mesquite.cont.lib
Class ContinuousDistribution

java.lang.Object
  mesquite.lib.characters.CharacterStates
      mesquite.cont.lib.ContinuousStates
          mesquite.cont.lib.ContinuousDistribution

All Implemented Interfaces:

ItemContainer, CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

ContinuousAdjustable, ContinuousEmbedded

public abstract class ContinuousDistribution
extends ContinuousStates
implements CharacterDistribution

Contains an array of continuous character states for one character, at each of the taxa or nodes See notes under ContinuousData regarding items

Field Summary

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, data, totalCreated

Constructor Summary

ContinuousDistribution(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.
AdjustableDistribution	getAdjustableClone() returns a CharacterDistribution that is adjustable and has the same states
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	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

Methods inherited from class mesquite.cont.lib.ContinuousStates

firstIsGreater, getCharacterDataClass, getCharacterState, getCharacterState, getDataTypeName, getDefaultModel, getItemName, getItemNumber, getItemReference, getItemReference, getNumItems, getState, getState, getStateClass, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, userQueryItem

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, toString, 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

ContinuousDistribution

public ContinuousDistribution(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

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

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

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

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