mesquite.cont.lib
Class MContinuousEmbedded

java.lang.Object
  mesquite.lib.characters.MCharactersStates
      mesquite.cont.lib.MContinuousStates
          mesquite.cont.lib.MContinuousDistribution
              mesquite.cont.lib.MContinuousEmbedded

All Implemented Interfaces:

ItemContainer, MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

public class MContinuousEmbedded
extends MContinuousDistribution

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

Field Summary

Fields inherited from class mesquite.lib.characters.MCharactersStates

data

Constructor Summary

MContinuousEmbedded(CharacterData data)

Method Summary

CharacterDistribution	getCharacterDistribution(int ic) return CharacterDistribution object for character ic
Double2DArray	getItem(int index)
java.lang.String	getItemName(int index)
int	getItemNumber(NameReference nr)
java.lang.String	getName() returns name
int	getNumberOfItems()
int	getNumChars()
int	getNumNodes() returns number of nodes for which MCharactersStates is defined (either terminal taxa, if MCharactersDistribution, or all nodes in tree, if MCharactersHistory)
int	getNumTaxa() returns number of terminal taxa for which MCharactersStates is defined
double	getState(int ic, int N) returns state of character ic in taxon/node it
double	getState(int ic, int N, int item) returns state of item item of character ic in taxon/node it

Methods inherited from class mesquite.cont.lib.MContinuousDistribution

adjustHistorySize, makeBlankAdjustable, makeCharacterData

Methods inherited from class mesquite.cont.lib.MContinuousStates

allCombinable, allCombinable, getCharacterDataClass, getCharacterState, getDataTypeName, getID, getItemReference, getItemReference, getMatrix, getNumItems, getStateClass, toString, userQueryItem

Methods inherited from class mesquite.lib.characters.MCharactersStates

checkIllegalNode, getBasisTree, getParentData, getTaxa, isCurrentlyIncluded, matrixToString, setBasisTree, setName, setTaxa

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface mesquite.lib.characters.MCharactersDistribution

getBasisTree, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

getCharacterDataClass, getCharacterState, getDataTypeName, getParentData, getStateClass, getTaxa, isCurrentlyIncluded

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MContinuousEmbedded

public MContinuousEmbedded(CharacterData data)

Method Detail

getItem

public Double2DArray getItem(int index)

Specified by:

getItem in class MContinuousDistribution

getItemName

public java.lang.String getItemName(int index)

Specified by:

getItemName in interface ItemContainer

Specified by:

getItemName in class MContinuousStates

getItemNumber

public int getItemNumber(NameReference nr)

Specified by:

getItemNumber in interface ItemContainer

Specified by:

getItemNumber in class MContinuousStates

getNumberOfItems

public int getNumberOfItems()

Specified by:

getNumberOfItems in class MContinuousStates

getState

public double getState(int ic,
                       int N,
                       int item)

Description copied from class: MContinuousStates

returns state of item item of character ic in taxon/node it

Specified by:

getState in class MContinuousStates

getState

public double getState(int ic,
                       int N)

Description copied from class: MContinuousStates

returns state of character ic in taxon/node it

Specified by:

getState in class MContinuousStates

getCharacterDistribution

public CharacterDistribution getCharacterDistribution(int ic)

Description copied from interface: MCharactersDistribution

return CharacterDistribution object for character ic

Specified by:

getCharacterDistribution in interface MCharactersDistribution

Specified by:

getCharacterDistribution in class MContinuousDistribution

getNumTaxa

public int getNumTaxa()

Description copied from interface: MCharactersStatesHolder

returns number of terminal taxa for which MCharactersStates is defined

getNumNodes

public int getNumNodes()

Description copied from interface: MCharactersStatesHolder

returns number of nodes for which MCharactersStates is defined (either terminal taxa, if MCharactersDistribution, or all nodes in tree, if MCharactersHistory)

Specified by:

getNumNodes in interface MCharactersStatesHolder

Overrides:

getNumNodes in class MCharactersStates

getNumChars

public int getNumChars()

getName

public java.lang.String getName()

Description copied from class: MCharactersStates

returns name

Specified by:

getName in interface Listable

Overrides:

getName in class MCharactersStates