mesquite.categ.lib
Class MCategoricalEmbedded

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

All Implemented Interfaces:

MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MDNAEmbedded, MProteinEmbedded

public class MCategoricalEmbedded
extends MCategoricalDistribution

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

MCategoricalEmbedded(CharacterData data)

Method Summary

CharacterDistribution	getCharacterDistribution(int ic) return CharacterDistribution object for character ic
java.lang.String	getName() returns name
int	getNumChars()
int	getNumTaxa() returns number of terminal taxa for which MCharactersStates is defined
long	getState(int ic, int it) returns state set of character ic in taxon
long	getStateRaw(int ic, int it) returns raw state set of character ic in taxon

Methods inherited from class mesquite.categ.lib.MCategoricalDistribution

adjustHistorySize, makeBlankAdjustable, makeCharacterData

Methods inherited from class mesquite.categ.lib.MCategoricalStates

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

Methods inherited from class mesquite.lib.characters.MCharactersStates

checkIllegalNode, getBasisTree, 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, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

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

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MCategoricalEmbedded

public MCategoricalEmbedded(CharacterData data)

Method Detail

getState

public long getState(int ic,
                     int it)

returns state set of character ic in taxon

Specified by:

getState in class MCategoricalStates

getStateRaw

public long getStateRaw(int ic,
                        int it)

returns raw state set of character ic in taxon

Overrides:

getStateRaw in class MCategoricalDistribution

getCharacterDistribution

public CharacterDistribution getCharacterDistribution(int ic)

return CharacterDistribution object for character ic

getNumTaxa

public int getNumTaxa()

Description copied from interface: MCharactersStatesHolder

returns number of terminal taxa for which MCharactersStates is defined

getNumChars

public int getNumChars()

getName

public java.lang.String getName()

Description copied from class: MCharactersStates

returns name

Specified by:

getName in interface Listable

Overrides:

getName in class MCharactersStates