mesquite.lib
Class MesquiteProject

java.lang.Object
  mesquite.lib.Listened
      mesquite.lib.MesquiteProject

All Implemented Interfaces:

Commandable, HNode, HTMLDescribable, Listable, Listenable, MesquiteListener

public class MesquiteProject
extends Listened
implements Listable, MesquiteListener, Commandable, HNode, HTMLDescribable

An object of this class represents a collection of information (data matrices, tree blocks, etc.) that may reside in more than one file (MesquiteFile, which represents files on disk or at a URL). More than one project can be open at once. Information from different projects generally doesn't interact (e.g., a data matrix from one project can't belong to a set of taxa from another project), but within a single project information can interact regardless of what file the information belongs to.

Although more than one file can belong to the project, the first file opened is treated as the "home file". In the future the idea of a "project" may be made stronger, and a separate sort of file (the project file) may be created. tHis would eliminate the need for a "home file".

Field Summary

MesquiteWindow	activeWindowOfProject
boolean	autosave
protected ModelVector	charModels Character models belonging to the project.
ListableVector	datas Vector of data sets (including matrix) within the project.
boolean	developing
MesquiteCommand	exportCommand
MesquiteCommand	getInfoCommand
boolean	isDoomed
MesquiteCommand	newLinkFileCommand
protected ListableVector	nexusBlocks Nexus blocks belonging to the files in the project.
protected ListableVector	otherElements Other file elements belonging to the project.
FileCoordinator	ownerModule The file coordinator module that owns this object
int	projectColor Background color scheme for project's windows
long	startupTime
ListableVector	taxas A vector of the sets of taxa within the project.
static int	totalCreated
static int	totalDisposed
static int	totalFinalized
MesquiteWindow	windowToActivate

Fields inherited from class mesquite.lib.Listened

allListeners, classes, classesNotified, listeners, listenersRemaining, notifications

Fields inherited from interface mesquite.lib.MesquiteListener

ANNOTATION_ADDED, ANNOTATION_CHANGED, ANNOTATION_DELETED, ASSOCIATED_CHANGED, BRANCHES_REARRANGED, BRANCHLENGTHS_CHANGED, COMMAND_CANCELLED, DATA_CHANGED, ELEMENT_CHANGED, ITEMS_ADDED, NAMES_CHANGED, OBJECT_DESTROYED, PARTS_ADDED, PARTS_CHANGED, PARTS_DELETED, PARTS_MOVED, SELECTION_CHANGED, TAXA_SUBSTITUTED, TEXTFIELD_EDITED, UNKNOWN, VALUE_CHANGED

Fields inherited from interface mesquite.lib.HNode

MOUSEDOWN, MOUSEEXIT, MOUSEMOVE

Fields inherited from interface mesquite.lib.HTMLDescribable

verbose

Constructor Summary

MesquiteProject(FileCoordinator ownerModule)

