mesquite.categ.lib
Class CategoricalData

java.lang.Object
  mesquite.lib.Listened
      mesquite.lib.Attachable
          mesquite.lib.Associable
              mesquite.lib.AssociableWithSpecs
                  mesquite.lib.FileElement
                      mesquite.lib.characters.CharacterData
                          mesquite.categ.lib.CategoricalData

All Implemented Interfaces:

Annotatable, Commandable, CompatibilityChecker, Doomable, Explainable, FileDirtier, HNode, HTMLDescribable, Identifiable, Listable, Listenable, MesquiteListener, Renamable, Selectionable, Showable, StringLister

Direct Known Subclasses:

MolecularData

public class CategoricalData
extends CharacterData

A subclass of CharacterData for data stored as Categorical sets (e.g, "{0, 2}"). Associated with the CharacterState subclass CategoricalState.

Field Summary

protected static char	ANDseparator
protected static char[]	defaultSymbols
protected static char	ORseparator
protected java.lang.String	puncString
protected char[]	symbols

Fields inherited from class mesquite.lib.characters.CharacterData

COMMENT, defaultInapplicableChar, defaultInventUniqueIDs, defaultMatchChar, defaultMissingChar, defaultRequireChangeAuthority, defaultSaveChangeHistory, EOL, ERROR, interleaved, interleavedLength, inventUniqueIDs, linkedDatas, matrixManager, nAdd, nDel, nMove, numChars, numTaxa, OK, OUTOFBOUNDS, requireChangeAuthority, saveChangeHistory, suppressChecksum, totalCreated, totalDisposed

Fields inherited from class mesquite.lib.FileElement

assignedIDNumber, assignedIDString, classesCreated, classesFinalized, countsOfClasses, countsOfClassesDisposed, DIRTY, disposed, doomed, IN_USE, name, totalFinalized

Fields inherited from class mesquite.lib.AssociableWithSpecs

SPECSSET_CHANGED

Fields inherited from class mesquite.lib.Associable

comment, comments, numParts, rememberDefaultOrder, selected, versionNumber

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

CategoricalData(CharMatrixManager manager, int numTaxa, int numChars, Taxa taxa)

