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 - Variable in class mesquite.align.lib.PairwiseAligner

A - Static variable in class mesquite.categ.lib.DNAState

A - Static variable in class mesquite.molec.lib.GeneticCode

AAProperty - Class in mesquite.molec.lib

AAProperty() - Constructor for class mesquite.molec.lib.AAProperty

Abortable - Interface in mesquite.lib

aboutToReturnText(int, int) - Method in class mesquite.lib.table.EditorPanel

ABOVE - Static variable in class mesquite.lib.TaxaDisplayExtra

ABOVE - Static variable in class mesquite.lib.TreeDisplayExtra

abs() - Method in class mesquite.lib.MesquiteNumber

Sets to absolute value

abs(double[][]) - Static method in class mesquite.rhetenor.lib.MatrixUtil

ABSENT - Static variable in class mesquite.categ.lib.ProteinData

absolute(double) - Static method in class mesquite.cont.lib.ContinuousState

ACCEPTABLETOUCHWIDTH - Static variable in class mesquite.lib.TreeDrawing

acceptParameters() - Method in class mesquite.lib.ParametersDialog

acceptProvisionalValue() - Method in class mesquite.lib.MesquiteParameter

acceptText() - Method in interface mesquite.lib.MiniControl

acceptText() - Method in class mesquite.lib.MiniNumberEditor

acceptText() - Method in class mesquite.lib.MiniScroll

acceptText() - Method in class mesquite.lib.MiniSliderWithText

acceptText() - Method in class mesquite.lib.MiniStringEditor

accumulate(Commandable, CommandChecker) - Static method in class mesquite.lib.CommandChecker

Accumulates (menus and ) commands from the given commandable and passes back a vector of strings describing the (menus and ) commands.

accumulateOnlyFrom(Class) - Method in class mesquite.lib.CommandChecker

Sets what exact class the checker is to accumulate commands from (will not accumulate from super or subclasses).

accumulateParameters(String) - Method in interface mesquite.lib.duties.BooleanForItem

accumulateParameters(String) - Method in interface mesquite.lib.duties.ItemsSource

accumulateParameters(String) - Method in interface mesquite.lib.duties.NumberForItem

accumulateParameters(String) - Method in class mesquite.lib.MesquiteModule

accumulateTerminals(int, int[], MesquiteInteger) - Method in class mesquite.lib.MesquiteTree

Places into the passed array (which must have been sized correctly in advance) the taxon numbers in the clade

actionPerformed(ActionEvent) - Method in class mesquite.genesis.lib.ProbSubModelCurator

actionPerformed(ActionEvent) - Method in class mesquite.genesis.lib.StateFreqUserModel

actionPerformed(ActionEvent) - Method in class mesquite.lib.ChecklistDialog

actionPerformed(ActionEvent) - Method in class mesquite.lib.ExtensibleDialog

This displays the help note.

actionPerformed(ActionEvent) - Method in class mesquite.lib.ExtensibleListDialog

If you override this to add more buttons, make sure you call super.actonPerformed()

actionPerformed(ActionEvent) - Method in class mesquite.lib.MesquiteCheckMenuItem

actionPerformed(ActionEvent) - Method in class mesquite.lib.MesquiteMenuItem

actionPerformed(ActionEvent) - Method in class mesquite.lib.MesquiteSubmenu

actionPerformed(ActionEvent) - Method in class mesquite.lib.MiniScroll

actionPerformed(ActionEvent) - Method in class mesquite.lib.MiniSliderWithText

actionPerformed(ActionEvent) - Method in class mesquite.lib.MiniStringEditor

actionPerformed(ActionEvent) - Method in class mesquite.lib.MRPopup

actionPerformed(ActionEvent) - Method in class mesquite.lib.StringIntegerDialog

actionPerformed(ActionEvent) - Method in class mesquite.lib.TwoIntegersDialog

actionPerformed(ActionEvent) - Method in class mesquite.lists.lib.GroupDialog

activeWindow - Static variable in class mesquite.lib.MesquiteFrame

activeWindowOfProject - Variable in class mesquite.lib.MesquiteProject

actUponDroppedFileContents(FileInterpreter, String) - Method in interface mesquite.lib.MesquiteDroppedFileHandler

actUponDroppedFileContents(FileInterpreter, String) - Method in class mesquite.lib.MousePanel

Method for panels to override in order to do something with dropped file contents

add(Component, int) - Method in class mesquite.lib.ContentArea

add(Component, Object, int) - Method in class mesquite.lib.ContentArea

add(Component, Object) - Method in class mesquite.lib.ContentArea

add(Component) - Method in class mesquite.lib.ContentArea

add(String, Component) - Method in class mesquite.lib.ContentArea

add(Component) - Method in class mesquite.lib.MesquiteDialog

add(Component, String) - Method in class mesquite.lib.MesquiteDialog

add(String, Component) - Method in class mesquite.lib.MesquiteDialog

add(MesquiteDialog) - Method in class mesquite.lib.MesquiteDialogParent

add(double) - Method in class mesquite.lib.MesquiteDouble

Adds to current value.

add(double, double) - Static method in class mesquite.lib.MesquiteDouble

Adds two doubles.

