mesquite.cont.lib
Class MContinuousStates

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

All Implemented Interfaces:

ItemContainer, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MContinuousDistribution, MGeographicStates

public abstract class MContinuousStates
extends MCharactersStates
implements ItemContainer

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

MContinuousStates(Taxa taxa)

Method Summary

boolean	allCombinable()
boolean	allCombinable(int item)
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterState	getCharacterState(CharacterState cs, int ic, int it) get CharacterState at node N
java.lang.String	getDataTypeName() returns the name of the type of data stored
long	getID()
abstract Double2DArray	getItem(int index)
abstract java.lang.String	getItemName(int index)
abstract int	getItemNumber(NameReference nr)
NameReference	getItemReference(int n)
NameReference	getItemReference(java.lang.String name)
double[][]	getMatrix(int index)
abstract int	getNumberOfItems()
int	getNumItems()
abstract double	getState(int ic, int it) returns state of character ic in taxon/node it
abstract double	getState(int ic, int it, int item) returns state of item item of character ic in taxon/node it
java.lang.Class	getStateClass() Indicates the type of character stored
java.lang.String	toString()
int	userQueryItem(java.lang.String message, MesquiteModule module)

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.MCharactersStatesHolder

getNumChars, getNumTaxa

Constructor Detail

MContinuousStates

public MContinuousStates(Taxa taxa)

Method Detail

getID

public long getID()

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface MCharactersStatesHolder

Specified by:

getStateClass in class MCharactersStates

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

returns the corresponding CharacterData subclass

Specified by:

getCharacterDataClass in interface MCharactersStatesHolder

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

Specified by:

getDataTypeName in interface MCharactersStatesHolder

Specified by:

getDataTypeName in class MCharactersStates

getState

public abstract double getState(int ic,
                                int it)

returns state of character ic in taxon/node it

getState

public abstract double getState(int ic,
                                int it,
                                int item)

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

getItem

public abstract Double2DArray getItem(int index)

getMatrix

public double[][] getMatrix(int index)

userQueryItem

public int userQueryItem(java.lang.String message,
                         MesquiteModule module)

getItemName

public abstract java.lang.String getItemName(int index)

Specified by:

getItemName in interface ItemContainer

getItemNumber

public abstract int getItemNumber(NameReference nr)

Specified by:

getItemNumber in interface ItemContainer

getNumberOfItems

public abstract int getNumberOfItems()

getNumItems

public int getNumItems()

Specified by:

getNumItems in interface ItemContainer

allCombinable

public boolean allCombinable()

allCombinable

public boolean allCombinable(int item)

getItemReference

public NameReference getItemReference(int n)

Specified by:

getItemReference in interface ItemContainer

getItemReference

public NameReference getItemReference(java.lang.String name)

Specified by:

getItemReference in interface ItemContainer

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int ic,
                                        int it)

get CharacterState at node N

Specified by:

getCharacterState in interface MCharactersStatesHolder

Specified by:

getCharacterState in class MCharactersStates

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object