mesquite.lib
Class MesquiteProject

java.lang.Object
  mesquite.lib.MesquiteProject

All Implemented Interfaces:

Commandable, HNode, Listable

public class MesquiteProject

extends java.lang.Object

implements Listable, Commandable, HNode

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 interface mesquite.lib.HNode

MOUSEDOWN, MOUSEEXIT, MOUSEMOVE

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.
CharacterData	chooseData(java.awt.Frame frame, MesquiteFile file, Taxa taxa, java.lang.Object dataClass, java.lang.String message, boolean askEvenIfOne, CommandRecord commandRec)
CharacterData	chooseData(java.awt.Frame frame, MesquiteFile file, Taxa taxa, java.lang.Object dataClass, java.lang.String message, CommandRecord commandRec)
CharacterData	chooseData(java.awt.Frame frame, Taxa taxa, java.lang.Object dataClass, CommandRecord commandRec)
CharacterData	chooseData(java.awt.Frame frame, Taxa taxa, java.lang.Object dataClass, java.lang.String message, CommandRecord commandRec)
MesquiteFile	chooseFile(CommandRecord commandRec, java.lang.String message) Select one of the currently linked files; selects first if only one or if scripting.
Taxa	chooseTaxa(java.awt.Frame frame, java.lang.String message, boolean askEvenIfOne, CommandRecord commandRec)
Taxa	chooseTaxa(java.awt.Frame frame, java.lang.String message, CommandRecord commandRec)
Taxa	createTaxaBlock(int numTaxa)
void	dispose() Disposes of the components of the project.
java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandRecord commandRec, 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.
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	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 permitAltMatchingTaxa, CommandRecord commandRec, java.lang.String messageIfNoneFound, java.lang.String messageForChoice) returns a data matrix that is of the same class as that passed, but is a different one.
CharacterData	getDifferentButCompatibleMatrix(CharacterData data, boolean permitAltMatchingTaxa, CommandRecord commandRec, 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.
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
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
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()
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.
void	setHomeFile(MesquiteFile file) DOCUMENT
TreeVector	storeTree(java.awt.Frame parent, Tree tree, CommandRecord commandRec)

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

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.

finalize

public void finalize()
              throws java.lang.Throwable

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,
                                  CommandRecord commandRec,
                                  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 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(CommandRecord commandRec,
                               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

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

getTaxa

public Taxa getTaxa(int taxaNumber)

returns the Taxa of given number

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(java.awt.Frame frame,
                       java.lang.String message,
                       CommandRecord commandRec)

chooseTaxa

public Taxa chooseTaxa(java.awt.Frame frame,
                       java.lang.String message,
                       boolean askEvenIfOne,
                       CommandRecord commandRec)

getNumberTaxas

public int getNumberTaxas(MesquiteFile f)

returns the number of Taxa objects stored in project belonging to a file

getNumberTaxas

public int getNumberTaxas(java.lang.String uniqueID)

getNumberTaxas

public int getNumberTaxas()

returns the number of Taxa objects stored in project

storeTree

public TreeVector storeTree(java.awt.Frame parent,
                            Tree tree,
                            CommandRecord commandRec)

getCharacterMatrices

public ListableVector getCharacterMatrices()

returns jth data set in file

getCharacterMatrix

public CharacterData getCharacterMatrix(int j)

returns jth data set in file

getCharacterMatrix

public CharacterData getCharacterMatrix(Taxa taxa,
                                        int j)

returns the jth data set belonging to given taxa.

getCharacterMatrix

public CharacterData getCharacterMatrix(int j,
                                        java.lang.Object dataClass)

returns the jth data set for given CharacterState subclass.

getCharacterMatrix

public CharacterData getCharacterMatrix(Taxa taxa,
                                        int j,
                                        java.lang.Object dataClass)

returns the jth data set belonging to given taxa for given CharacterState subclass.

