mesquite.cont.lib
Class MContinuousDistribution

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

All Implemented Interfaces:

ItemContainer, MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MContinuousAdjustable, MContinuousEmbedded

public abstract class MContinuousDistribution
extends MContinuousStates
implements MCharactersDistribution

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

MContinuousDistribution(Taxa taxa)

Method Summary

MCharactersHistory	adjustHistorySize(Tree tree, MCharactersHistory charStates) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
abstract CharacterDistribution	getCharacterDistribution(int ic) return CharacterDistribution object for character ic
abstract Double2DArray	getItem(int index)
MAdjustableDistribution	makeBlankAdjustable() return blank adjustable MContinuousDistribution if this same type
CharacterData	makeCharacterData(CharMatrixManager manager, Taxa taxa) return CharacterData filled with same values as this matrix

Methods inherited from class mesquite.cont.lib.MContinuousStates

allCombinable, allCombinable, getCharacterDataClass, getCharacterState, getDataTypeName, getID, getItemName, getItemNumber, getItemReference, getItemReference, getMatrix, getNumberOfItems, getNumItems, getState, getState, getStateClass, toString, userQueryItem

Methods inherited from class mesquite.lib.characters.MCharactersStates

checkIllegalNode, getBasisTree, getName, getNumNodes, 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, getNumChars, getNumNodes, getNumTaxa, getParentData, getStateClass, getTaxa, isCurrentlyIncluded

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Constructor Detail

MContinuousDistribution

public MContinuousDistribution(Taxa taxa)

Method Detail

getCharacterDistribution

public abstract CharacterDistribution getCharacterDistribution(int ic)

Description copied from interface: MCharactersDistribution

return CharacterDistribution object for character ic

Specified by:

getCharacterDistribution in interface MCharactersDistribution

getItem

public abstract Double2DArray getItem(int index)

Specified by:

getItem in class MContinuousStates

makeBlankAdjustable

public MAdjustableDistribution makeBlankAdjustable()

return blank adjustable MContinuousDistribution if this same type

Specified by:

makeBlankAdjustable in interface MCharactersDistribution

makeCharacterData

public CharacterData makeCharacterData(CharMatrixManager manager,
                                       Taxa taxa)

return CharacterData filled with same values as this matrix

Specified by:

makeCharacterData in interface MCharactersDistribution

adjustHistorySize

public MCharactersHistory adjustHistorySize(Tree tree,
                                            MCharactersHistory 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 MCharactersDistribution