Method Summary

void	addFile(MesquiteFile file) add a file to list of currently linked files
void	addFileElement(FileElement element) Adds the passed element to the project.
void	addNexusBlock(NexusBlock block) Adds the passed NEXUS block to the project.
void	changed(java.lang.Object caller, java.lang.Object obj, Notification notification) passes which object changed, along with optional Notification object with details (e.g., code number (type of change) and integers (e.g.
CharacterData	chooseData(MesquiteWindow frame, MesquiteFile file, Taxa taxa, java.lang.Object dataClass, java.lang.String message)
CharacterData	chooseData(MesquiteWindow frame, MesquiteFile file, Taxa taxa, java.lang.Object dataClass, java.lang.String message, boolean askEvenIfOne)
CharacterData	chooseData(MesquiteWindow frame, Taxa taxa, java.lang.Object dataClass)
CharacterData	chooseData(MesquiteWindow frame, Taxa taxa, java.lang.Object dataClass, java.lang.String message)
MesquiteFile	chooseFile(java.lang.String message) Select one of the currently linked files; selects first if only one or if scripting.
Taxa	chooseTaxa(MesquiteWindow frame, java.lang.String message)
Taxa	chooseTaxa(MesquiteWindow frame, java.lang.String message, boolean askEvenIfOne)
Taxa	createTaxaBlock(int numTaxa)
void	dispose() Disposes of the components of the project.
void	disposing(java.lang.Object obj) passes which object was disposed
java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandChecker checker) Here as a placeholder; doesn't do anything at the moment.
void	fileSaved(MesquiteFile f) Sets elements of file as not dirty (i.e.
void	finalize()
Author	findAuthor(java.lang.String s, boolean tryName)
ListableVector	getAuthors()
CentralModelListener	getCentralModelListener()
CharacterData	getCharacterData(MesquiteFile f, java.lang.String ref) gets the data set of given reference string (ref.
CharacterData	getCharacterData(MesquiteFile f, Taxa taxa, java.lang.Object dataClass, java.lang.String ref) gets the data set of given reference string (ref.
CharacterData	getCharacterData(MesquiteFile f, Taxa taxa, java.lang.String ref) gets the data set of given reference string (ref.
CharacterData	getCharacterData(java.lang.String name) gets the data set of given reference string (ref.
CharacterData	getCharacterDataReverseOrder(MesquiteFile file, java.lang.String name) gets the data set of given reference string (ref.
CharacterData	getCharacterDataReverseOrder(MesquiteFile f, Taxa taxa, java.lang.Object dataClass, java.lang.String ref) gets the data set of given reference string (ref.
CharacterData	getCharacterDataReverseOrder(java.lang.String name) gets the data set of given reference string (ref.
ListableVector	getCharacterMatrices() returns jth data set in file
CharacterData	getCharacterMatrix(int j) returns jth data set in file
CharacterData	getCharacterMatrix(int j, java.lang.Object dataClass) returns the jth data set for given CharacterState subclass.
CharacterData	getCharacterMatrix(MesquiteFile f, int j) returns the jth of data sets belonging to a given file
CharacterData	getCharacterMatrix(MesquiteFile f, Taxa taxa, java.lang.Object dataClass, int j) returns the jth of data sets belonging to a given file
CharacterData	getCharacterMatrix(java.lang.String uniqueID, int j) returns the jth of data sets with given unique ID
CharacterData	getCharacterMatrix(Taxa taxa, int j) returns the jth data set belonging to given taxa.
CharacterData	getCharacterMatrix(Taxa taxa, int j, java.lang.Object dataClass) returns the jth data set belonging to given taxa for given CharacterState subclass.
CharacterData	getCharacterMatrixByID(long id) returns jth data set in file
CharacterData	getCharacterMatrixPAMT(Taxa taxa, java.lang.Object dataClass, int j) returns the jth of data sets belonging to a given file*, permitting matrices with different but equivalent taxa
CharacterModel	getCharacterModel(java.lang.Class c, boolean allowBuiltIn, int index) returns the index'th character model that is a subclass of c.
CharacterModel	getCharacterModel(java.lang.Class c, int index) returns the index'th character model that is a subclass of c.
CharacterModel	getCharacterModel(int index) returns the index'th character model.
CharacterModel	getCharacterModel(ModelCompatibilityInfo mci, int index) returns the index'th character model that is a subclass of c.
CharacterModel	getCharacterModel(ModelCompatibilityInfo mci, java.lang.String name) returns the character model of name "name' that is a subclass of c.
CharacterModel	getCharacterModel(java.lang.String name) returns the character model with the given name
ModelVector	getCharacterModels() returns the vector of stored character models
Listable[]	getCharacterModels(java.lang.Class c, java.lang.Class stateClass) returns a vector of stored character models that are subclasses of the given class
Listable[]	getCharacterModels(ModelCompatibilityInfo mci, java.lang.Class stateClass) returns a vector of stored character models that are compatible with the passed information
java.lang.String	getCharMatrixReferenceExternal(CharacterData data) returns a string that can be used to refer to taxa block
java.lang.String	getCharMatrixReferenceInternal(CharacterData data) returns a string that can be used to refer to taxa block
MesquiteCommand	getCloseCommand() returns command to close a file
MesquiteCommand	getCloseFilesCommand() returns command to close project (linked files)
Listable[]	getCompatibleFileElements(java.lang.Class c, java.lang.Object condition) Returns a vector of FileElements that are of the given class or are of its subclasses, and which are compatible with the passed object.
FileCoordinator	getCoordinatorModule() returns the file coordinator module in charge of the project
CharacterData	getDifferentButCompatibleMatrix(CharacterData data, boolean permitOtherTaxa, java.lang.String messageIfNoneFound, java.lang.String messageForChoice, boolean subclassOK) returns a data matrix that is of the same class as that passed, but is a different one.
FileElement	getElementByID(java.lang.Class c, int id) Returns the number of FileElements that are subclasses of the given class.
MesquiteFile	getFile(int num) returns a currently linked file
MesquiteFile	getFile(java.lang.String name) returns a currently linked file
MesquiteFile	getFileByID(int id) returns a currently linked file
FileElement	getFileElement(java.lang.Class c, int i) Returns the ith FileElement that is a subclass of the given class.
int	getFileElementNumber(FileElement f, java.lang.Class c) Returns the index position of the FileElement among others of its the subclass c.
Listable[]	getFileElements(java.lang.Class c) Returns a vector of FileElements that are of the given class or are of its subclasses.