getCharacterMatrix

public CharacterData getCharacterMatrix(MesquiteFile f,
                                        int j)

returns the jth of data sets belonging to a given file

getLatestMatrix

public CharacterData getLatestMatrix()

returns most recently added matrix.

getCharacterMatrix

public CharacterData getCharacterMatrix(MesquiteFile f,
                                        Taxa taxa,
                                        java.lang.Object dataClass,
                                        int j)

returns the jth of data sets belonging to a given file

getCharacterMatrixPAMT

public 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

getCharacterMatrix

public CharacterData getCharacterMatrix(java.lang.String uniqueID,
                                        int j)

returns the jth of data sets with given unique ID

getCharacterData

public CharacterData getCharacterData(java.lang.String name)

gets the data set of given reference string (ref. number, name, number) from the project

getCharacterData

public CharacterData getCharacterData(MesquiteFile f,
                                      java.lang.String ref)

gets the data set of given reference string (ref. number, name, number) from the project

getCharacterData

public CharacterData getCharacterData(MesquiteFile f,
                                      Taxa taxa,
                                      java.lang.String ref)

gets the data set of given reference string (ref. number, name, number) from the project

getCharacterData

public CharacterData getCharacterData(MesquiteFile f,
                                      Taxa taxa,
                                      java.lang.Object dataClass,
                                      java.lang.String ref)

gets the data set of given reference string (ref. number, name, number) from the project

getDifferentButCompatibleMatrix

public CharacterData getDifferentButCompatibleMatrix(CharacterData data,
                                                     boolean permitAltMatchingTaxa,
                                                     CommandRecord commandRec,
                                                     java.lang.String messageIfNoneFound,
                                                     java.lang.String messageForChoice)

returns a data matrix that is of the same class as that passed, but is a different one.

getDifferentButCompatibleMatrix

public CharacterData getDifferentButCompatibleMatrix(CharacterData data,
                                                     boolean permitAltMatchingTaxa,
                                                     CommandRecord commandRec,
                                                     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.

getMatrixNumber

public int getMatrixNumber(java.lang.String name)

gets the number (index position) of the data set of given name.

getMatrixNumber

public int getMatrixNumber(CharacterData data)

gets the number (index position) of the data set.

getMatrixNumber

public int getMatrixNumber(MesquiteFile file,
                           CharacterData data)

gets the number (index position) of the data set.

getCharMatrixReferenceInternal

public java.lang.String getCharMatrixReferenceInternal(CharacterData data)

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

getCharMatrixReferenceExternal

public java.lang.String getCharMatrixReferenceExternal(CharacterData data)

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

getNumberCharMatrices

public int getNumberCharMatrices()

returns number of data sets in file

getNumberCharMatrices

public int getNumberCharMatrices(Taxa taxa)

returns number of data sets belonging to given taxa

getNumberCharMatrices

public 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

getNumberCharMatrices

public int getNumberCharMatrices(java.lang.Object dataClass)

returns number of data sets of a given data class (CharacterState subclass is passed)

getNumberCharMatrices

public int getNumberCharMatrices(MesquiteFile f)

returns number of data sets belonging to a given file

getNumberCharMatrices

public 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. If permitTaxaMatching is true, * considers taxa equal if names coincide

getNumberCharMatricesPAMT

public 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. If permitTaxaMatching is true, * considers taxa equal if names coincide

getNumberCharMatrices

public int getNumberCharMatrices(long ref)

returns number of data sets of given reference string (ref. number, name, number) from the project

getNumberCharMatrices

public int getNumberCharMatrices(java.lang.String uniqueID)

returns number of data sets of given reference string (ref. number, name, number) from the project

resolveCharMatrixIDs

public void resolveCharMatrixIDs()

gets the data set of given reference string (ref. number, name, number) from the project

chooseData

public CharacterData chooseData(java.awt.Frame frame,
                                Taxa taxa,
                                java.lang.Object dataClass,
                                CommandRecord commandRec)