mesquite.categ.lib
Class MCategoricalDistribution

java.lang.Object
  mesquite.lib.characters.MCharactersStates
      mesquite.categ.lib.MCategoricalStates
          mesquite.categ.lib.MCategoricalDistribution

All Implemented Interfaces:

MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MCategoricalAdjustable, MCategoricalEmbedded

public abstract class MCategoricalDistribution
extends MCategoricalStates
implements MCharactersDistribution

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

Field Summary

Fields inherited from class mesquite.categ.lib.MCategoricalStates

extraFrequencies, frequencies

Fields inherited from class mesquite.lib.characters.MCharactersStates

data, totalCreated

Constructor Summary

MCategoricalDistribution(Taxa taxa)

Method Summary

MCharactersHistory	adjustHistorySize(Tree tree, MCharactersHistory charStates) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
long	getStateRaw(int ic, int it) returns raw state set of character ic in taxon
MAdjustableDistribution	makeBlankAdjustable() return blank adjustable MCharactersDistribution if this same type
CharacterData	makeCharacterData(CharMatrixManager manager, Taxa taxa) return CharacterData filled with same values as this matrix

Methods inherited from class mesquite.categ.lib.MCategoricalStates

copyExtraFrequencies, copyFrequencies, disposeExtraFrequencies, disposeFrequencies, extraFrequenciesExist, frequenciesExist, getAllStates, getCharacterDataClass, getCharacterState, getDataTypeName, getExtraFrequencies, getExtraFrequency, getFrequencies, getFrequency, getNumExtraFreqCateg, getNumFreqCateg, getState, getStateClass, setExtraFrequencies, setExtraFrequencies, setFrequencies, setFrequencies

Methods inherited from class mesquite.lib.characters.MCharactersStates

checkIllegalNode, getBasisTree, getName, getNumNodes, getParentData, getTaxa, isCurrentlyIncluded, matrixToString, setBasisTree, setName, setTaxa

Methods inherited from class java.lang.Object

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

Methods inherited from interface mesquite.lib.characters.MCharactersDistribution

getBasisTree, getCharacterDistribution, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

getCharacterDataClass, getCharacterState, getDataTypeName, getNumChars, getNumNodes, getNumTaxa, getParentData, getStateClass, getTaxa, isCurrentlyIncluded

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MCategoricalDistribution

public MCategoricalDistribution(Taxa taxa)

Method Detail

makeBlankAdjustable

public MAdjustableDistribution makeBlankAdjustable()

return blank adjustable MCharactersDistribution if this same type

Specified by:

makeBlankAdjustable in interface MCharactersDistribution

makeCharacterData

public CharacterData makeCharacterData(CharMatrixManager manager,
                                       Taxa taxa)

return CharacterData filled with same values as this matrix

Specified by:

makeCharacterData in interface MCharactersDistribution

adjustHistorySize

public MCharactersHistory adjustHistorySize(Tree tree,
                                            MCharactersHistory charStates)

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

Specified by:

adjustHistorySize in interface MCharactersDistribution

getStateRaw

public long getStateRaw(int ic,
                        int it)

returns raw state set of character ic in taxon