add(int) - Method in class mesquite.lib.MesquiteInteger

Adds to current value.

add(int, int) - Static method in class mesquite.lib.MesquiteInteger

Adds two ints.

add(long) - Method in class mesquite.lib.MesquiteLong

Adds to current value.

add(long, long) - Static method in class mesquite.lib.MesquiteLong

Adds two doubles.

add(MenuItem) - Method in class mesquite.lib.MesquiteMenu

add(Menu, MenuItem) - Static method in class mesquite.lib.MesquiteMenu

add(Menu) - Method in class mesquite.lib.MesquiteMenuBar

add(int) - Method in class mesquite.lib.MesquiteNumber

Adds value to current value

add(long) - Method in class mesquite.lib.MesquiteNumber

Adds value to current value

add(double) - Method in class mesquite.lib.MesquiteNumber

Adds value to current value

add(MesquiteNumber) - Method in class mesquite.lib.MesquiteNumber

Adds value to current value

add(Component) - Method in class mesquite.lib.MesquitePanel

add(boolean) - Method in class mesquite.lib.table.MesquiteTable

Sets whether or not different the message panel is visible.

add(double[][], double[][]) - Static method in class mesquite.rhetenor.lib.MatrixUtil

addAButton(String, Panel) - Method in class mesquite.lib.ExtensibleDialog

addAButton(String, Panel, GridBagConstraints) - Method in class mesquite.lib.ExtensibleDialog

addAdditionalButtonsBesideList() - Method in class mesquite.lib.ExtensibleListDialog

override this to to add new buttons beside list; use addNewButtonBesideList to add them

addAListenedButton(String, Panel, ActionListener) - Method in class mesquite.lib.ExtensibleDialog

addAListenedImage(String, String, String, boolean, Panel, ImagePanelListener) - Method in class mesquite.lib.ExtensibleDialog

addAndFillNextUnassigned(String) - Method in class mesquite.lib.StringArray

addAnEmptyImage(Panel) - Method in class mesquite.lib.ExtensibleDialog

addAssistantTask(TaxaDisplayAssistant) - Method in class mesquite.lib.duties.DrawTaxaCoordinator

Add taxa display assistant

addAssistantTask(TreeDisplayAssistant) - Method in class mesquite.lib.duties.DrawTreeCoordinator

Add tree display assistant

addAuthorBlockByDefault - Static variable in class mesquite.lib.Author

addAuxiliaryDefaultPanels() - Method in class mesquite.lib.ExtensibleDialog

Can be overrided to provide extra panels above button row

addAuxiliaryDefaultPanels() - Method in class mesquite.lib.ExtensibleExplDialog

Can be overrided to provide extra panels above button row

addAuxiliaryDefaultPanels() - Method in class mesquite.lib.StringIntegerListDlog

addAuxiliaryMenu(String) - Method in class mesquite.lib.MenuOwner

This requests an auxiliary menu for the MesquiteModule

addBlankLine() - Method in class mesquite.lib.ExtensibleDialog

addBlock(NexusBlock) - Method in class mesquite.lib.duties.NexusFileInterpreter

adds nexus block to project (block contains reference to the file it belongs to)

addBlockListener(MesquiteListener) - Method in class mesquite.lib.duties.TreesManager

addBoldLabel(String) - Method in class mesquite.lib.ExtensibleDialog

addButton(String) - Method in class mesquite.lib.ExtensibleDialog

addCharacters(int, int, boolean) - Method in class mesquite.lib.characters.CharacterData

A equivalent of addParts but with notification added

addCheckBox(String, boolean) - Method in class mesquite.lib.ExtensibleDialog

addCheckMenuItem(MesquiteMenuSpec, String, MesquiteCommand, MesquiteBoolean) - Method in class mesquite.lib.MenuOwner

Add check menu item.

addCheckMenuItemToSubmenu(MesquiteMenuSpec, MesquiteSubmenuSpec, String, MesquiteCommand, MesquiteBoolean) - Method in class mesquite.lib.MenuOwner

Adds a menu item to the given submenu of the given menu.

addChoice(String) - Method in class mesquite.lib.PanelOfCards

addChoice(String) - Method in class mesquite.lib.PopUpPanelOfCards

addClade(String) - Method in class mesquite.lib.Clades

addColumnDelimiterPopUpPanel() - Method in class mesquite.io.lib.DistanceMatrixExporterDialog

addColumns(long[][], int, long, int, int) - Static method in class mesquite.lib.Long2DArray

addColumns(long[][], long, int, int) - Static method in class mesquite.lib.Long2DArray

addColumns(short[][], int, short, int, int) - Static method in class mesquite.lib.Short2DArray

addColumns(short[][], short, int, int) - Static method in class mesquite.lib.Short2DArray

addCommand(String, String) - Method in class mesquite.lib.FileBlock

addComponent(MesquiteDialog, Component, int, int, int, int, int, int, int, int) - Static method in class mesquite.lib.MesquiteDialog

addComponent(Container, Component, int, int, int, int, int, int, int, int) - Static method in class mesquite.lib.MesquiteDialog

addComponentPlease(Component) - Method in class mesquite.lib.MesquiteChart

addComponentPlease(Component) - Method in class mesquite.lib.TaxaTreeDisplay

addControlButton(MesquiteButton) - Method in class mesquite.lib.table.MesquiteTable

