev.TreePane
 
treePane - Variable in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
TreePaneController - Class in jebl.gui.trees.treeviewer_dev
 
TreePaneController(TreePane) - Constructor for class jebl.gui.trees.treeviewer_dev.TreePaneController
 
TreePaneListener - Interface in jebl.gui.trees.treeviewer_dev
 
TreePaneRuler - Class in jebl.gui.trees.treeviewer
 
TreePaneRuler(TreePane) - Constructor for class jebl.gui.trees.treeviewer.TreePaneRuler
 
TreePaneRuler - Class in jebl.gui.trees.treeviewer_dev
 
TreePaneRuler(TreePane) - Constructor for class jebl.gui.trees.treeviewer_dev.TreePaneRuler
 
TreePaneSelector - Class in jebl.gui.trees.treeviewer
 
TreePaneSelector(TreePane) - Constructor for class jebl.gui.trees.treeviewer.TreePaneSelector
 
treePaneSelector - Variable in class jebl.gui.trees.treeviewer.TreeViewer
 
TreePaneSelector - Class in jebl.gui.trees.treeviewer_dev
 
TreePaneSelector(TreePane) - Constructor for class jebl.gui.trees.treeviewer_dev.TreePaneSelector
 
treePaneSelector - Variable in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
TreePaneSelector.DragMode - Enum in jebl.gui.trees.treeviewer
 
TreePaneSelector.DragMode - Enum in jebl.gui.trees.treeviewer_dev
 
TreePaneSelector.SelectionMode - Enum in jebl.gui.trees.treeviewer
 
TreePaneSelector.SelectionMode - Enum in jebl.gui.trees.treeviewer_dev
 
treePaneSettingsChanged() - Method in interface jebl.gui.trees.treeviewer_dev.TreePaneListener
 
TreeSelectionListener - Interface in jebl.gui.trees.treeviewer
 
TreeSelectionListener - Interface in jebl.gui.trees.treeviewer_dev
 
TreeSimulator - Class in jebl.evolution.trees
This class provides the framework for (backwards-through-time) tree simulation.
TreeSimulator(IntervalGenerator, String, int) - Constructor for class jebl.evolution.trees.TreeSimulator
A constructor for a given number of taxa, all sampled at the same time
TreeSimulator(IntervalGenerator, String, double[]) - Constructor for class jebl.evolution.trees.TreeSimulator
 
TreeSimulator(IntervalGenerator, String, int[], double[]) - Constructor for class jebl.evolution.trees.TreeSimulator
 
TreeSimulator(IntervalGenerator, Collection<Taxon>, String) - Constructor for class jebl.evolution.trees.TreeSimulator
A constructor for a given collection of taxa.
TreeViewer - Class in jebl.gui.trees.treeviewer
 
TreeViewer() - Constructor for class jebl.gui.trees.treeviewer.TreeViewer
Creates new TreeViewer
TreeViewer(int, BasicControlPalette.DisplayMode) - Constructor for class jebl.gui.trees.treeviewer.TreeViewer
 
TreeViewer(int) - Constructor for class jebl.gui.trees.treeviewer.TreeViewer
 
TreeViewer(ControlPalette, int) - Constructor for class jebl.gui.trees.treeviewer.TreeViewer
Creates new TreeViewer
TreeViewer - Class in jebl.gui.trees.treeviewer_dev
 
TreeViewer() - Constructor for class jebl.gui.trees.treeviewer_dev.TreeViewer
Creates new TreeViewer
TreeViewer(TreePane) - Constructor for class jebl.gui.trees.treeviewer_dev.TreeViewer
Creates new TreeViewer
TreeViewer.SearchType - Enum in jebl.gui.trees.treeviewer
 
TreeViewer.SearchType - Enum in jebl.gui.trees.treeviewer_dev
 
TreeViewer.TreeLayoutType - Enum in jebl.gui.trees.treeviewer
 
TreeViewerController - Class in jebl.gui.trees.treeviewer_dev
 
TreeViewerController(TreeViewer) - Constructor for class jebl.gui.trees.treeviewer_dev.TreeViewerController
 
TreeViewerController.TreeLayoutType - Enum in jebl.gui.trees.treeviewer_dev
 
TreeViewerListener - Interface in jebl.gui.trees.treeviewer_dev
 
TreeViewerPanel - Class in jebl.gui.trees.treeviewer_dev
This is a panel that has a TreeViewer and a BasicControlPalette with the default Controllers and Painters.
TreeViewerPanel(TreeViewer, ControlPalette) - Constructor for class jebl.gui.trees.treeviewer_dev.TreeViewerPanel
 
trimExtensions(String, String[]) - Static method in class org.virion.jam.app.Utils
This function takes a file name and an array of extensions (specified without the leading '.').

