mesquite.categ.lib
Class CategoricalAdjustable

java.lang.Object
  mesquite.lib.characters.CharacterStates
      mesquite.categ.lib.CategoricalStates
          mesquite.categ.lib.CategoricalDistribution
              mesquite.categ.lib.CategoricalAdjustable

All Implemented Interfaces:

AdjustableDistribution, CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

CategoricalHistory, DNACharacterAdjustable, ProteinAdjustable

public class CategoricalAdjustable
extends CategoricalDistribution
implements AdjustableDistribution

A class for an array of categorical character states for one character, at each of the taxa or nodes

Field Summary

protected int	numNodes
long[]	states

Fields inherited from class mesquite.categ.lib.CategoricalStates

allStates, enforcedMaxState, extraFrequencies, extraFrequencyColors, extraFrequencyNames, frequencies, maxFound, maxState, minFound, minState

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, data, totalCreated

Constructor Summary

CategoricalAdjustable(Taxa taxa)

CategoricalAdjustable(Taxa taxa, int num)

Method Summary

AdjustableDistribution	adjustSize(Taxa taxa) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
void	deassignStates() set all states to missing (unassigned)
int	getNumNodes() get number of nodes available in this categorical character.
int	getNumTaxa() get number of taxa available in this categorical character.
long	getState(int N) get stateset at node N
void	setCharacterState(int N, CharacterState cs) sets state at node N to stateset passed
void	setState(int N, long d) sets state at node N to stateset passed
void	setStates(long[] sStates) Set states array to be one passed
void	setWatchPoint(int N) set watchpoint at node N.
void	tradeStatesBetweenTaxa(int it, int it2) Trade states of nodes it and it2

Methods inherited from class mesquite.categ.lib.CategoricalDistribution

adjustHistorySize, fullSet, getAdjustableClone, getMaxState, hasInapplicable, hasInapplicable, hasMissing, hasMissing, hasMultipleStatesInTaxon, hasMultipleStatesInTaxon, isBinary, isBinary, isBinaryCombinable, isBinaryNoMissing, isConstant, isConstant, makeAdjustable

Methods inherited from class mesquite.categ.lib.CategoricalStates

copyExtraFrequencies, copyFrequencies, disposeExtraFrequencies, disposeFrequencies, extraFrequenciesExist, firstIsGreater, frequenciesExist, getAllStates, getAllStates, getCharacterDataClass, getCharacterState, getCharacterState, getDataTypeName, getDefaultModel, getExtraFrequencies, getExtraFrequency, getExtraFrequencyColors, getExtraFrequencyNames, getExtraNumFreqCategories, getFrequencies, getFrequency, getNumFreqCategories, getSetFromFrequencies, getStateClass, isInapplicable, isUnassigned, isUncertain, logStates, setExtraFrequencies, setExtraFrequency, setExtraFrequencyColors, setExtraFrequencyNames, setFrequencies, setFrequency, setNumExtraFreqCategories, setNumFreqCategories, statesEqual, toString, toString

Methods inherited from class mesquite.lib.characters.CharacterStates

checkIllegalNode, getName, getParentCharacter, getParentData, getTaxa, makeCharacterState, setName, setParentCharacter, setParentData, setTaxa, toExternal, toInternal, toStringWithDetails

Methods inherited from class java.lang.Object

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

Methods inherited from interface mesquite.lib.characters.AdjustableDistribution

setParentCharacter, setParentData

Methods inherited from interface mesquite.lib.characters.CharacterStatesHolder

firstIsGreater, getCharacterDataClass, getCharacterState, getCharacterState, getDefaultModel, getParentCharacter, getParentData, getStateClass, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, toStringWithDetails

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Field Detail

states

public long[] states

numNodes

protected int numNodes

Constructor Detail

CategoricalAdjustable

public CategoricalAdjustable(Taxa taxa,
                             int num)

CategoricalAdjustable

public CategoricalAdjustable(Taxa taxa)

Method Detail

getNumTaxa

public int getNumTaxa()

get number of taxa available in this categorical character.

Specified by:

getNumTaxa in interface CharacterStatesHolder

getNumNodes

public int getNumNodes()

get number of nodes available in this categorical character.

Specified by:

getNumNodes in interface CharacterStatesHolder

Overrides:

getNumNodes in class CategoricalDistribution

deassignStates

public void deassignStates()

set all states to missing (unassigned)

Specified by:

deassignStates in interface AdjustableDistribution

setStates

public void setStates(long[] sStates)

Set states array to be one passed

getState

public long getState(int N)

get stateset at node N

Specified by:

getState in class CategoricalStates

setState

public void setState(int N,
                     long d)

sets state at node N to stateset passed

setCharacterState

public void setCharacterState(int N,
                              CharacterState cs)

sets state at node N to stateset passed

Specified by:

setCharacterState in interface AdjustableDistribution

setWatchPoint

public void setWatchPoint(int N)

set watchpoint at node N. Subsequently moniters to see if its value changed and gives notification. May not work well (changes may not be checked in all places.

tradeStatesBetweenTaxa

public void tradeStatesBetweenTaxa(int it,
                                   int it2)

Trade states of nodes it and it2

Specified by:

tradeStatesBetweenTaxa in interface AdjustableDistribution

adjustSize

public AdjustableDistribution adjustSize(Taxa taxa)

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

Specified by:

adjustSize in interface AdjustableDistribution