Adds a button to the control strip at lower left of table.

addControlButton(MesquiteButton) - Method in class mesquite.lib.table.TableWindow

Adds a button to the control strip at lower left of table.

addDefaultPanelsListener(boolean, ActionListener) - Method in class mesquite.lib.ExtensibleDialog

addDialogElements(ExtensibleDialog) - Method in class mesquite.lib.CircleSymbol

addDialogElements(ExtensibleDialog) - Method in class mesquite.lib.FillableMesquiteSymbol

addDialogElements(ExtensibleDialog) - Method in class mesquite.lib.MesquiteSymbol

addDoubleField(String, double, int, double, double) - Method in class mesquite.lib.ExtensibleDialog

addDoubleField(String, double, int) - Method in class mesquite.lib.ExtensibleDialog

addDoubleField(String, int) - Method in class mesquite.lib.ExtensibleDialog

addElement(Listable, boolean) - Method in class mesquite.lib.ListableVector

addElement(Listable, boolean) - Method in class mesquite.lib.TreeVector

addElements(ListableVector, boolean) - Method in class mesquite.lib.ListableVector

addEvent(Author, long, String) - Method in class mesquite.lib.ChangeHistory

addEvent(ChangeEvent) - Method in class mesquite.lib.ChangeHistory

addExtra(ChartExtra) - Method in class mesquite.lib.MesquiteChart

addExtra(TaxaDisplayExtra) - Method in class mesquite.lib.TaxaDisplay

addExtra(TreeDisplayExtra) - Method in class mesquite.lib.TreeDisplay

addExtraButtons(Panel, ActionListener) - Method in class mesquite.lib.ExtensibleDialog

addExtraButtons(Panel) - Method in class mesquite.lib.ExtensibleDialog

addExtraSubcommand(String, boolean) - Method in class mesquite.lib.AttachedNote

addExtraSubcommand(String) - Method in class mesquite.lib.ImageLabel

addFile(MesquiteFile) - Method in class mesquite.lib.MesquiteProject

add a file to list of currently linked files

addFileElement(FileElement) - Method in class mesquite.lib.MesquiteFile

Adds the passed FileElement to the file.

addFileElement(FileElement) - Method in class mesquite.lib.MesquiteProject

Adds the passed element to the project.

addGraphicsPanel(DialogGraphicsPanel) - Method in class mesquite.lib.ExtensibleDialog

addGuestModule(MesquiteModule) - Method in class mesquite.lib.MesquiteMenuSpec

addHelpButtons(Panel) - Method in class mesquite.lib.ExtensibleDialog

addHorizontalLine(int) - Method in class mesquite.lib.ExtensibleDialog

addHorizontalLine(int, int) - Method in class mesquite.lib.ExtensibleDialog

addInLinked(int, int, boolean) - Method in class mesquite.lib.characters.CharacterData

Adds characters in linked data files.

addIntegerField(String, int, int, int, int) - Method in class mesquite.lib.ExtensibleDialog

addIntegerField(String, int, int) - Method in class mesquite.lib.ExtensibleDialog

addIntegerField(String, int) - Method in class mesquite.lib.ExtensibleDialog

addInternodeEvent(int, CategInternodeEvent) - Method in class mesquite.categ.lib.CategoricalHistory

addItem(NameReference) - Method in class mesquite.cont.lib.ContinuousAdjustable

addItem(String) - Method in class mesquite.cont.lib.ContinuousAdjustable

addItem(String) - Method in class mesquite.cont.lib.ContinuousData

Make an item with the passed name.

addItem(NameReference) - Method in class mesquite.cont.lib.MContinuousAdjustable

addItem(String) - Method in class mesquite.cont.lib.MContinuousAdjustable

addItem(String, MesquiteModule, MesquiteCommand, String) - Method in class mesquite.lib.MesquitePopup

addItem(String, MesquiteCommand, String) - Method in class mesquite.lib.MesquitePopup

addItem(String, MesquiteModule, MesquiteCommand) - Method in class mesquite.lib.MesquitePopup

addItems(String[], MesquiteModule[], MesquiteCommand[]) - Method in class mesquite.lib.MesquitePopup

addItemToSubmenu(MesquiteMenuSpec, MesquiteSubmenuSpec, String, MesquiteCommand) - Method in class mesquite.lib.MenuOwner

Adds a menu item to the given submenu of the given menu.

addItemToSubmenu(MesquiteMenuSpec, MesquiteSubmenuSpec, MesquiteMenuItemSpec) - Method in class mesquite.lib.MenuOwner

Adds a menu item to the given submenu of the given menu.

additionalDoCommands(String, String, CommandChecker) - Method in class mesquite.trees.lib.ManyTreesFromFileLib

additionalSnapshot(Snapshot) - Method in class mesquite.trees.lib.ManyTreesFromFileLib

additionalText(Taxa) - Method in class mesquite.lib.TaxaDisplayExtra

return any additional explanatory text, e.g.