U

U_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
union(FixedBitSet) - Method in class jebl.util.FixedBitSet
 
uniqueNewick(RootedTree, Node) - Static method in class jebl.evolution.trees.RootedTreeUtils
Recursive function for constructing a newick tree representation in the given buffer.
UnivariateFunction - Interface in jebl.math
interface for a function of one variable
UnivariateMinimum - Class in jebl.math
minimization of a real-valued function of one variable without using derivatives.
UnivariateMinimum() - Constructor for class jebl.math.UnivariateMinimum
 
UNIVERSAL - Static variable in class jebl.evolution.sequences.GeneticCode
 
UNKNOWN_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
UNKNOWN_STATE - Static variable in class jebl.evolution.sequences.Codons
 
UNKNOWN_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
unreadCharacter(char) - Method in class jebl.evolution.io.ImportHelper
 
updateByRelativeRates(double[][]) - Method in class jebl.evolution.substmodel.MatrixExponential
 
updatedDistance(int) - Method in class jebl.evolution.trees.ClusteringTreeBuilder
compute updated distance between the new cluster (besti,bestj) to any other cluster k.
updatedDistance(int) - Method in class jebl.evolution.trees.NeighborJoiningTreeBuilder
 
updateMatrixExp() - Method in class jebl.evolution.substmodel.AbstractRateMatrix
 
updateProgress(double) - Method in interface jebl.math.MinimiserMonitor
Inform monitor of current progress (as a number between 0 and 1), or -1 to reset
updateUI() - Method in class org.virion.jam.table.HeaderRenderer
 
UPPER_ATTRIBUTE - Static variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
upperSolve(double[][], double[], double) - Static method in class jebl.math.MatrixCalc
upperSolve back substitution with optional over-riding diagonal
userMessage() - Method in exception jebl.evolution.io.ImportException.MissingFieldException
 
userMessage() - Method in exception jebl.evolution.io.ImportException
 
Utils - Class in jebl.evolution.graphs
A collection of utility functions for graphs.
Utils() - Constructor for class jebl.evolution.graphs.Utils
 
Utils - Class in jebl.evolution.sequences
 
Utils() - Constructor for class jebl.evolution.sequences.Utils
 
Utils - Class in jebl.evolution.trees
A collection of utility functions for trees.
Utils() - Constructor for class jebl.evolution.trees.Utils
 
Utils - Class in jebl.util
Provides some miscellaneous methods.
Utils() - Constructor for class jebl.util.Utils
 
Utils - Class in org.virion.jam.app
 
Utils() - Constructor for class org.virion.jam.app.Utils
 
Utils - Class in org.virion.jam.mac
 
Utils() - Constructor for class org.virion.jam.mac.Utils
 
Utils - Class in org.virion.jam.util
 
Utils() - Constructor for class org.virion.jam.util.Utils
 

V

V_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
V_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
validate() - Method in class jebl.gui.trees.treeviewer.treelayouts.AbstractTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer.treelayouts.RadialTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer.treelayouts.RectilinearTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.AbstractTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RadialTreeLayout
 
validate() - Method in class jebl.gui.trees.treeviewer_dev.treelayouts.RectilinearTreeLayout
 
