mesquite.categ.lib
Class CategoricalStates

java.lang.Object
  mesquite.lib.characters.CharacterStates
      mesquite.categ.lib.CategoricalStates

All Implemented Interfaces:

CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

CategoricalDistribution

public abstract class CategoricalStates
extends CharacterStates

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

Field Summary

protected long	allStates
protected int	enforcedMaxState
protected double[][]	extraFrequencies
protected ColorDistribution	extraFrequencyColors
protected java.lang.String[]	extraFrequencyNames
protected double[][]	frequencies
protected boolean	maxFound
protected int	maxState
protected boolean	minFound
protected int	minState

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, data, totalCreated

Constructor Summary

CategoricalStates(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	firstIsGreater(int N, int M) returns true if statesets have single element each, and that at node N is greater than that at node M.
boolean	frequenciesExist() return if frequencies exist for states at each node.
long	getAllStates() get union of all statesets, including multiple-state uncertainties (but not missing, gap)
long	getAllStates(Tree tree, int node) get union of all statesets, including multiple-state uncertainties (but not missing, gap), in the tree
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
CharacterModel	getDefaultModel(MesquiteProject file, java.lang.String paradigm) Get the default CharacterModel for the given paradigm (e.g., "Parsimony")
double[]	getExtraFrequencies(int node) get extra freqency information at a particular node
double	getExtraFrequency(int node, int category) get extra freqency of particular category at a particular node
ColorDistribution	getExtraFrequencyColors() get extra frequency colors
java.lang.String[]	getExtraFrequencyNames() get extra frequency names
int	getExtraNumFreqCategories()
double[]	getFrequencies(int node) get freqency information at a particular node
double	getFrequency(int node, int category) get freqency of particular category at a particular node
int	getNumFreqCategories()
long	getSetFromFrequencies(int node) get state set represented by frequences at a particular node
abstract long	getState(int N) get stateset at node N
java.lang.Class	getStateClass() Indicates the type of character stored
boolean	isInapplicable(int N) returns whether state at node N is inapplicable
boolean	isUnassigned(int N) returns whether state at node N is unassigned (missing data)(
boolean	isUncertain(int N) returns whether state at node N is uncertain (partial missing or ambiguous data)(
void	logStates() Dump a listing of the states to the log.
void	setExtraFrequencies(int node, double[] freqs) set extra freqency information
void	setExtraFrequency(int node, int category, double freq) set extra freqency information.
void	setExtraFrequencyColors(ColorDistribution colors) Set extra frequency colors
void	setExtraFrequencyNames(java.lang.String[] names) Set extra frequency names
void	setFrequencies(int node, double[] freqs) set freqency information
void	setFrequency(int node, int category, double freq) set freqency information.
void	setNumExtraFreqCategories(int numExtraCategories)
void	setNumFreqCategories(int numCategories)
boolean	statesEqual(int N, int M) returns true if states at nodes N and M are equal
java.lang.String	toString() returns string describing states at nodes.
java.lang.String	toString(int node, java.lang.String lineEnding) returns string describing character states at node

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.CharacterStatesHolder

getNumNodes, getNumTaxa

Field Detail

maxState

protected int maxState

minState

protected int minState

allStates

protected long allStates

minFound

protected boolean minFound

maxFound

protected boolean maxFound

frequencies

protected double[][] frequencies

extraFrequencies

protected double[][] extraFrequencies

extraFrequencyColors

protected ColorDistribution extraFrequencyColors

extraFrequencyNames

protected java.lang.String[] extraFrequencyNames

enforcedMaxState

protected int enforcedMaxState

Constructor Detail

CategoricalStates

public CategoricalStates(Taxa taxa)

Method Detail

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

returns the corresponding CharacterData subclass

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

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.

copyExtraFrequencies

public static void copyExtraFrequencies(CategoricalStates source,
                                        CategoricalStates sink)

Copy extra frequency information from first to second CategoricalStates.

setExtraFrequencyColors

public void setExtraFrequencyColors(ColorDistribution colors)

Set extra frequency colors

getExtraFrequencyColors

public ColorDistribution getExtraFrequencyColors()

get extra frequency colors

setExtraFrequencyNames

public void setExtraFrequencyNames(java.lang.String[] names)

Set extra frequency names

getExtraFrequencyNames

public java.lang.String[] getExtraFrequencyNames()

get extra frequency names

setNumFreqCategories

public void setNumFreqCategories(int numCategories)

getNumFreqCategories

public int getNumFreqCategories()

setFrequencies

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

set freqency information

setFrequency

public void setFrequency(int node,
                         int category,
                         double freq)

set freqency information.

getFrequencies

public double[] getFrequencies(int node)

get freqency information at a particular node

getFrequency

public double getFrequency(int node,
                           int category)

get freqency of particular category at a particular node

setNumExtraFreqCategories

public void setNumExtraFreqCategories(int numExtraCategories)

getExtraNumFreqCategories

public int getExtraNumFreqCategories()

setExtraFrequencies

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

set extra freqency information

setExtraFrequency

public void setExtraFrequency(int node,
                              int category,
                              double freq)

set extra freqency information.

getExtraFrequencies

public double[] getExtraFrequencies(int node)

get extra freqency information at a particular node

getExtraFrequency

public double getExtraFrequency(int node,
                                int category)

get extra freqency of particular category at a particular node

getSetFromFrequencies

public long getSetFromFrequencies(int node)

get state set represented by frequences at a particular node

disposeFrequencies

public void disposeFrequencies()

dispose frequency information (frees memory).

disposeExtraFrequencies

public void disposeExtraFrequencies()

dispose extra frequency information (frees memory).

getDefaultModel

public CharacterModel getDefaultModel(MesquiteProject file,
                                      java.lang.String paradigm)

Get the default CharacterModel for the given paradigm (e.g., "Parsimony")

getAllStates

public long getAllStates()

get union of all statesets, including multiple-state uncertainties (but not missing, gap)

getAllStates

public long getAllStates(Tree tree,
                         int node)

get union of all statesets, including multiple-state uncertainties (but not missing, gap), in the tree

getState

public abstract long getState(int N)

get stateset at node N

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int N)

returns CharacterState at node N

getCharacterState

public CharacterState getCharacterState()

returns blank CharacterState object

isInapplicable

public boolean isInapplicable(int N)

returns whether state at node N is inapplicable

isUnassigned

public boolean isUnassigned(int N)

returns whether state at node N is unassigned (missing data)(

isUncertain

public boolean isUncertain(int N)

returns whether state at node N is uncertain (partial missing or ambiguous data)(

logStates

public void logStates()

Dump a listing of the states to the log.

toString

public java.lang.String toString(int node,
                                 java.lang.String lineEnding)

returns string describing character states at node

toString

public java.lang.String toString()

returns string describing states at nodes.

Overrides:

toString in class java.lang.Object

firstIsGreater

public boolean firstIsGreater(int N,
                              int M)

returns true if statesets have single element each, and that at node N is greater than that at node M.

statesEqual

public boolean statesEqual(int N,
                           int M)

returns true if states at nodes N and M are equal