additionalText(Tree, int) - Method in class mesquite.lib.TreeDecorator

additionalText(Tree, int) - Method in class mesquite.lib.TreeDisplayExtra

return any additional explanatory text, e.g.

additionStartJobItems() - Method in class mesquite.trees.lib.ManyTreesFromFileLib

addKeyListener(MesquiteWindow, KeyListener) - Static method in class mesquite.lib.MesquiteWindow

addKeyListener(MesquiteWindow, KeyListener, boolean) - Static method in class mesquite.lib.MesquiteWindow

addKeyListenerToAll(Component, KeyListener, boolean) - Static method in class mesquite.lib.MesquiteWindow

addLabel(ImageLabel) - Method in class mesquite.lib.AttachedNote

addLabel(String, int, boolean, boolean) - Method in class mesquite.lib.ExtensibleDialog

addLabel(String, int, boolean) - Method in class mesquite.lib.ExtensibleDialog

addLabel(String) - Method in class mesquite.lib.ExtensibleDialog

addLabel(String, int) - Method in class mesquite.lib.ExtensibleDialog

addLargeOrSmallTextLabel(String) - Method in class mesquite.lib.ExtensibleDialog

addLargeTextLabel(String, Font) - Method in class mesquite.lib.ExtensibleDialog

addLargeTextLabel(String) - Method in class mesquite.lib.ExtensibleDialog

addLedgePanel(MousePanel, int) - Method in class mesquite.lib.ContentArea

addLedgePanel(MousePanel, int) - Method in class mesquite.lib.MesquiteWindow

requests that a ledge panel be added to main graphics panel

addLine(String) - Method in class mesquite.lib.LightLabel

addLine(String) - Method in class mesquite.lib.MesquiteLabel

addLine(String, MesquiteModule) - Method in class mesquite.lib.Snapshot

Add the given command to the list of commands.

addLine(String) - Method in class mesquite.lib.Snapshot

Add the given command to the list of commands.

addLineEndPopUpPanel() - Method in class mesquite.lib.ExporterDialog

addLineIfAnythingToTell(String, MesquiteModule) - Method in class mesquite.lib.Snapshot

Add command if there is any snapshot from module

addLineToSubmenu(MesquiteMenuSpec, MesquiteSubmenuSpec) - Method in class mesquite.lib.MenuOwner

Adds a dividing line to the given submenu of the given menu.

addList(Object, MesquiteInteger, String) - Method in class mesquite.lib.ExtensibleDialog

addListAndButtons() - Method in class mesquite.lib.ExtensibleListDialog

addListAssistant(ListAssistant) - Method in class mesquite.lists.lib.ListWindow

addListener(MesquiteListener) - Method in interface mesquite.lib.Listenable

adds a listener to notify if the element changes

addListener(MesquiteListener) - Method in class mesquite.lib.Listened

adds a listener to notify if the element changes

addListenerHighPriority(MesquiteListener) - Method in interface mesquite.lib.Listenable

adds a listener to notify if the element changes; add to start of listener vector so it will be notified early

addListenerHighPriority(MesquiteListener) - Method in class mesquite.lib.Listened

adds a listener to notify if the element changes

addLongField(String, long, int) - Method in class mesquite.lib.ExtensibleDialog

addMacro(MesquiteMacro) - Method in class mesquite.lib.MesquiteModuleInfo

addMenuItem(String, MesquiteCommand) - Method in class mesquite.lib.MenuOwner

Adds a menu item to the module's containing menu.

addMenuItem(MesquiteMenuSpec, String, MesquiteCommand) - Method in class mesquite.lib.MenuOwner

Adds a menu item to the given menu.

addMenuItem(MesquiteMenuSpec, MesquiteMenuItemSpec) - Method in class mesquite.lib.MenuOwner

Adds a menu item to the given menu..

addMenuLine() - Method in class mesquite.lib.MenuOwner

Adds a dividing line to the module's containing menu.

addModel(CharacterModel) - Method in class mesquite.lib.characters.CentralModelListener

addModelOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.ProbSubModel

addModuleMenuItems(MesquiteMenuSpec, MesquiteCommand, Class) - Method in class mesquite.lib.MenuOwner

Adds a series of menu items, one for each of the modules belonging to the given dutyClass, to a menu.

addNewButtonBesideList(String) - Method in class mesquite.lib.ExtensibleListDialog

addNewCard(String) - Method in class mesquite.lib.PanelOfCards

addNewDialogPanel(Panel, GridBagConstraints) - Method in class mesquite.lib.ExtensibleDialog

addNewDialogPanel() - Method in class mesquite.lib.ExtensibleDialog

addNewDialogPanel(Panel) - Method in class mesquite.lib.ExtensibleDialog

addNewDialogPanel(GridBagConstraints) - Method in class mesquite.lib.ExtensibleDialog

addNewElement(Listable, String) - Method in class mesquite.lib.ExtensibleListDialog

addNEXUSBlock(NexusBlock) - Method in class mesquite.lib.MesquiteModule

Adds NEXUS block to the file.

addNexusBlock(NexusBlock) - Method in class mesquite.lib.MesquiteProject

Adds the passed NEXUS block to the project.

