mesquite.cont.lib
Class ContinuousEmbedded

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

All Implemented Interfaces:

ItemContainer, CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

public class ContinuousEmbedded
extends ContinuousDistribution

Contains an array of continuous character states for one character, at each of the taxa or nodes

Field Summary

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, totalCreated

Constructor Summary

ContinuousEmbedded(ContinuousData data, int ic)

Method Summary

java.lang.String	getItemName(int index)
int	getItemNumber(NameReference nr)
NameReference	getItemReference(int index)
NameReference	getItemReference(java.lang.String name)
java.lang.String	getName() returns name
int	getNumItems()
int	getNumTaxa() This is the same as getNumNodes.
CharacterData	getParentData() returns parent data of this CharacterStates.
double	getState(int N)
double	getState(int N, int item)
java.lang.Class	getStateClass() Indicates the type of character stored

Methods inherited from class mesquite.cont.lib.ContinuousDistribution

adjustHistorySize, getAdjustableClone, getNumNodes, hasInapplicable, hasInapplicable, hasMissing, hasMissing, isConstant, isConstant

Methods inherited from class mesquite.cont.lib.ContinuousStates

firstIsGreater, getCharacterDataClass, getCharacterState, getCharacterState, getDataTypeName, getDefaultModel, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, userQueryItem

Methods inherited from class mesquite.lib.characters.CharacterStates

checkIllegalNode, getParentCharacter, 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, getParentCharacter, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, toStringWithDetails

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

ContinuousEmbedded

public ContinuousEmbedded(ContinuousData data,
                          int ic)

Method Detail

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface CharacterStatesHolder

Overrides:

getStateClass in class ContinuousStates

getParentData

public CharacterData getParentData()

Description copied from class: CharacterStates

returns parent data of this CharacterStates. There is not a corresponding set procedure because the parent data is set either by the constructor (for Embedded distributions) or by a set procedure (for History or Adjustables)

Specified by:

getParentData in interface CharacterStatesHolder

Overrides:

getParentData in class CharacterStates

getNumItems

public int getNumItems()

Specified by:

getNumItems in interface ItemContainer

Specified by:

getNumItems in class ContinuousStates

getItemReference

public NameReference getItemReference(java.lang.String name)

Specified by:

getItemReference in interface ItemContainer

Specified by:

getItemReference in class ContinuousStates

getItemReference

public NameReference getItemReference(int index)

Specified by:

getItemReference in interface ItemContainer

Specified by:

getItemReference in class ContinuousStates

getItemNumber

public int getItemNumber(NameReference nr)

Specified by:

getItemNumber in interface ItemContainer

Specified by:

getItemNumber in class ContinuousStates

getItemName

public java.lang.String getItemName(int index)

Specified by:

getItemName in interface ItemContainer

Specified by:

getItemName in class ContinuousStates

getNumTaxa

public int getNumTaxa()

Description copied from interface: CharacterStatesHolder

This is the same as getNumNodes. This may be unexpected, because it does NOT necessarily give the same results as getTaxa().getNumTaxa(). For instance, if this is a CharacterHistory, then this is the same as number of nodes, not the number of terminal taxa. The reason for this unusual usage is that

getState

public double getState(int N,
                       int item)

Specified by:

getState in class ContinuousStates

getState

public double getState(int N)

Specified by:

getState in class ContinuousStates

getName

public java.lang.String getName()

Description copied from class: CharacterStates

returns name

Specified by:

getName in interface Listable

Overrides:

getName in class CharacterStates