Method Summary

boolean	addParts(int starting, int num) Adds num characters after position "starting"; returns true iff successful.
boolean	addTaxa(int starting, int num) Adds num taxa after position "starting"; returns true iff successful.
long	calculateChecksum(java.util.zip.CRC32 crc32)
long	calculateDataChecksum(int icStart, int icEnd, int itStart, int itEnd, java.util.zip.CRC32 crc32)
CharacterData	cloneData() clone this CharacterData and return new copy.
void	copyData(CharacterData sourceData) copy the basic data.
boolean	deleteParts(int starting, int num) Deletes num characters from position "starting"; returns true iff successful.
boolean	deleteTaxa(int starting, int num) Deletes num taxa from position "starting"; returns true iff successful.
void	dispose() Deletes the file element.
void	equalizeCharacter(CharacterData oData, int oic, int ic)
void	examineCheckSum(int icStart, int icEnd, int itStart, int itEnd, java.lang.String warning, MesquiteBoolean warnCheckSum, long originalCheckSum)
static DefaultReference	findDefaultReference(NameReference paradigm)
long	fromChar(char state) Given a character, what state set is implied.
long	fromString(int ic, Parser parser, boolean fromEditor, MesquiteInteger resultCode, MesquiteString result) Set the state at character ic from the string s, beginning at position pos in the string.
long	getAllStates(int ic) returns the set of states in character ic
long[]	getCharacter(int ic) extract character ic and return as an array of long's
CharacterDistribution	getCharacterDistribution(int ic) return a CharacterDistribution that points to character ic
CharacterState	getCharacterState(CharacterState cs, int ic, int it) returns the state of character ic in taxon it
java.awt.Color	getColorOfState(int ic, int istate) Returns the color for the given state of character ic.
java.awt.Color	getColorOfState(int ic, int istate, int maxState) returns Color for state of character, scaled to maxState (e.g.
java.awt.Color	getColorOfState(int ic, int istate, int maxState, MesquiteColorTable colors) returns Color for state of character, scaled to maxState (e.g.
java.awt.Color	getColorOfStates(int ic, int it) Gets the color representing state(s) of character ic in taxon it
java.lang.String	getDataTypeName() returns the name of the type of data stored
CharacterModel	getDefaultModel(java.lang.String paradigm) returns the default character model for the paradigm (e.g., "parsimony") given in the String
long	getDefaultState()
static java.lang.String	getDefaultStateSymbol(java.lang.Class dataClass, int state) gets state symbol for state "state", returned as string.
static java.lang.String	getDefaultStateSymbol(int state) gets state symbol for state "state", returned as string.
double[]	getFrequencies(boolean includeAmbiguous, boolean ambiguousBasedOnFreq, int it1, int it2) returns the maximum possible state
long[]	getLongArray(int icStart, int length, int it, boolean includeGaps) returns an array of longs for the cells in taxon it, starting at character icStart, for length "length"
int	getMaxPossibleState() returns the maximum possible state
int	getMaxState() returns the maximum state in the matrix
int	getMaxState(int ic) returns the maximum state in character ic
int	getMaxSymbolDefined() returns the maximum symbol defined
MCharactersDistribution	getMCharactersDistribution() get matrix and return as StsOfCharacters
int	getNumChars() returns number of characters in data matrix
int	getNumChars(boolean notifyIfError) returns number of characters in data matrix
int	getNumTaxa() returns number of taxa in data matrix
int	getNumTaxa(boolean notifyIfError) returns number of taxa in data matrix
long	getState(int ic, int it) return stateset in node it and character ic.
long	getState(long[] sequence, int ic) return stateset in node it and character ic.
AttachedNotesVector	getStateAnnotationsVector(int ic, int state) gets state name of state "state" of character ic
java.lang.Class	getStateClass() Indicates the type of character stored
int[]	getStateFrequencyArray(int ic) returns an integer array summarizing the frequencies of states of a character.
java.lang.String	getStateFrequencyString(int ic) returns a String summarizing the frequencies of states of a character .
java.lang.String	getStateName(int ic, int state) gets state name of state "state" of character ic
java.lang.String	getStateNote(int ic, int state) gets state name of state "state" of character ic
long	getStateRaw(int ic, int it) return stateset in node it and character ic, raw, as in matrix.
java.lang.String	getStatesSummary(int ic) returns a String summarizing the states of a character (e.g., "2 states", "0.1-0.9").
java.lang.String	getStateSymbol(int ic, int state) gets state symbol for state "state" of character ic, returned as string.
char	getSymbol(int st) Get symbol for state st.
java.lang.String[]	getSymbols() Get String[] of symbols
int	getTotalBitsInStateSet() returns the maximum possible state
boolean	hasStateAnnotations(int ic, int s) returns true if state name for state s is available for character ic
boolean	hasStateFootnote(int ic, int s) returns true if state name for state s is available for character ic
boolean	hasStateName(int ic, int s) returns true if state name for state s is available for character ic
boolean	hasStateNames() returns true if state names are available for matrix
boolean	hasStateNames(int ic) returns true if state names are available for character ic
boolean	isAcceptableCharForState(char c) returns whether a given char is acceptable as the value for a character state
