mesquite.categ.lib
Class MCategoricalHistory

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

All Implemented Interfaces:

Annotatable, MAdjustableDistribution, MCharactersDistribution, MCharactersHistory, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MDNAHistory, MProteinHistory

public class MCategoricalHistory
extends MCategoricalAdjustable
implements MCharactersHistory

DOCUMENT

Field Summary

Fields inherited from class mesquite.categ.lib.MCategoricalStates

extraFrequencies, frequencies

Fields inherited from class mesquite.lib.characters.MCharactersStates

data, totalCreated

Constructor Summary

MCategoricalHistory(Taxa taxa, int numChars, int numNodes)

Method Summary

long	getAllStates() returns the union of all state sets
CharacterHistory	getCharacterHistory(int ic) extract the states of character ic and return as CharacterHistory
int	getNumNodes() returns number of nodes for which MCharactersStates is defined (either terminal taxa, if MCharactersDistribution, or all nodes in tree, if MCharactersHistory)
void	transferFrom(int ic, CharacterHistory s) obtain states of character ic from passed CharacterHistory object

Methods inherited from class mesquite.categ.lib.MCategoricalAdjustable

deassignStates, getAnnotation, getCharacterDistribution, getNumChars, getNumTaxa, getState, makeCharacterData, setAnnotation, setCharacterState, setParentData, setSize, setState, tradeStatesBetweenTaxa, transferFrom

Methods inherited from class mesquite.categ.lib.MCategoricalDistribution

adjustHistorySize, getStateRaw, makeBlankAdjustable

Methods inherited from class mesquite.categ.lib.MCategoricalStates

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

Methods inherited from class mesquite.lib.characters.MCharactersStates

checkIllegalNode, getBasisTree, getName, 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.MAdjustableDistribution

deassignStates, setCharacterState, setParentData, setSize, setTaxa, tradeStatesBetweenTaxa, transferFrom

Methods inherited from interface mesquite.lib.characters.MCharactersDistribution

adjustHistorySize, getBasisTree, getCharacterDistribution, makeBlankAdjustable, makeCharacterData, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

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

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Methods inherited from interface mesquite.lib.Annotatable

getAnnotation, setAnnotation

Constructor Detail

MCategoricalHistory

public MCategoricalHistory(Taxa taxa,
                           int numChars,
                           int numNodes)

Method Detail

getNumNodes

public int getNumNodes()

Description copied from interface: MCharactersStatesHolder

returns number of nodes for which MCharactersStates is defined (either terminal taxa, if MCharactersDistribution, or all nodes in tree, if MCharactersHistory)

Specified by:

getNumNodes in interface MCharactersStatesHolder

Overrides:

getNumNodes in class MCharactersStates

getCharacterHistory

public CharacterHistory getCharacterHistory(int ic)

extract the states of character ic and return as CharacterHistory

Specified by:

getCharacterHistory in interface MCharactersHistory

transferFrom

public void transferFrom(int ic,
                         CharacterHistory s)

obtain states of character ic from passed CharacterHistory object

Specified by:

transferFrom in interface MCharactersHistory

getAllStates

public long getAllStates()

returns the union of all state sets

Overrides:

getAllStates in class MCategoricalStates