addNormalHorizontalLine(int) - Method in class mesquite.lib.ExtensibleDialog

addNote(AttachedNote, boolean) - Method in class mesquite.lib.AttachedNotesVector

addNoteFirst(AttachedNote, boolean) - Method in class mesquite.lib.AttachedNotesVector

addOneTaxon() - Method in class mesquite.lib.TaxaDrawing

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.CharRatesCodePos

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.CharRatesEqual

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.CharRatesGamma

adds items to extensible dialog box used for setting parameter values

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.CharRatesGammaInvar

adds items to extensible dialog box used for setting parameter values

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.CharRatesInvar

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.CompositProbCategModel

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.ProbSubModel

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.RateMatrixEqualDNAModel

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.RateMatrixGTRModel

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.RateMatrixTiTvModel

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.StateFreqDNAEmpir

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.StateFreqDNAEqual

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.StateFreqDNASpecif

addOptions(ExtensibleDialog) - Method in class mesquite.genesis.lib.StateFreqUserModel

addOptionsOnCards(ExtensibleDialog) - Method in class mesquite.genesis.lib.CompositProbCategModel

addPage(MesquiteWindow) - Method in class mesquite.lib.MesquiteFrame

addPanelPlease(Panel) - Method in class mesquite.lib.ChartExtra

addPanelPlease(Panel) - Method in class mesquite.lib.MesquiteChart

addPanelPlease(Panel) - Method in class mesquite.lib.TaxaDisplayExtra

addPanelPlease(Panel) - Method in class mesquite.lib.TaxaTreeDisplay

addPanelPlease(Panel) - Method in class mesquite.lib.TreeDisplayExtra

addParts(int, int) - Method in class mesquite.categ.lib.CategoricalData

Adds num characters after position "starting"; returns true iff successful.

addParts(int, int) - Method in class mesquite.categ.lib.MolecularData

Adds num characters after position "starting".

addParts(int, int) - Method in class mesquite.cont.lib.ContinuousData

Adds num characters after position "starting"; returns true iff successful.

addParts(int, int) - Method in class mesquite.lib.Associable

addParts(int, int) - Method in class mesquite.lib.AssociableWithSpecs

addParts(int, int) - Method in class mesquite.lib.Bits

Inserts num (cleared) bits just after bit "starting"

addParts(boolean[], int, int) - Static method in class mesquite.lib.Bits

Inserts num (cleared) bits just after bit "starting"

addParts(int, int) - Method in class mesquite.lib.BitsSpecsSet

Add num parts just after "starting" (filling with default values)

addParts(int, int) - Method in class mesquite.lib.characters.CharacterData

Adds num characters after position "starting".

addParts(int, int) - Method in interface mesquite.lib.characters.CharSpecsSet

Add num characters just after "starting" (filling with default values)

addParts(int, int) - Method in class mesquite.lib.characters.CodonPositionsSet

Add num parts just after "starting" (filling with default values)

addParts(int, int) - Method in class mesquite.lib.DoubleArray

addParts(double[], int, int) - Static method in class mesquite.lib.DoubleArray

addParts(int, int) - Method in class mesquite.lib.IntegerArray

addParts(int[], int, int) - Static method in class mesquite.lib.IntegerArray

addParts(int, int, long) - Method in class mesquite.lib.LongArray

addParts(long[], int, int, long) - Static method in class mesquite.lib.LongArray

addParts(int, int) - Method in class mesquite.lib.NumberArray

addParts(int, int) - Method in class mesquite.lib.NumSpecsSet

Add num parts just after "starting" (filling with default values)

addParts(int, int) - Method in class mesquite.lib.ObjectArray

addParts(Object[], int, int) - Static method in class mesquite.lib.ObjectArray

addParts(int, int) - Method in class mesquite.lib.ObjectSpecsSet

Add num characters just after "starting" (filling with default values)

addParts(int, int, short) - Method in class mesquite.lib.ShortArray

addParts(short[], int, int, short) - Static method in class mesquite.lib.ShortArray

addParts(int, int) - Method in class mesquite.lib.SpecsSet

Add num parts just after "starting" (filling with default values)

addParts(int, int) - Method in class mesquite.lib.StringArray

addParts(String[], int, int) - Static method in class mesquite.lib.StringArray

addParts(int, int) - Method in class mesquite.lib.Taxa

Adds new taxa starting just after taxon "starting"

addParts(int, int) - Method in class mesquite.lib.TaxaBitsSet

Add num taxa just after "starting" (filling with default values)

addParts(int, int) - Method in interface mesquite.lib.TaxaSpecsSet

Add num taxa just after "starting" (filling with default values)

addParts(int, int) - Method in class mesquite.lib.TaxaStringsSet

Add num taxa just after "starting" (filling with default values)

addPath(TaxaPath) - Method in class mesquite.pairwise.lib.TaxaPairing

addPath(int, int, int) - Method in class mesquite.pairwise.lib.TaxaPairing

addPoint(MesquiteNumber, MesquiteNumber) - Method in class mesquite.lib.MesquiteChart

addPoint(MesquiteNumber, MesquiteNumber, MesquiteNumber) - Method in class mesquite.lib.MesquiteChart