boolean	isAmbiguousOrPolymorphic(int ic, int it) returns whether the state of character ic is missing in taxon it
boolean	isInapplicable(int ic, int it) returns whether the character ic is inapplicable to taxon it
boolean	isMultistateUncertainty(int ic, int it) returns whether the state of character ic is missing in taxon it
boolean	isUnassigned(int ic, int it) returns whether the state of character ic is missing in taxon it
void	logMatrix() Dump matrix to log
CharacterData	makeCharacterData() Return CharacterData object with same number of taxa & characters as this object (but not with any particular data; just so that of same data type)
CharacterData	makeCharacterData(CharMatrixManager manager, Taxa taxa) creates an empty CharacterData object of the same data type as CharacterData subclass used, based on CharMatrixManager & Taxa passed.
CharacterData	makeCharacterData(int ntaxa, int nchars) Return CharacterData object with passed number of taxa & characters (but not with any particular data; just so that of same data type)
CharacterDistribution	makeCharacterDistribution() Return CharacterDistribution object with same number of taxa as this object (but not with any particular data; just so that of same data type)
CharacterState	makeCharacterState() creates an empty CharacterState object of the same data type as CharacterData subclass used.
int	maxStateWithDefinition(int ic) returns state number for last state scored, with name, with footnote, or with annotation for character ic
int	maxStateWithName(int ic) returns state number for last state with name for character ic
void	mergeSecondTaxonIntoFirst(int it1, int it2) merges the states for taxon it2 into it1 within this Data object
void	mergeTaxa(int sinkTaxon, boolean[] taxaToMerge) merges the states for the taxa recorded in taxaToMerge into taxon it within this Data object
boolean	moveParts(int first, int num, int justAfter) move num characters starting at first to just after character justAfter
boolean	moveTaxa(int starting, int num, int justAfter) moves num taxa from position "starting" to just after position "justAfter"; returns true iff successful.
protected boolean	notInStorage(int ic, int it)
boolean	recodeStates(int ic, long[] rules, int maxState) recodes stateA to stateB in character IC
static void	registerDefaultModel(java.lang.String paradigm, java.lang.String name)
void	reverse(int icStart, int icEnd, int it, boolean reverseTerminalGaps, boolean adjustCellLinked) Reverses the data from character icStart to icEnd in taxon it.
java.lang.String	searchData(java.lang.String s, MesquiteString commandResult)
void	setInapplicableSymbol(char inapp) sets the symbol used for inapplicable character (e.g., gap)
void	setMatrix(MCharactersDistribution states) Fills matrix with data from passed StsOfCharacters object.
void	setState(int ic, int it, char c) Set stateset in node it and character ic to state indicated by state symbol.
void	setState(int ic, int it, CharacterState cs) sets the state of character ic in taxon it from CharacterState cs
void	setState(int ic, int it, long states) Set stateset in node it and character ic to states.
int	setState(int ic, int it, Parser parser, boolean fromEditor, MesquiteString result) Set the state at character ic and taxon it from the string of the parser, beginning at current position of the parser.
void	setStateAnnotationsVector(int ic, int state, AttachedNotesVector v) sets state name of state "state" of character ic to name
void	setStateName(int ic, int state, java.lang.String name) sets state name of state "state" of character ic to name
void	setStateNote(int ic, int state, java.lang.String name) sets state name of state "state" of character ic to name
boolean	setSymbol(int st, char symbol) Set symbol for state st.
void	setSymbolDirect(int st, char symbol) Set symbol for state st.
void	setUnassignedSymbol(char mc) sets the symbol used for missing data (unassigned) character
void	statesIntoNEXUSStringBuffer(int ic, int it, java.lang.StringBuffer sb) appends to buffer string describing the state(s) of character ic in taxon it.
void	statesIntoStringBuffer(int ic, int it, java.lang.StringBuffer sb, boolean forDisplay) appends to buffer string describing the state(s) of character ic in taxon it.�
void	statesIntoStringBuffer(int ic, int it, java.lang.StringBuffer sb, boolean forDisplay, boolean includeInapplicable, boolean includeUnassigned) appends to buffer string describing the state(s) of character ic in taxon it.�
void	statesIntoStringBufferCore(int ic, long s, java.lang.StringBuffer sb, boolean forDisplay) appends to buffer string describing the state(s) of character ic in taxon it.
void	statesIntoStringBufferCore(int ic, long s, java.lang.StringBuffer sb, boolean forDisplay, boolean includeInapplicable, boolean includeUnassigned) appends to buffer string describing the state(s) of character ic in taxon it.
long	storeCheckSum(int icStart, int icEnd, int itStart, int itEnd)
boolean	swapParts(int first, int second) swaps characters first and second
void	tradeStatesBetweenCharacters(int ic, int ic2, int it, boolean adjustCellLinked) Trades the states of character ic and ic2 in taxon it.
protected void	tradeStatesBetweenCharactersInternal(int ic, int ic2, int it, boolean adjustCellLinked, boolean adjustDirections) Trades the states of character ic and ic2 in taxon it.
void	tradeStatesBetweenTaxa(int ic, int it, int it2) trades the states of character ic between taxa it and it2.
boolean	usingShortMatrix()