int	getFileNumber(MesquiteFile f) returns the index of a currently linked file
ListableVector	getFiles() returns currently linked files
MesquiteFrame	getFrame()
java.awt.Color	getHColor()
HNode[]	getHDaughters() for HNode interface
java.awt.Image	getHImage()
HNode	getHMother() for HNode interface
java.lang.String	getHomeDirectoryName() Returns name of directory of home file.
MesquiteFile	getHomeFile() DOCUMENT
java.lang.String	getHomeFileName() Returns name of home file.
java.net.URL	getHomeURL() DOCUMENT
boolean	getHShow()
long	getID() instantiations of projects are numbered sequentially so they can be referred to by number
MesquiteCommand	getIncludeFileCommand() returns command to incorporate file
MesquiteCommand	getIncludeURLCommand() returns command to incorporate file
CharacterData	getLatestMatrix() returns most recently added matrix.
MesquiteCommand	getLinkFileCommand() returns command to link file
MesquiteCommand	getLinkURLCommand() returns command to link file
int	getMatrixNumber(CharacterData data) gets the number (index position) of the data set.
int	getMatrixNumber(MesquiteFile file, CharacterData data) gets the number (index position) of the data set.
int	getMatrixNumber(java.lang.String name) gets the number (index position) of the data set of given name.
java.lang.String	getName() Returns the name of the project.
MesquiteCommand	getNewLinkFileCommand() returns command to make new linked file
ListableVector	getNexusBlocks() Returns the ListableVector of NEXUS blocks in the project.
NexusBlock[]	getNexusBlocks(java.lang.Class c, MesquiteFile f) Returns an array of NEXUS blocks of the given type and belonging to the given file.
NexusBlock[]	getNexusBlocks(java.lang.String typeName) Returns an array of NEXUS blocks of the given type name.
int	getNumberCharMatrices() returns number of data sets in file
int	getNumberCharMatrices(long ref) returns number of data sets of given reference string (ref.
int	getNumberCharMatrices(MesquiteFile f) returns number of data sets belonging to a given file
int	getNumberCharMatrices(MesquiteFile file, Taxa taxa, java.lang.Object dataClass) returns number of data sets of a given data class (CharacterState subclass is passed) belonging to given taxa.
int	getNumberCharMatrices(java.lang.Object dataClass) returns number of data sets of a given data class (CharacterState subclass is passed)
int	getNumberCharMatrices(java.lang.String uniqueID) returns number of data sets of given reference string (ref.
int	getNumberCharMatrices(Taxa taxa) returns number of data sets belonging to given taxa
int	getNumberCharMatrices(Taxa taxa, java.lang.Object dataClass) returns number of data sets of a given data class (CharacterState subclass is passed) belonging to given taxa
int	getNumberCharMatricesPAMT(Taxa taxa, java.lang.Object dataClass) returns number of data sets of a given data class (CharacterState subclass is passed) belonging to given taxa.
int	getNumberLinkedFiles() returns number of currently linked files
int	getNumberOfFileElements(java.lang.Class c) Returns the number of FileElements that are subclasses of the given class.
int	getNumberTaxas() returns the number of Taxa objects stored in project
int	getNumberTaxas(MesquiteFile f) returns the number of Taxa objects stored in project belonging to a file
int	getNumberTaxas(java.lang.String uniqueID)
int	getNumModels() returns the number of character models stored
int	getNumSupplements() for HNode interface
int	getProjectColor() Returns the background color scheme for the project's windows.
MesquiteCommand	getSaveAsCommand() returns command to save as
MesquiteCommand	getSaveCommand() returns command to save a file
MesquiteCommand	getSaveFilesCommand() returns command to save project (linked files)
MesquiteCommand	getSaveLinkagesCommand() returns command to save as project (linked files)
java.lang.String	getSupplementName(int index) for HNode interface
Taxa	getTaxa(int taxaNumber) returns the Taxa of given number
Taxa	getTaxa(MesquiteFile f, int taxaNumber) returns the Taxa of given number belonging to given file
Taxa	getTaxa(MesquiteFile f, java.lang.String ref) returns the Taxa of given reference, name or number (as indicated by string passed)
Taxa	getTaxa(java.lang.String name) returns the Taxa of given name
Taxa	getTaxa(java.lang.String uniqueID, int j) returns the jth of taxa blocks with given unique ID
Taxa	getTaxaByID(long id) returns the Taxa with given id number
Taxa	getTaxaLastFirst(MesquiteFile f, java.lang.String ref) returns the Taxa of given reference, name or number (as indicated by string passed)
Taxa	getTaxaLastFirst(java.lang.String name) returns the Taxa of given name
int	getTaxaNumber(MesquiteFile file, Taxa taxa) returns the number (index position) of the Taxa
int	getTaxaNumber(java.lang.String name) returns the number (index position) of the Taxa of given name
int	getTaxaNumber(Taxa taxa) returns the number (index position) of the Taxa
java.lang.String	getTaxaReference(Taxa taxa) This is deprecated and should be avoided
java.lang.String	getTaxaReferenceExternal(Taxa taxa) returns a string that can be used to refer to taxa block
java.lang.String	getTaxaReferenceInternal(Taxa taxa) returns a string that can be used to refer to taxa block
ListableVector	getTaxas() returns the list of Taxa
java.lang.String	getTypeName() for HNode interface
int	getWhichCharacterModel(ModelCompatibilityInfo mci, CharacterModel model) returns the index of the passed character model among compatible models.
void	hNodeAction(java.awt.Container c, int x, int y, int action) for HNode interface
void	hSupplementTouched(int index) for HNode interface
boolean	isDirty() returns whether any files are dirty
void	mergeFile(MesquiteFile file) Puts all file elements belonging to passed file into home file, and gets rid of record of file.
int	numAuthors()
boolean	okToDispose(java.lang.Object obj, int queryUser) Asks whether it's ok to delete the object as far as the listener is concerned (e.g., is it in use?)
void	refreshProjectWindow()
void	removeFile(MesquiteFile file) remove a file from list of currently linked files
void	removeFileElement(FileElement element) DOCUMENT
void	removeNexusBlock(NexusBlock block) Removes the passed NEXUS block from the project.
void	removeNexusBlocks(MesquiteFile f) Returns those NEXUS blocks belonging to the given file.
void	resolveCharMatrixIDs() gets the data set of given reference string (ref.
java.lang.String	searchData(java.lang.String s, MesquiteString commandResult)
void	setFrame(MesquiteFrame f)
void	setHomeFile(MesquiteFile file) DOCUMENT
TreeVector	storeTree(MesquiteWindow parent, Tree tree)
java.lang.String	toHTMLStringDescription()