valueOf(String) - Static method in enum jebl.evolution.coalescent.IntervalList.IntervalType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.io.DistanceMatrixImporter.Triangle
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.io.NexusImporter.NexusBlock
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.trees.TransformedRootedTree.Transform
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.DistanceModel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.evolution.trees.TreeBuilderFactory.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.painters.BasicLabelPainter.PainterIntent
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.painters.Painter.Justification
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.painters.Painter.Orientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout.TaxonLabelPosition
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.treelayouts.TreeLayout.AxisType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.TreePaneSelector.DragMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.TreePaneSelector.SelectionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.TreeViewer.SearchType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer.TreeViewer.TreeLayoutType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter.PainterIntent
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapeController.NodePainterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter.NodeShape
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.painters.Painter.Justification
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.painters.Painter.Orientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout.TipLabelPosition
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout.AxisType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.TreePaneSelector.DragMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.TreePaneSelector.SelectionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.TreeViewer.SearchType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum jebl.gui.trees.treeviewer_dev.TreeViewerController.TreeLayoutType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.virion.jam.controlpalettes.BasicControlPalette.DisplayMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.virion.jam.controlpanels.BasicControlPalette.DisplayMode
Returns the enum constant of this type with the specified name.
values() - Static method in enum jebl.evolution.coalescent.IntervalList.IntervalType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.io.DistanceMatrixImporter.Triangle
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.io.NexusImporter.NexusBlock
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.trees.ConsensusTreeBuilder.Method
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.trees.SortedRootedTree.BranchOrdering
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.trees.TransformedRootedTree.Transform
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.ConsensusMethod
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.DistanceModel
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.evolution.trees.TreeBuilderFactory.Method
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.painters.BasicLabelPainter.PainterIntent
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.painters.Painter.Justification
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.painters.Painter.Orientation
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.treelayouts.PolarTreeLayout.TaxonLabelPosition
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.treelayouts.TreeLayout.AxisType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.TreePaneSelector.DragMode
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.TreePaneSelector.SelectionMode
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.TreeViewer.SearchType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer.TreeViewer.TreeLayoutType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.painters.BasicLabelPainter.PainterIntent
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapeController.NodePainterType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter.NodeShape
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.painters.Painter.Justification
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.painters.Painter.Orientation
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.treelayouts.PolarTreeLayout.TipLabelPosition
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.treelayouts.TreeLayout.AxisType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.TreePaneSelector.DragMode
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.TreePaneSelector.SelectionMode
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.TreeViewer.SearchType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum jebl.gui.trees.treeviewer_dev.TreeViewerController.TreeLayoutType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.virion.jam.controlpalettes.BasicControlPalette.DisplayMode
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.virion.jam.controlpanels.BasicControlPalette.DisplayMode
Returns an array containing the constants of this enum type, in the order they're declared.
VERTEBRATE_MT - Static variable in class jebl.evolution.sequences.GeneticCode
 
verticalExpansionAllowed() - Method in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
viewport - Variable in class jebl.gui.trees.treeviewer.TreeViewer
 
viewport - Variable in class jebl.gui.trees.treeviewer_dev.TreeViewer
 
VOLUME_CLASSIFICATION - Static variable in class jebl.evolution.sequences.AminoAcids
 

W

W_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
W_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
WAG - Class in jebl.evolution.substmodel
WAG model of amino acid evolution (S.
WAG(double[]) - Constructor for class jebl.evolution.substmodel.WAG
constructor
WARNING - Static variable in class org.virion.jam.panels.StatusPanel
 
websiteAction - Variable in class org.virion.jam.framework.Application
 
WholeNumberCellEditor - Class in org.virion.jam.table
 
WholeNumberCellEditor(int, int) - Constructor for class org.virion.jam.table.WholeNumberCellEditor
 
WholeNumberField - Class in org.virion.jam.components
 
WholeNumberField() - Constructor for class org.virion.jam.components.WholeNumberField
 
WholeNumberField(int, int) - Constructor for class org.virion.jam.components.WholeNumberField
 
WIDTH_ATTRIBUTE - Static variable in class jebl.gui.trees.treeviewer_dev.painters.NodeShapePainter
 
WORKING - Static variable in class org.virion.jam.panels.StatusPanel
 
writer - Variable in class jebl.evolution.io.NexusExporter
 
writeToFile(File) - Method in class org.virion.jam.console.ConsoleFrame
 
writeToFile(File) - Method in class org.virion.jam.demo.DemoFrame
 
writeToFile(File) - Method in class org.virion.jam.framework.DocumentFrame
 

X

X_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 

Y

Y_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 
Y_STATE - Static variable in class jebl.evolution.sequences.Nucleotides
 
YEAST - Static variable in class jebl.evolution.sequences.GeneticCode
 

Z

Z_STATE - Static variable in class jebl.evolution.sequences.AminoAcids
 

_

_setIndeterminateProgress() - Method in class jebl.util.CompositeProgressListener
 
_setIndeterminateProgress() - Method in class jebl.util.ProgressListener
This method is a hook called from ProgressListener.setIndeterminateProgress() to allow subclasses a custom reaction to setIndeterminateProgress events.
_setMessage(String) - Method in class jebl.util.CompositeProgressListener
 
_setMessage(String) - Method in class jebl.util.ProgressListener
This method is a hook called from ProgressListener.setMessage(java.lang.String) to allow subclasses a custom reaction to setMessage events.
_setProgress(double) - Method in class jebl.util.CompositeProgressListener
 
_setProgress(double) - Method in class jebl.util.ProgressListener
This method is a hook called from ProgressListener.setProgress(double) to allow subclasses a custom reaction to setProgress events.

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