Methods inherited from class mesquite.lib.characters.CharacterData

addCharacters, addInLinked, addToBrowserPopup, addToFile, addToLinkageGroup, canAddCharacters, canMoveChars, changed, characterHasName, characterNamesExist, checkCellMoveDistanceAvailable, checkNameLegality, checkTaxaIDs, colorCellsByDefault, compareChecksums, copyCurrentToPreviousOrderInLinked, dataMatches, dataMatches, decrementSuppressHistoryStamp, deleteCharacters, deleteInLinked, deleteUniqueIDs, doAfterNotify, doCommand, entirelyInapplicable, findByUniqueID, firstApplicable, getAnnotation, getBasisTree, getCellContentsDescription, getCellObject, getCellObjectDisplay, getCellObjectsVector, getChangedSinceSave, getCharacterName, getCharacterStateArray, getChecksum, getDarkDefaultCharacterColor, getDataLinkages, getDefaultCharacterColor, getDefaultColumnWidth, getEditorInhibition, getExplanation, getFootnotes, getHColor, getHImage, getHShow, getID, getIDOrderedFullChecksum, getIllustration, getIllustrationPath, getInapplicableSymbol, getIndependentMCharactersDistribution, getInventUniqueIDs, getMatchChar, getMatrixManager, getMaxNumChars, getName, getNameOfCellEntry, getNumCharsIncluded, getOrMakeCellObjects, getSnapshot, getStatesVersion, getStrings, getTaxa, getTaxaInfo, getTypeName, getUnassignedSymbol, getUndoInstructionsAllData, getUniqueID, getUniqueID, getWhichCellObjects, hasTitle, incrementStatesVersion, incrementSuppressHistoryStamp, isCompatible, isCurrentlyIncluded, isLinked, isLinked, isMolecularSequence, lastApplicable, moveCells, moveCharacters, moveInLinked, moveOne, notifyInLinked, okToDispose, pleaseAutoSizeColumns, recordCurrentOrderInLinked, recordPreviousOrderInLinked, resetChangedSinceSave, resignFromLinkageGroup, restoreToPreviousOrderInLinked, setAnnotation, setAutoSizeColumns, setBasisTree, setCellObject, setCellObjectDisplay, setCharacterName, setDirty, setEditorInhibition, setIllustration, setInventUniqueIDs, setMatchChar, setMatrixManager, setName, setUniqueID, setUniqueID, shiftSequence, showList, showMatrix, stampHistoryChange, stampHistoryChange, stampUniqueID, stampUniqueIDs, swapInLinked, thisOrNextApplicableChar, thisOrPreviousApplicableChar, toHTMLStringDescription, toString, toStringsContig, uniquelyNamed

Methods inherited from class mesquite.lib.FileElement

deleteMe, doom, fileDirtiedByCommand, finalize, getAssignedID, getAssignedIDNumber, getCIPResIDString, getFile, getFileName, getHDaughters, getHMother, getLastModifiedAuthor, getManager, getNexusBlock, getNumSupplements, getProject, getSupplementName, hNodeAction, hSupplementTouched, isDisposed, isDoomed, okToClose, setAssignedIDNumber, setCIPResIDString, setFile, setManager, setProject, show, showMe, stampLastModifiedAuthor

Methods inherited from class mesquite.lib.AssociableWithSpecs

disposing, equalizeParts, getCurrentSpecsSet, getNumSpecsSets, getSpecSetsVector, getSpecSetsVectorVector, getSpecsSet, getSpecsSet, listAssociates, prepareSpecsSetVector, removeSpecsSet, setCurrentSpecsSet, storeSpecsSet

Methods inherited from class mesquite.lib.Associable

anyAssociatedObject, anySelected, clearAllAssociatedBits, contiguousSelection, contiguousSelectionOld, copyCurrentToPreviousOrder, deassignAllAssociatedLongs, deassignAssociated, deassignAssociated, deleteJustAdded, deselectAll, equalizeParts, exchangeAssociated, firstSelected, getAnnotation, getAnnotation, getAssociatedBit, getAssociatedBits, getAssociatedDouble, getAssociatedDoubles, getAssociatedLong, getAssociatedLongs, getAssociatedObject, getAssociatedObjects, getDefaultPosition, getDirty, getJustAdded, getNumberAssociatedBits, getNumberAssociatedDoubles, getNumberAssociatedLongs, getNumberAssociatedObjects, getNumberOfParts, getNumberOfSelectableParts, getSelected, getSelectedBits, getVersionNumber, getWhichAssociatedBits, getWhichAssociatedDouble, getWhichAssociatedLong, getWhichAssociatedObject, inBounds, lastSelected, makeAssociatedBits, makeAssociatedDoubles, makeAssociatedLongs, makeAssociatedObjects, numberSelected, numberSelected, readAssociated, recordCurrentOrder, recordDefaultOrder, recordPreviousOrder, removeAssociatedBits, removeAssociatedDoubles, removeAssociatedLongs, removeAssociatedObjects, resetDefaultOrderToCurrent, resetJustAdded, restoreToPreviousOrder, selectAll, setAnnotation, setAnnotation, setAssociatedBit, setAssociatedDouble, setAssociatedLong, setAssociatedObject, setAssociateds, setDefaultPosition, setDirty, setJustAdded, setNumberOfParts, setSelected, transferAssociated, writeAssociated, zeroAllAssociatedDoubles, zeroAllAssociatedLongs, zeroAllAssociatedObjects