Methods inherited from class mesquite.lib.Listened

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, doAfterNotify, getRemainingListeners, incrementNotifySuppress, listListeners, notifyDisposing, notifyListeners, notifyListeners, removeListener, reportListeners, setDumpNotified

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

taxas

public ListableVector taxas

A vector of the sets of taxa within the project.

datas

public ListableVector datas

Vector of data sets (including matrix) within the project.

charModels

protected ModelVector charModels

Character models belonging to the project.

otherElements

protected ListableVector otherElements

Other file elements belonging to the project.

nexusBlocks

protected ListableVector nexusBlocks

Nexus blocks belonging to the files in the project.

startupTime

public long startupTime

windowToActivate

public MesquiteWindow windowToActivate

activeWindowOfProject

public MesquiteWindow activeWindowOfProject

exportCommand

public MesquiteCommand exportCommand

newLinkFileCommand

public MesquiteCommand newLinkFileCommand

getInfoCommand

public MesquiteCommand getInfoCommand

ownerModule

public FileCoordinator ownerModule

The file coordinator module that owns this object

projectColor

public int projectColor

Background color scheme for project's windows

totalCreated

public static int totalCreated

totalDisposed

public static int totalDisposed

totalFinalized

public static int totalFinalized

developing

public boolean developing

autosave

public boolean autosave

isDoomed

public boolean isDoomed

Constructor Detail

MesquiteProject

public MesquiteProject(FileCoordinator ownerModule)

Method Detail

refreshProjectWindow

public void refreshProjectWindow()

toHTMLStringDescription

public java.lang.String toHTMLStringDescription()

Specified by:

toHTMLStringDescription in interface HTMLDescribable

searchData

public java.lang.String searchData(java.lang.String s,
                                   MesquiteString commandResult)

setFrame

public void setFrame(MesquiteFrame f)

getFrame

public MesquiteFrame getFrame()

getID

public long getID()

instantiations of projects are numbered sequentially so they can be referred to by number

dispose

public void dispose()

Disposes of the components of the project.

