mesquite.categ.lib
Class CategoricalEmbedded

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

All Implemented Interfaces:

CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

DNAEmbedded, ProteinEmbedded

public class CategoricalEmbedded
extends CategoricalDistribution

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

Field Summary

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, totalCreated

Constructor Summary

CategoricalEmbedded(CategoricalData data, int ic)

Method Summary

java.lang.String	getName() returns name
int	getNumTaxa() get number of taxa available in this categorical character.
CharacterData	getParentData() returns parent data of this CharacterStates.
long	getState(int N) get stateset at node N
java.lang.Class	getStateClass() Indicates the type of character stored
java.lang.String	toString() returns string describing states at nodes.

Methods inherited from class mesquite.categ.lib.CategoricalDistribution

adjustHistorySize, fullSet, getAdjustableClone, getMaxState, getNumNodes, 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, isInapplicable, isUnassigned, isUncertain, logStates, setExtraFrequencies, setExtraFrequency, setExtraFrequencyColors, setExtraFrequencyNames, setFrequencies, setFrequency, setNumExtraFreqCategories, setNumFreqCategories, statesEqual, toString

Methods inherited from class mesquite.lib.characters.CharacterStates

checkIllegalNode, getParentCharacter, 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.CharacterStatesHolder

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

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

CategoricalEmbedded

public CategoricalEmbedded(CategoricalData data,
                           int ic)

Method Detail

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface CharacterStatesHolder

Overrides:

getStateClass in class CategoricalStates

getParentData

public CharacterData getParentData()

Description copied from class: CharacterStates

returns parent data of this CharacterStates. There is not a corresponding set procedure because the parent data is set either by the constructor (for Embedded distributions) or by a set procedure (for History or Adjustables)

Specified by:

getParentData in interface CharacterStatesHolder

Overrides:

getParentData in class CharacterStates

getNumTaxa

public int getNumTaxa()

get number of taxa available in this categorical character.

getState

public long getState(int N)

get stateset at node N

Specified by:

getState in class CategoricalStates

getName

public java.lang.String getName()

Description copied from class: CharacterStates

returns name

Specified by:

getName in interface Listable

Overrides:

getName in class CharacterStates

toString

public java.lang.String toString()

Description copied from class: CategoricalStates

returns string describing states at nodes.

Overrides:

toString in class CategoricalStates