Methods inherited from class mesquite.lib.Attachable

anyAttachments, attach, attachIfUniqueName, detach, getAttachment, getAttachment, getAttachments, listAttachments, readAttachments, setAttachments, writeAttachments

Methods inherited from class mesquite.lib.Listened

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface mesquite.lib.MesquiteListener

disposing

Methods inherited from interface mesquite.lib.Annotatable

getAnnotation, setAnnotation

Methods inherited from interface mesquite.lib.Listenable

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, incrementNotifySuppress, listListeners, notifyListeners, removeListener

Field Detail

symbols

protected char[] symbols

defaultSymbols

protected static final char[] defaultSymbols

ANDseparator

protected static char ANDseparator

ORseparator

protected static char ORseparator

puncString

protected java.lang.String puncString

Constructor Detail

CategoricalData

public CategoricalData(CharMatrixManager manager,
                       int numTaxa,
                       int numChars,
                       Taxa taxa)

Method Detail

searchData

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

Overrides:

searchData in class CharacterData

usingShortMatrix

public boolean usingShortMatrix()

getDefaultState

public long getDefaultState()

getLongArray

public long[] getLongArray(int icStart,
                           int length,
                           int it,
                           boolean includeGaps)

returns an array of longs for the cells in taxon it, starting at character icStart, for length "length"

dispose

public void dispose()

Description copied from class: FileElement

Deletes the file element. Should typically be called via close() to make sure that the file element is not in use etc.

Overrides:

dispose in class CharacterData

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in class CharacterData

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Specified by:

getDataTypeName in class CharacterData

copyData

public void copyData(CharacterData sourceData)

copy the basic data. Does not copy the associated specs sets etc.

Specified by:

copyData in class CharacterData

cloneData

public CharacterData cloneData()

clone this CharacterData and return new copy. Does not clone the associated specs sets etc.

Specified by:

cloneData in class CharacterData

getNumTaxa

public int getNumTaxa()

Description copied from class: CharacterData

returns number of taxa in data matrix

Overrides:

getNumTaxa in class CharacterData

getNumTaxa

public int getNumTaxa(boolean notifyIfError)

Description copied from class: CharacterData

returns number of taxa in data matrix

Overrides:

getNumTaxa in class CharacterData

getNumChars

public int getNumChars()

Description copied from class: CharacterData

returns number of characters in data matrix

Overrides:

getNumChars in class CharacterData

getNumChars

public int getNumChars(boolean notifyIfError)

Description copied from class: CharacterData

returns number of characters in data matrix

Overrides:

getNumChars in class CharacterData

recodeStates

public boolean recodeStates(int ic,
                            long[] rules,
                            int maxState)

recodes stateA to stateB in character IC

swapParts

public boolean swapParts(int first,
                         int second)

swaps characters first and second

Overrides:

swapParts in class CharacterData

moveParts

public boolean moveParts(int first,
                         int num,
                         int justAfter)

move num characters starting at first to just after character justAfter

Overrides:

moveParts in class CharacterData

addParts

public boolean addParts(int starting,
                        int num)

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

Overrides:

addParts in class CharacterData

deleteParts

public boolean deleteParts(int starting,
                           int num)

Deletes num characters from position "starting"; returns true iff successful.

Overrides:

deleteParts in class CharacterData

addTaxa

public boolean addTaxa(int starting,
                       int num)

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

Overrides:

addTaxa in class CharacterData

deleteTaxa

public boolean deleteTaxa(int starting,
                          int num)

Deletes num taxa from position "starting"; returns true iff successful.