Overrides:

dispose in class Listened

finalize

public void finalize()
              throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable

isDirty

public boolean isDirty()

returns whether any files are dirty

doCommand

public java.lang.Object doCommand(java.lang.String commandName,
                                  java.lang.String arguments,
                                  CommandChecker checker)

Here as a placeholder; doesn't do anything at the moment.

Specified by:

doCommand in interface Commandable

getProjectColor

public int getProjectColor()

Returns the background color scheme for the project's windows. This is 0, unless multiple projects are open simultaneously, in which case other colors are used as well (to distinguish windows belonging to different projects).

getHomeDirectoryName

public java.lang.String getHomeDirectoryName()

Returns name of directory of home file.

getHomeFileName

public java.lang.String getHomeFileName()

Returns name of home file.

getName

public java.lang.String getName()

Returns the name of the project. Currently (temporarily?), the name is based upon the name of the home file.

Specified by:

getName in interface HNode

Specified by:

getName in interface Listable

getHomeURL

public java.net.URL getHomeURL()

DOCUMENT

setHomeFile

public void setHomeFile(MesquiteFile file)

DOCUMENT

getHomeFile

public MesquiteFile getHomeFile()

DOCUMENT

addFile

public void addFile(MesquiteFile file)

add a file to list of currently linked files

removeFile

public void removeFile(MesquiteFile file)

remove a file from list of currently linked files

mergeFile

public void mergeFile(MesquiteFile file)

Puts all file elements belonging to passed file into home file, and gets rid of record of file.

getNumberLinkedFiles

public int getNumberLinkedFiles()

returns number of currently linked files

getFileNumber

public int getFileNumber(MesquiteFile f)

returns the index of a currently linked file

getFile

public MesquiteFile getFile(java.lang.String name)

returns a currently linked file

getFile

public MesquiteFile getFile(int num)

returns a currently linked file

getFileByID

public MesquiteFile getFileByID(int id)

returns a currently linked file

getFiles

public ListableVector getFiles()

returns currently linked files

chooseFile

public MesquiteFile chooseFile(java.lang.String message)

Select one of the currently linked files; selects first if only one or if scripting. 12 Jan 02

getCloseCommand

public MesquiteCommand getCloseCommand()

returns command to close a file

getCloseFilesCommand

public MesquiteCommand getCloseFilesCommand()

returns command to close project (linked files)

getSaveCommand

public MesquiteCommand getSaveCommand()

returns command to save a file

getSaveFilesCommand

public MesquiteCommand getSaveFilesCommand()

returns command to save project (linked files)

getLinkFileCommand

public MesquiteCommand getLinkFileCommand()

returns command to link file

getNewLinkFileCommand

public MesquiteCommand getNewLinkFileCommand()

returns command to make new linked file

getLinkURLCommand

public MesquiteCommand getLinkURLCommand()

returns command to link file

getIncludeFileCommand

public MesquiteCommand getIncludeFileCommand()

returns command to incorporate file

getIncludeURLCommand

public MesquiteCommand getIncludeURLCommand()

returns command to incorporate file

getSaveAsCommand

public MesquiteCommand getSaveAsCommand()

returns command to save as

getSaveLinkagesCommand

public MesquiteCommand getSaveLinkagesCommand()

returns command to save as project (linked files)

getCoordinatorModule

public FileCoordinator getCoordinatorModule()

returns the file coordinator module in charge of the project

changed

public void changed(java.lang.Object caller,
                    java.lang.Object obj,
                    Notification notification)

passes which object changed, along with optional Notification object with details (e.g., code number (type of change) and integers (e.g. which character))

Specified by:

changed in interface MesquiteListener

disposing

public void disposing(java.lang.Object obj)

passes which object was disposed

Specified by:

disposing in interface MesquiteListener

okToDispose

public boolean okToDispose(java.lang.Object obj,
                           int queryUser)

Asks whether it's ok to delete the object as far as the listener is concerned (e.g., is it in use?)

