mesquite.categ.lib
Class RNACharacterHistory

java.lang.Object
  mesquite.lib.characters.CharacterStates
      mesquite.categ.lib.CategoricalStates
          mesquite.categ.lib.CategoricalDistribution
              mesquite.categ.lib.CategoricalAdjustable
                  mesquite.categ.lib.CategoricalHistory
                      mesquite.categ.lib.DNACharacterHistory
                          mesquite.categ.lib.RNACharacterHistory

All Implemented Interfaces:

AdjustableDistribution, CharacterDistribution, CharacterHistory, CharacterStatesHolder, Listable, Renamable, WithStringDetails

public class RNACharacterHistory
extends DNACharacterHistory

A subclass of CharacterHistory forRNA data. Enforces max state at 3

Field Summary

Fields inherited from class mesquite.categ.lib.CategoricalAdjustable

numNodes, states

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, data, totalCreated

Constructor Summary

RNACharacterHistory(Taxa taxa)

RNACharacterHistory(Taxa taxa, int num)

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
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterState	getCharacterState() returns blank CharacterState object
CharacterState	getCharacterState(CharacterState cs, int N) returns CharacterState at node N
java.lang.String	getDataTypeName() returns the name of the type of data stored
java.lang.Class	getStateClass() Indicates the type of character stored
CategoricalAdjustable	makeAdjustable(Taxa taxa)
CharacterHistory	makeHistory(Tree tree)

Methods inherited from class mesquite.categ.lib.DNACharacterHistory

clone, getAllStates, getColorTable, getDefaultColor, getLegendStates, prepareColors, toString, toString

Methods inherited from class mesquite.categ.lib.CategoricalHistory

addInternodeEvent, adjustSize, deassignStates, getColorsAtNode, getColorSequenceAtNode, getColorsOfState, getInternodeEvent, getInternodeHistoryVector, getNumberOfEvents, getObservedStates, getStatesAtTips, polymorphToUncertainties, prepareInternodeHistories, setObservedStates

Methods inherited from class mesquite.categ.lib.CategoricalAdjustable

adjustSize, getNumNodes, getNumTaxa, getState, setCharacterState, setState, setStates, setWatchPoint, tradeStatesBetweenTaxa

Methods inherited from class mesquite.categ.lib.CategoricalDistribution

getAdjustableClone, getMaxState, 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, getDefaultModel, getExtraFrequencies, getExtraFrequency, getExtraFrequencyColors, getExtraFrequencyNames, getExtraNumFreqCategories, getFrequencies, getFrequency, getNumFreqCategories, getSetFromFrequencies, isInapplicable, isUnassigned, isUncertain, logStates, setExtraFrequencies, setExtraFrequency, setExtraFrequencyColors, setExtraFrequencyNames, setFrequencies, setFrequency, setNumExtraFreqCategories, setNumFreqCategories, statesEqual

Methods inherited from class mesquite.lib.characters.CharacterStates

checkIllegalNode, getName, getParentCharacter, getParentData, 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.AdjustableDistribution

adjustSize, setCharacterState, setParentCharacter, setParentData, tradeStatesBetweenTaxa

Methods inherited from interface mesquite.lib.characters.CharacterStatesHolder

firstIsGreater, getDefaultModel, getNumNodes, getNumTaxa, getParentCharacter, getParentData, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toStringWithDetails

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

RNACharacterHistory

public RNACharacterHistory(Taxa taxa)

RNACharacterHistory

public RNACharacterHistory(Taxa taxa,
                           int num)

Method Detail

getCharacterState

public CharacterState getCharacterState()

returns blank CharacterState object

Specified by:

getCharacterState in interface CharacterStatesHolder

Overrides:

getCharacterState in class DNACharacterHistory

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface CharacterStatesHolder

Overrides:

getStateClass in class DNACharacterHistory

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

returns the corresponding CharacterData subclass

Specified by:

getCharacterDataClass in interface CharacterStatesHolder

Overrides:

getCharacterDataClass in class DNACharacterHistory

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Overrides:

getDataTypeName in class DNACharacterHistory

fullSet

public long fullSet()

Returns full set of allowed states

Overrides:

fullSet in class DNACharacterHistory

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int N)

returns CharacterState at node N

Specified by:

getCharacterState in interface CharacterStatesHolder

Overrides:

getCharacterState in class DNACharacterHistory

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 DNACharacterHistory

makeHistory

public CharacterHistory makeHistory(Tree tree)

Overrides:

makeHistory in class DNACharacterHistory

makeAdjustable

public CategoricalAdjustable makeAdjustable(Taxa taxa)

Overrides:

makeAdjustable in class DNACharacterHistory