mesquite.categ.lib
Class MCategoricalStates

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

All Implemented Interfaces:

MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MCategoricalDistribution

public abstract class MCategoricalStates
extends MCharactersStates

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

Field Summary

protected double[][][]	extraFrequencies
protected double[][][]	frequencies

Fields inherited from class mesquite.lib.characters.MCharactersStates

data, totalCreated

Constructor Summary

MCategoricalStates(Taxa taxa)

Method Summary

static void	copyExtraFrequencies(CategoricalStates source, CategoricalStates sink) Copy extra frequency information from first to second CategoricalStates.
static void	copyFrequencies(CategoricalStates source, CategoricalStates sink) Copy frequency information from first to second CategoricalStates.
void	disposeExtraFrequencies() dispose extra frequency information (frees memory).
void	disposeFrequencies() dispose frequency information (frees memory).
boolean	extraFrequenciesExist() return if frequencies exist for states at each node.
boolean	frequenciesExist() return if frequencies exist for states at each node.
long	getAllStates() returns the union of all state sets
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterState	getCharacterState(CharacterState cs, int ic, int it) get CharacterState at node N
java.lang.String	getDataTypeName() returns the name of the type of data stored
double[][]	getExtraFrequencies(int node) get extra freqency information at a particular node
double	getExtraFrequency(int ic, int node, int category) get extra freqency of particular category at a particular node
double[][]	getFrequencies(int node) get freqency information at a particular node
double	getFrequency(int ic, int node, int category) get freqency of particular category at a particular node
protected int	getNumExtraFreqCateg()
protected int	getNumFreqCateg()
abstract long	getState(int ic, int it) returns state set of character ic in taxon
java.lang.Class	getStateClass() Indicates the type of character stored
void	setExtraFrequencies(int node, double[][] freqs) set extra freqency information
void	setExtraFrequencies(int ic, int node, double[] freqs) set extra freqency information
void	setFrequencies(int node, double[][] freqs) set freqency information
void	setFrequencies(int ic, int node, double[] freqs) set freqency information

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.MCharactersStatesHolder

getNumChars, getNumTaxa

Field Detail

frequencies

protected double[][][] frequencies

extraFrequencies

protected double[][][] extraFrequencies

Constructor Detail

MCategoricalStates

public MCategoricalStates(Taxa taxa)

Method Detail

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface MCharactersStatesHolder

Specified by:

getStateClass in class MCharactersStates

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

Description copied from interface: MCharactersStatesHolder

returns the corresponding CharacterData subclass

frequenciesExist

public boolean frequenciesExist()

return if frequencies exist for states at each node.

extraFrequenciesExist

public boolean extraFrequenciesExist()

return if frequencies exist for states at each node.

copyFrequencies

public static void copyFrequencies(CategoricalStates source,
                                   CategoricalStates sink)

Copy frequency information from first to second CategoricalStates.

getNumFreqCateg

protected int getNumFreqCateg()

setFrequencies

public void setFrequencies(int node,
                           double[][] freqs)

set freqency information

setFrequencies

public void setFrequencies(int ic,
                           int node,
                           double[] freqs)

set freqency information

getFrequencies

public double[][] getFrequencies(int node)

get freqency information at a particular node

getFrequency

public double getFrequency(int ic,
                           int node,
                           int category)

get freqency of particular category at a particular node

disposeFrequencies

public void disposeFrequencies()

dispose frequency information (frees memory).

copyExtraFrequencies

public static void copyExtraFrequencies(CategoricalStates source,
                                        CategoricalStates sink)

Copy extra frequency information from first to second CategoricalStates.

getNumExtraFreqCateg

protected int getNumExtraFreqCateg()

setExtraFrequencies

public void setExtraFrequencies(int node,
                                double[][] freqs)

set extra freqency information

setExtraFrequencies

public void setExtraFrequencies(int ic,
                                int node,
                                double[] freqs)

set extra freqency information

getExtraFrequencies

public double[][] getExtraFrequencies(int node)

get extra freqency information at a particular node

getExtraFrequency

public double getExtraFrequency(int ic,
                                int node,
                                int category)

get extra freqency of particular category at a particular node

disposeExtraFrequencies

public void disposeExtraFrequencies()

dispose extra frequency information (frees memory).

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Specified by:

getDataTypeName in interface MCharactersStatesHolder

Specified by:

getDataTypeName in class MCharactersStates

getState

public abstract long getState(int ic,
                              int it)

returns state set of character ic in taxon

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int ic,
                                        int it)

get CharacterState at node N

Specified by:

getCharacterState in interface MCharactersStatesHolder

Specified by:

getCharacterState in class MCharactersStates

getAllStates

public long getAllStates()

returns the union of all state sets