Specified by:

okToDispose in interface MesquiteListener

addFileElement

public void addFileElement(FileElement element)

Adds the passed element to the project.

removeFileElement

public void removeFileElement(FileElement element)

DOCUMENT

getNumberOfFileElements

public int getNumberOfFileElements(java.lang.Class c)

Returns the number of FileElements that are subclasses of the given class.

fileSaved

public void fileSaved(MesquiteFile f)

Sets elements of file as not dirty (i.e. saved).

getFileElements

public Listable[] getFileElements(java.lang.Class c)

Returns a vector of FileElements that are of the given class or are of its subclasses.

getCompatibleFileElements

public Listable[] getCompatibleFileElements(java.lang.Class c,
                                            java.lang.Object condition)

Returns a vector of FileElements that are of the given class or are of its subclasses, and which are compatible with the passed object.

getFileElement

public FileElement getFileElement(java.lang.Class c,
                                  int i)

Returns the ith FileElement that is a subclass of the given class.

getFileElementNumber

public int getFileElementNumber(FileElement f,
                                java.lang.Class c)

Returns the index position of the FileElement among others of its the subclass c.

addNexusBlock

public void addNexusBlock(NexusBlock block)

Adds the passed NEXUS block to the project.

removeNexusBlock

public void removeNexusBlock(NexusBlock block)

Removes the passed NEXUS block from the project.

removeNexusBlocks

public void removeNexusBlocks(MesquiteFile f)

Returns those NEXUS blocks belonging to the given file.

getNexusBlocks

public NexusBlock[] getNexusBlocks(java.lang.Class c,
                                   MesquiteFile f)

Returns an array of NEXUS blocks of the given type and belonging to the given file.

getNexusBlocks

public NexusBlock[] getNexusBlocks(java.lang.String typeName)

Returns an array of NEXUS blocks of the given type name. 12 Jan 02

getNexusBlocks

public ListableVector getNexusBlocks()

Returns the ListableVector of NEXUS blocks in the project.

getAuthors

public ListableVector getAuthors()

numAuthors

public int numAuthors()

findAuthor

public Author findAuthor(java.lang.String s,
                         boolean tryName)

createTaxaBlock

public Taxa createTaxaBlock(int numTaxa)

getTaxas

public ListableVector getTaxas()

returns the list of Taxa

getElementByID

public FileElement getElementByID(java.lang.Class c,
                                  int id)

Returns the number of FileElements that are subclasses of the given class.

getTaxa

public Taxa getTaxa(int taxaNumber)

returns the Taxa of given number

getTaxaByID

public Taxa getTaxaByID(long id)

returns the Taxa with given id number

getTaxaLastFirst

public Taxa getTaxaLastFirst(java.lang.String name)

returns the Taxa of given name

getTaxaLastFirst

public Taxa getTaxaLastFirst(MesquiteFile f,
                             java.lang.String ref)

returns the Taxa of given reference, name or number (as indicated by string passed)

getTaxa

public Taxa getTaxa(java.lang.String name)

returns the Taxa of given name

getTaxa

public Taxa getTaxa(MesquiteFile f,
                    java.lang.String ref)

returns the Taxa of given reference, name or number (as indicated by string passed)

getTaxa

public Taxa getTaxa(java.lang.String uniqueID,
                    int j)

returns the jth of taxa blocks with given unique ID

getTaxa

public Taxa getTaxa(MesquiteFile f,
                    int taxaNumber)

returns the Taxa of given number belonging to given file

getTaxaNumber

public int getTaxaNumber(java.lang.String name)

returns the number (index position) of the Taxa of given name

getTaxaNumber

public int getTaxaNumber(MesquiteFile file,
                         Taxa taxa)

returns the number (index position) of the Taxa

getTaxaNumber

public int getTaxaNumber(Taxa taxa)

returns the number (index position) of the Taxa

getTaxaReferenceInternal

public java.lang.String getTaxaReferenceInternal(Taxa taxa)

returns a string that can be used to refer to taxa block

getTaxaReferenceExternal

public java.lang.String getTaxaReferenceExternal(Taxa taxa)

returns a string that can be used to refer to taxa block

getTaxaReference

public java.lang.String getTaxaReference(Taxa taxa)

This is deprecated and should be avoided

chooseTaxa

public Taxa chooseTaxa(MesquiteWindow frame,
                       java.lang.String message)

chooseTaxa

public Taxa chooseTaxa(MesquiteWindow frame,
                       java.lang.String message,
                       boolean askEvenIfOne)

getNumberTaxas

public int getNumberTaxas(