Overrides:

deleteTaxa in class CharacterData

moveTaxa

public boolean moveTaxa(int starting,
                        int num,
                        int justAfter)

moves num taxa from position "starting" to just after position "justAfter"; returns true iff successful.

Overrides:

moveTaxa in class CharacterData

getSymbols

public java.lang.String[] getSymbols()

Get String[] of symbols

getSymbol

public char getSymbol(int st)

Get symbol for state st.

setSymbolDirect

public void setSymbolDirect(int st,
                            char symbol)

Set symbol for state st. Does not check for duplicate symbols

setSymbol

public boolean setSymbol(int st,
                         char symbol)

Set symbol for state st. Returns whether setting implied duplicate symbol

setInapplicableSymbol

public void setInapplicableSymbol(char inapp)

sets the symbol used for inapplicable character (e.g., gap)

Overrides:

setInapplicableSymbol in class CharacterData

setUnassignedSymbol

public void setUnassignedSymbol(char mc)

sets the symbol used for missing data (unassigned) character

Overrides:

setUnassignedSymbol in class CharacterData

reverse

public void reverse(int icStart,
                    int icEnd,
                    int it,
                    boolean reverseTerminalGaps,
                    boolean adjustCellLinked)

Reverses the data from character icStart to icEnd in taxon it. If reverseTerminalGaps is true, then it reversed the entire stretch; if it is false, it only reverses from the first non-gap to last non-gap in the stretch. If adjustLinks is true, then the linked matrices will also have their cells reversed. adjustLinks should be true in almost all cases, as reversing without it will disrupt linkages between matrices and cause features in Mesquite to fail (e.g., within Chromaseq).

tradeStatesBetweenCharacters

public void tradeStatesBetweenCharacters(int ic,
                                         int ic2,
                                         int it,
                                         boolean adjustCellLinked)

Trades the states of character ic and ic2 in taxon it. Used for sorting by characters or reversing sequences (for example). If adjustCellLinked is true, then linked matrices will also have their cells traded. This should generally be set to true; if you set it to false, then you must trade states of linked matrices yourself. This is the public version; the internal version is used internally to distinguish between the internal call from reverse (which will handle directions otherwise) and external calls (which should do the direction bookkeeping for the user)

Overrides:

tradeStatesBetweenCharacters in class CharacterData

tradeStatesBetweenCharactersInternal

protected void tradeStatesBetweenCharactersInternal(int ic,
                                                    int ic2,
                                                    int it,
                                                    boolean adjustCellLinked,
                                                    boolean adjustDirections)

Trades the states of character ic and ic2 in taxon it. Used for sorting by characters or reversing sequences (for example). If adjustCellLinked is true, then linked matrices will also have their cells traded. This should generally be set to true; if you set it to false, then you must trade states of linked matrices yourself.

tradeStatesBetweenTaxa

public void tradeStatesBetweenTaxa(int ic,
                                   int it,
                                   int it2)

trades the states of character ic between taxa it and it2. Used for reshuffling.

Overrides:

tradeStatesBetweenTaxa in class CharacterData

logMatrix

public void logMatrix()

Dump matrix to log

Specified by:

logMatrix in class CharacterData

setMatrix

public void setMatrix(MCharactersDistribution states)

Fills matrix with data from passed StsOfCharacters object.

Specified by:

setMatrix in class CharacterData

getMCharactersDistribution

public MCharactersDistribution getMCharactersDistribution()

get matrix and return as StsOfCharacters

Specified by:

getMCharactersDistribution in class CharacterData

getCharacterDistribution

public CharacterDistribution getCharacterDistribution(int ic)

return a CharacterDistribution that points to character ic

Specified by:

getCharacterDistribution in class CharacterData

getCharacter

public long[] getCharacter(int ic)

extract character ic and return as an array of long's

makeCharacterDistribution

public CharacterDistribution makeCharacterDistribution()

Return CharacterDistribution object with same number of taxa as this object (but not with any particular data; just so that of same data type)

Specified by:

makeCharacterDistribution in class CharacterData

makeCharacterState

public CharacterState makeCharacterState()

creates an empty CharacterState object of the same data type as CharacterData subclass used.

Specified by:

makeCharacterState in class CharacterData

makeCharacterData

pu