mesquite.categ.lib
Class MCategoricalAdjustable

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

All Implemented Interfaces:

Annotatable, MAdjustableDistribution, MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MCategoricalHistory, MDNAAdjustable, MProteinAdjustable

public class MCategoricalAdjustable
extends MCategoricalDistribution
implements MAdjustableDistribution

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

MCategoricalAdjustable()

MCategoricalAdjustable(Taxa taxa)

MCategoricalAdjustable(Taxa taxa, int numChars, int numTaxa)

Method Summary

void	deassignStates() assign missing data (unassigned) to all characters and nodes
java.lang.String	getAnnotation()
CharacterDistribution	getCharacterDistribution(int ic) return CharacterDistribution object for character ic
int	getNumChars()
int	getNumTaxa() returns number of terminal taxa for which MCharactersStates is defined
long	getState(int ic, int N) returns state set of character ic at node
CharacterData	makeCharacterData(CharMatrixManager manager, Taxa taxa) return CharacterData filled with same values as this matrix
void	setAnnotation(java.lang.String s, boolean notify)
void	setCharacterState(CharacterState s, int ic, int it) sets the character state of character ic and taxon it to that in the passed CharacterState
void	setParentData(CharacterData cd) sets the parent CharacterData from which this CharacterDistribution is derived or related
void	setSize(int numChars, int numTaxa) Set the size of the matrix
void	setState(int ic, int N, long d) set state set of character ic at node to d
void	tradeStatesBetweenTaxa(int ic, int it, int it2) trades the states of character ic between taxa it and it2.
void	transferFrom(int ic, CharacterDistribution s) obtain states of character ic from passed CharacterDistribution object

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, 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, getName, 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.MAdjustableDistribution

setTaxa

Methods inherited from interface mesquite.lib.characters.MCharactersDistribution

adjustHistorySize, getBasisTree, makeBlankAdjustable, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

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

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MCategoricalAdjustable

public MCategoricalAdjustable(Taxa taxa,
                              int numChars,
                              int numTaxa)

MCategoricalAdjustable

public MCategoricalAdjustable(Taxa taxa)

MCategoricalAdjustable

public MCategoricalAdjustable()

Method Detail

setAnnotation

public void setAnnotation(java.lang.String s,
                          boolean notify)

Specified by:

setAnnotation in interface Annotatable

getAnnotation

public java.lang.String getAnnotation()

Specified by:

getAnnotation in interface Annotatable

setParentData

public void setParentData(CharacterData cd)

sets the parent CharacterData from which this CharacterDistribution is derived or related

Specified by:

setParentData in interface MAdjustableDistribution

setSize

public void setSize(int numChars,
                    int numTaxa)

Description copied from interface: MAdjustableDistribution

Set the size of the matrix

Specified by:

setSize in interface MAdjustableDistribution

deassignStates

public void deassignStates()

assign missing data (unassigned) to all characters and nodes

Specified by:

deassignStates in interface MAdjustableDistribution

getState

public long getState(int ic,
                     int N)

returns state set of character ic at node

Specified by:

getState in class MCategoricalStates

setState

public void setState(int ic,
                     int N,
                     long d)

set state set of character ic at node to d

setCharacterState

public void setCharacterState(CharacterState s,
                              int ic,
                              int it)

sets the character state of character ic and taxon it to that in the passed CharacterState

Specified by:

setCharacterState in interface MAdjustableDistribution

tradeStatesBetweenTaxa

public void tradeStatesBetweenTaxa(int ic,
                                   int it,
                                   int it2)

trades the states of character ic between taxa it and it2. Used for reshuffling.

Specified by:

tradeStatesBetweenTaxa in interface MAdjustableDistribution

transferFrom

public void transferFrom(int ic,
                         CharacterDistribution s)

obtain states of character ic from passed CharacterDistribution object

Specified by:

transferFrom in interface MAdjustableDistribution

getCharacterDistribution

public CharacterDistribution getCharacterDistribution(int ic)

return CharacterDistribution object for character ic

Specified by:

getCharacterDistribution in interface MCharactersDistribution

makeCharacterData

public CharacterData makeCharacterData(CharMatrixManager manager,
                                       Taxa taxa)

return CharacterData filled with same values as this matrix

Specified by:

makeCharacterData in interface MCharactersDistribution

Overrides:

makeCharacterData in class MCategoricalDistribution

getNumTaxa

public int getNumTaxa()

Description copied from interface: MCharactersStatesHolder

returns number of terminal taxa for which MCharactersStates is defined

Specified by:

getNumTaxa in interface MCharactersStatesHolder

getNumChars

public int getNumChars()

Specified by:

getNumChars in interface MCharactersStatesHolder