addPopUpMenu(Label, String[], int) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenu(String, String[], int) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenu(String, String, String, String, String, int) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenu(String, Listable[], int) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenu(String, String, String, String, int) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenu(String, String, String, int) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenu(String) - Method in class mesquite.lib.ExtensibleDialog

addPopUpMenuItems() - Method in class mesquite.align.lib.BlockMover

addPopUpPanelOfCards(String) - Method in class mesquite.lib.ExtensibleDialog

addPrimaryButtonRow(String, String, String) - Method in class mesquite.lib.ExtensibleDialog

addPrimaryButtonRow(String, String) - Method in class mesquite.lib.ExtensibleDialog

addPrimaryButtonRow(String) - Method in class mesquite.lib.ExtensibleDialog

addPrimaryButtonRowListener(String, String, ActionListener) - Method in class mesquite.lib.ExtensibleDialog

addProject(MesquiteProject) - Method in class mesquite.lib.MesquiteTrunk

add a project to Mesquite's list of currently active projects

addProject(MesquiteProject) - Method in class mesquite.lib.Projects

Add project to the list of projects.

addRadioButtons(String[], int) - Method in class mesquite.lib.ExtensibleDialog

addRow() - Method in class mesquite.lists.lib.ListModule

addRows(boolean[][], int, int) - Static method in class mesquite.lib.Bits

addRows(Object[][], int, int) - Static method in class mesquite.lib.Object2DArray

addRows(String[][], int, int) - Static method in class mesquite.lib.StringArray

addRows(int) - Method in class mesquite.lists.lib.ListWindow

addRowsNotify(int, int) - Method in class mesquite.lists.lib.ListWindow

addSidePanel(MousePanel, int) - Method in class mesquite.lib.ContentArea

addSidePanel(MousePanel, int) - Method in class mesquite.lib.MesquiteWindow

requests that a side panel be added to main graphics panel

addSingleLineTextArea(String, int) - Method in class mesquite.lib.ExtensibleDialog

addSpecSet(Listable) - Method in class mesquite.lib.SpecsSetVector

Add specs set to vector

addSplash(MesquiteModuleInfo) - Method in class mesquite.lib.MesquiteTrunk

add a package splash banner to Mesquite's list of currently active packages

addStackedLabels(String, String, String, int) - Method in class mesquite.lib.ExtensibleDialog

Adds a panel with three labels closely stacked, one on top of the other.

addStackedLabels(String, String, int) - Method in class mesquite.lib.ExtensibleDialog

Adds a panel with two labels closely stacked, one on top of the other.

addStackedLabelsBottomSmall(String, String) - Method in class mesquite.lib.ExtensibleDialog

Adds a panel with two labels closely stacked, one on top of the other, with the second on in a smaller font.

addString(String) - Method in class mesquite.lib.CommandChecker

Adds a string to the vector of strings being accumulated by the checker.

addSubmenu(MesquiteMenuSpec, String) - Method in class mesquite.lib.MenuOwner

Adds a submenu of the given name.

addSubmenu(MesquiteMenuSpec, String, MesquiteCommand) - Method in class mesquite.lib.MenuOwner

Adds a submenu of the given name.

addSubmenu(MesquiteMenuSpec, String, MesquiteCommand, Class) - Method in class mesquite.lib.MenuOwner

Adds a submenu of the given name with all the modules belonging to the given dutyClass.

addSubmenu(MesquiteMenuSpec, String, MesquiteCommand, ListableVector) - Method in class mesquite.lib.MenuOwner

Adds a submenu of the given name with all the items in the ListableVector listed as items.

addSubmenu(MesquiteMenuSpec, String, MesquiteCommand, StringLister) - Method in class mesquite.lib.MenuOwner

Adds a submenu of the given name with all the items in the String array listed as items.

addSubmodelCuratorsPopup(ExtensibleDialog, Class, String) - Method in class mesquite.genesis.lib.SimulationDNAModel

addSubmodelPopup(ExtensibleDialog, ProbSubModel, Listable[], String) - Method in class mesquite.genesis.lib.SimulationDNAModel

addSubsequentThread(ProjectReadThread) - Method in class mesquite.lib.ProjectReadThread

addSumPoint(MesquiteNumber, MesquiteNumber) - Method in class mesquite.lib.MesquiteChart

addTaxa(int, int) - Method in class mesquite.categ.lib.CategoricalData

Adds num taxa after position "starting"; returns true iff successful.

addTaxa(int, int) - Method in class mesquite.categ.lib.MolecularData

Adds num taxa after position "starting"; returns true iff successful.

addTaxa(int, int) - Method in class mesquite.cont.lib.ContinuousData

Adds num taxa after position "starting"; returns true iff successful.

addTaxa(int, int) - Method in class mesquite.lib.characters.CharacterData

Adds num taxa after position "starting"; returns true iff successful.

addTaxa(int, int, boolean) - Method in class mesquite.lib.Taxa

An equivalent to addParts but with notification added.

