mesquite.categ.lib
Class CategoricalDistribution

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

All Implemented Interfaces:

CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

CategoricalAdjustable, CategoricalEmbedded

public abstract class CategoricalDistribution
extends CategoricalStates
implements CharacterDistribution

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

Field Summary

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

CategoricalDistribution(Taxa taxa)

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
AdjustableDistribution	getAdjustableClone() returns a CharacterDistribution that is adjustable and has the same states
int	getMaxState() Returns largest state value
int	getNumNodes() returns number of nodes for which CharacterStates is defined (either terminal taxa, if CharacterDistribution, or all nodes in tree, if CharacterHistory)
boolean	hasInapplicable() Returns whether or not the character has inapplicable codings (gaps)
boolean	hasInapplicable(Tree tree, int node) Returns whether or not the character has inapplicable codings (gaps) in the taxa of the tree
boolean	hasMissing() Returns whether or not the character has missing (unassigned) data
boolean	hasMissing(Tree tree, int node) Returns whether or not the character has missing (unassigned) data in the taxa of the tree
boolean	hasMultipleStatesInTaxon() Returns whether or not the character has polymorphic or multstate uncertain data
boolean	hasMultipleStatesInTaxon(Tree tree, int node) Returns whether or not the character has polymorphic or multstate uncertain data in the taxa of the tree
static boolean	isBinary(CharacterDistribution dist, Tree tree) Returns whether or not the character is all binary in the taxa of the tree
boolean	isBinary(int node) Returns whether or not the character is binary
boolean	isBinaryCombinable(int node) Returns whether or not the character is binary and with an actual state
static boolean	isBinaryNoMissing(CharacterDistribution dist, Tree tree) Returns whether or not the character is all binary and no missing in the taxa of the tree
boolean	isConstant() Returns whether or not the character is constant (all states are the same)
boolean	isConstant(Tree tree, int node) Returns whether or not the character is constant (all states are the same) in the taxa of the tree
CategoricalAdjustable	makeAdjustable(Taxa taxa)

Methods inherited from class mesquite.categ.lib.CategoricalStates

copyExtraFrequencies, copyFrequencies, disposeExtraFrequencies, disposeFrequencies, extraFrequenciesExist, firstIsGreater, frequenciesExist, getAllStates, getAllStates, getCharacterDataClass, getCharacterState, getCharacterState, getDataTypeName, getDefaultModel, getExtraFrequencies, getExtraFrequency, getExtraFrequencyColors, getExtraFrequencyNames, getExtraNumFreqCategories, getFrequencies, getFrequency, getNumFreqCategories, getSetFromFrequencies, getState, getStateClass, isInapplicable, isUnassigned, isUncertain, logStates, setExtraFrequencies, setExtraFrequency, setExtraFrequencyColors, setExtraFrequencyNames, setFrequencies, setFrequency, setNumExtraFreqCategories, setNumFreqCategories, statesEqual, toString, toString

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

firstIsGreater, getCharacterDataClass, getCharacterState, getCharacterState, getDefaultModel, getNumTaxa, getParentCharacter, getParentData, getStateClass, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, toStringWithDetails

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

CategoricalDistribution

public CategoricalDistribution(Taxa taxa)

Method Detail

getNumNodes

public int getNumNodes()

Description copied from interface: CharacterStatesHolder

returns number of nodes for which CharacterStates is defined (either terminal taxa, if CharacterDistribution, or all nodes in tree, if CharacterHistory)

Specified by:

getNumNodes in interface CharacterStatesHolder

fullSet

public long fullSet()

Returns full set of allowed states

getMaxState

public int getMaxState()

Returns largest state value

hasMultipleStatesInTaxon

public boolean hasMultipleStatesInTaxon()

Returns whether or not the character has polymorphic or multstate uncertain data

hasMissing

public boolean hasMissing()

Returns whether or not the character has missing (unassigned) data

Specified by:

hasMissing in interface CharacterDistribution

hasInapplicable

public boolean hasInapplicable()

Returns whether or not the character has inapplicable codings (gaps)

Specified by:

hasInapplicable in interface CharacterDistribution

hasMultipleStatesInTaxon

public boolean hasMultipleStatesInTaxon(Tree tree,
                                        int node)

Returns whether or not the character has polymorphic or multstate uncertain data in the taxa of the tree

hasMissing

public boolean hasMissing(Tree tree,
                          int node)

Returns whether or not the character has missing (unassigned) data in the taxa of the tree

Specified by:

hasMissing in interface CharacterDistribution

hasInapplicable

public boolean hasInapplicable(Tree tree,
                               int node)

Returns whether or not the character has inapplicable codings (gaps) in the taxa of the tree

Specified by:

hasInapplicable in interface CharacterDistribution

isBinaryNoMissing

public static boolean isBinaryNoMissing(CharacterDistribution dist,
                                        Tree tree)

Returns whether or not the character is all binary and no missing in the taxa of the tree

isBinary

public static boolean isBinary(CharacterDistribution dist,
                               Tree tree)

Returns whether or not the character is all binary in the taxa of the tree

isBinary

public boolean isBinary(int node)

Returns whether or not the character is binary

isBinaryCombinable

public boolean isBinaryCombinable(int node)

Returns whether or not the character is binary and with an actual state

isConstant

public boolean isConstant()

Returns whether or not the character is constant (all states are the same)

Specified by:

isConstant in interface CharacterDistribution

isConstant

public boolean isConstant(Tree tree,
                          int node)

Returns whether or not the character is constant (all states are the same) in the taxa of the tree

Specified by:

isConstant in interface CharacterDistribution

getAdjustableClone

public AdjustableDistribution getAdjustableClone()

returns a CharacterDistribution that is adjustable and has the same states

Specified by:

getAdjustableClone in interface CharacterDistribution

makeAdjustable

public CategoricalAdjustable makeAdjustable(Taxa taxa)

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