mesquite.categ.lib
Class ProteinEmbedded

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

All Implemented Interfaces:

CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

public class ProteinEmbedded
extends CategoricalEmbedded

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

ProteinEmbedded(ProteinData data, int ic)

Method Summary

CharacterHistory	adjustHistorySize(Tree tree, CharacterHistory charStates) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
long	fullSet() Returns full set of allowed states
long	getAllStates() returns the union of all state sets
CharacterState	getCharacterState(CharacterState cs, int N) returns CharacterState at node N
CategoricalAdjustable	makeAdjustable(Taxa taxa)

Methods inherited from class mesquite.categ.lib.CategoricalEmbedded

getName, getNumTaxa, getParentData, getState, getStateClass, toString

Methods inherited from class mesquite.categ.lib.CategoricalDistribution

getAdjustableClone, getMaxState, getNumNodes, hasInapplicable, hasInapplicable, hasMissing, hasMissing, hasMultipleStatesInTaxon, hasMultipleStatesInTaxon, isBinary, isBinary, isBinaryCombinable, isBinaryNoMissing, isConstant, isConstant

Methods inherited from class mesquite.categ.lib.CategoricalStates

copyExtraFrequencies, copyFrequencies, disposeExtraFrequencies, disposeFrequencies, extraFrequenciesExist, firstIsGreater, frequenciesExist, getAllStates, getCharacterDataClass, 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, getDefaultModel, getParentCharacter, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, toStringWithDetails

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

ProteinEmbedded

public ProteinEmbedded(ProteinData data,
                       int ic)

Method Detail

getAllStates

public long getAllStates()

returns the union of all state sets

Overrides:

getAllStates in class CategoricalStates

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int N)

returns CharacterState at node N

Specified by:

getCharacterState in interface CharacterStatesHolder

Overrides:

getCharacterState in class CategoricalStates

fullSet

public long fullSet()

Returns full set of allowed states

Overrides:

fullSet in class CategoricalDistribution

adjustHistorySize

public CharacterHistory adjustHistorySize(Tree tree,
                                          CharacterHistory 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 CharacterDistribution

Overrides:

adjustHistorySize in class CategoricalDistribution

makeAdjustable

public CategoricalAdjustable makeAdjustable(Taxa taxa)

Overrides:

makeAdjustable in class CategoricalDistribution