addTaxon(boolean) - Method in class mesquite.lib.Taxa

addTextArea(String, int, Font) - Method in class mesquite.lib.ExtensibleDialog

addTextArea(String, int, int, Font, int, boolean) - Method in class mesquite.lib.ExtensibleDialog

addTextArea(String, int, int, Font) - Method in class mesquite.lib.ExtensibleDialog

addTextArea(String, int) - Method in class mesquite.lib.ExtensibleDialog

addTextAreaSmallFont(String, int, int) - Method in class mesquite.lib.ExtensibleDialog

addTextAreaSmallFont(String, int) - Method in class mesquite.lib.ExtensibleDialog

addTextAreaSmallFontNoScroll(String, int, boolean) - Method in class mesquite.lib.ExtensibleDialog

addTextField(String, String, int, boolean) - Method in class mesquite.lib.ExtensibleDialog

addTextField(String, String, int) - Method in class mesquite.lib.ExtensibleDialog

addTextField(String, int) - Method in class mesquite.lib.ExtensibleDialog

addTextField(String) - Method in class mesquite.lib.ExtensibleDialog

addToBrowserPopup(MesquitePopup) - Method in class mesquite.lib.characters.CharacterData

addToBrowserPopup(MesquitePopup) - Method in class mesquite.lib.FileElement

addToBrowserPopup(MesquitePopup) - Method in class mesquite.lib.TreeVector

addToCharBlockValues(int) - Method in class mesquite.align.lib.CellBlock

addToDefaultPunctuationString(String) - Method in class mesquite.lib.Parser

addToDialog(Component, Object) - Method in class mesquite.lib.ExtensibleDialog

addToDialog(Component) - Method in class mesquite.lib.ExtensibleDialog

addToFile(MesquiteFile, MesquiteProject, ElementManager) - Method in class mesquite.lib.characters.CharacterData

addToFile(MesquiteFile, MesquiteProject, ElementManager) - Method in class mesquite.lib.characters.StoredCharacterHistory

addToFile(MesquiteFile, MesquiteProject, ElementManager) - Method in class mesquite.lib.FileElement

Adds the element to the given file and project, and assigns it the given manager.

addToJournal(String) - Method in class mesquite.lib.Journal

addToLinkageGroup(CharacterData) - Method in class mesquite.lib.characters.CharacterData

Adds the passed Character data into this's linkage group

addTool(MesquiteTool) - Method in class mesquite.lib.MesquiteWindow

addTool(MesquiteTool) - Method in class mesquite.lib.ToolPalette

addToSet(long, int) - Static method in class mesquite.categ.lib.CategoricalState

return the result of adding state e to state set s

addToSet(long, int) - Static method in class mesquite.lib.MesquiteSet

return the result of adding state e to state set s

addToStart(String[], String) - Static method in class mesquite.lib.StringArray

addToWindow(Component) - Method in class mesquite.lib.MesquiteWindow

The method to be called to add a component for display (adds it to the graphics[0] content area)

addTreeContextListener(TreeContextListener) - Method in interface mesquite.lib.TreeContext

addValue(int, int, MesquiteNumber) - Method in class mesquite.lib.Number2DArray

Add the value in the passed MesquiteNumber to that of element i,j.

addValue(int, MesquiteNumber) - Method in class mesquite.lib.NumberArray

Add the value in the passed MesquiteNumber to that of element "index".

addWindowListener(WindowListener) - Method in class mesquite.lib.MesquiteDialog

addWindowListener(WindowListener) - Method in class mesquite.lib.MesquiteWindow

AdjustableDistribution - Interface in mesquite.lib.characters

An interface to signal that a CharacterDistribution can be changed (i.e.

AdjustableTree - Interface in mesquite.lib

This interface matches some of the basic tree changing methods of MesquiteTree.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.CategoricalDistribution

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.DNACharacterAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.DNACharacterHistory

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.DNAEmbedded

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.categ.lib.MCategoricalDistribution

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.categ.lib.MDNAAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.categ.lib.MDNAEmbedded

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.categ.lib.MDNAHistory

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.categ.lib.MProteinAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.categ.lib.MProteinHistory

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.ProteinAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.ProteinCharacterHistory

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.ProteinEmbedded

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.RNACharacterAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.categ.lib.RNACharacterHistory

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in class mesquite.cont.lib.ContinuousDistribution

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, MCharactersHistory) - Method in class mesquite.cont.lib.MContinuousDistribution

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustHistorySize(Tree, CharacterHistory) - Method in interface mesquite.lib.characters.CharacterDistribution

Adjusts the size of the passed CharacterHistory to be of the same type as this CharacterHistory and to be prepared to store states for each of the nodes of the tree.

adjustHistorySize(Tree, MCharactersHistory) - Method in interface mesquite.lib.characters.MCharactersDistribution

Adjusts the size of the passed MCharacterHistory to be of the same type as this MCharactersDistribution and to be prepared to store states for each of the nodes of the tree.

adjustingColumnWidth - Variable in class mesquite.lib.table.MesquiteTable

adjustLocation() - Method in class mesquite.lib.Legend

adjustLocation() - Method in class mesquite.lib.TreeDisplayLegend

adjustmentValueChanged(AdjustmentEvent) - Method in class mesquite.assoc.lib.SimpleTaxaList

adjustmentValueChanged(AdjustmentEvent) - Method in class mesquite.lib.MesquiteScrollbar

adjustSize(Taxa) - Method in class mesquite.categ.lib.CategoricalAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustSize(Tree) - Method in class mesquite.categ.lib.CategoricalHistory

Get the information about states occurring in this object for a legend.

adjustSize(Taxa) - Method in class mesquite.cont.lib.ContinuousAdjustable

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustSize(Tree) - Method in class mesquite.cont.lib.ContinuousHistory

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

adjustSize(Taxa) - Method in interface mesquite.lib.characters.AdjustableDistribution

Adjusts the size of this to store states for each of the terminal taxa.

adjustSize(Tree) - Method in interface mesquite.lib.characters.CharacterHistory

Adjusts the size of this to store states for each of the terminal taxa.

ALA - Static variable in class mesquite.categ.lib.ProteinData

alert(String, String, String) - Method in class mesquite.lib.MesquiteModule

Displays an alert in log; also in dialog if flag is set.

alert(String) - Method in class mesquite.lib.MesquiteModule

Displays an alert in log; also in dialog if flag is set.

AlertDialog - Class in mesquite.lib

AlertDialog() - Constructor for class mesquite.lib.AlertDialog

aligner - Variable in class mesquite.align.lib.AlignScoreForTaxonGen

AlignMatch - Class in mesquite.align.lib

AlignMatch() - Constructor for class mesquite.align.lib.AlignMatch

AlignmentHelper - Class in mesquite.align.lib

AlignmentHelper() - Constructor for class mesquite.align.lib.AlignmentHelper

AlignmentHelperLinearSpace - Class in mesquite.align.lib

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, int, int) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, boolean, int[]) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, int, int, boolean, int[]) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, boolean) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, int, int, boolean) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, boolean, boolean, int[]) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperLinearSpace(int[], int[], int, int, int[][], int, int, int, int, int, boolean, boolean, int[]) - Constructor for class mesquite.align.lib.AlignmentHelperLinearSpace

AlignmentHelperQuadraticSpace - Class in mesquite.align.lib

AlignmentHelperQuadraticSpace(int[], int[], int, int, int[][], int, int, int) - Constructor for class mesquite.align.lib.AlignmentHelperQuadraticSpace

AlignmentHelperQuadraticSpace(int[], int[], int, int, int[][], int, int, int, int, int) - Constructor for class mesquite.align.lib.AlignmentHelperQuadraticSpace

AlignScoreForTaxonGen - Class in mesquite.align.lib

AlignScoreForTaxonGen() - Constructor for class mesquite.align.lib.AlignScoreForTaxonGen

alignSequences(MCategoricalDistribution, boolean[], int, int, int, int) - Method in class mesquite.align.lib.MultipleSequenceAligner

Subclasses can override this to have access to full information about data.

alignSequences(long[][]) - Method in class mesquite.align.lib.MultipleSequenceAligner

This method is not called directly by Mesquite, but modules preferring to receive and return the information as long[][] can override this and let the previous method call it.

alignSequences(long[], long[], boolean, MesquiteNumber) - Method in class mesquite.align.lib.PairwiseAligner

This method returns a 2d-long array ([site][taxon]) representing the alignment of the passed sequences.

alignSequences(MCategoricalDistribution, int, int, int, int, boolean, MesquiteNumber) - Method in class mesquite.align.lib.PairwiseAligner

This method returns a 2d-long array ([site][taxon]) representing the alignment of the sequences identified by the "taxon" and "site" arguments.

alignSequences(MCategoricalDistribution, int, int, int, int, boolean, MesquiteNumber) - Method in class mesquite.align.lib.TwoSequenceAligner

Subclasses can override this to have access to full information about data.

alignSequences(long[], long[], boolean, MesquiteNumber, CategoricalState) - Method in class mesquite.align.lib.TwoSequenceAligner

This method is not called directly by Mesquite, but modules preferring to receive and return the information as long[][] can override this and let the previous method call it.

alignSequences(MCategoricalDistribution, int, int, int, int, boolean, MesquiteNumber, boolean, Bits) - Method in class mesquite.align.lib.TwoSequenceAlignerGaps

As a subclass of TwoSequenceAligner, the methods here have passed into them some additional arguments that ideally would be dealt with.

alignSequences(MCategoricalDistribution, int, int, int, int, boolean, MesquiteNumber) - Method in class mesquite.align.lib.TwoSequenceAlignerGaps

alignSequences(long[], long[], boolean, MesquiteNumber, CategoricalState, boolean, Bits) - Method in class mesquite.align.lib.TwoSequenceAlignerGaps

This method is not called directly by Mesquite, but modules preferring to receive and return the information as long[][] can override this and let the previous method call it.

alignSequences(long[], long[], boolean, MesquiteNumber, CategoricalState) - Method in class mesquite.align.lib.TwoSequenceAlignerGaps

AlignTool - Class in mesquite.align.lib

This subclass of TableTool is used in data windows for aligning data; adds an edgeCursor for between cells.

AlignTool(Object, String, String, String, int, int, String, int, int, String, String, MesquiteCommand, MesquiteCommand, MesquiteCommand) - Constructor for class mesquite.align.lib.AlignTool

AlignUtil - Class in mesquite.align.lib

AlignUtil() - Constructor for class mesquite.align.lib.