mesquite.cont.lib
Class MContinuousAdjustable

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

All Implemented Interfaces:

ItemContainer, Annotatable, MAdjustableDistribution, MCharactersDistribution, MCharactersStatesHolder, Listable, Renamable

Direct Known Subclasses:

MContinuousHistory

public class MContinuousAdjustable
extends MContinuousDistribution
implements MAdjustableDistribution

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

Field Summary

protected Double2DArray	firstMatrix
protected java.util.Vector	matrices

Fields inherited from class mesquite.lib.characters.MCharactersStates

data

Constructor Summary

MContinuousAdjustable()

MContinuousAdjustable(Taxa taxa)

MContinuousAdjustable(Taxa taxa, int numChars, int numTaxa)

Method Summary

Double2DArray	addItem(NameReference nr)
Double2DArray	addItem(java.lang.String name)
void	deassignStates() assign missing data (unassigned) to all of the characters
Double2DArray	establishItem(NameReference nr) Make an item with the passed name.
Double2DArray	establishItem(java.lang.String name)
java.lang.String	getAnnotation()
CharacterDistribution	getCharacterDistribution(int ic) return CharacterDistribution object for character ic
Double2DArray	getItem(int index)
java.lang.String	getItemName(int index)
int	getItemNumber(NameReference nr)
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
void	removeItem(int item) Removes item.
void	setAnnotation(java.lang.String s, boolean notify)
void	setCharacterState(CharacterState cs, int ic, int it) sets the state of character ic in taxon it from CharacterState cs.
void	setItemReference(int index, NameReference nr) Sets the name reference for the item number "index".
void	setItemsAs(ItemContainer iCont)
void	setParentData(CharacterData cd) sets the parent CharacterData from which this CharacterDistribution is derived or related
void	setSize(int numChars, int numTaxa) Set the size of the matrix
void	setState(int ic, int N, double d)
void	setState(int ic, int N, int item, double d)
void	setStates(Double2DArray matrix)
void	setStates(java.util.Vector matrices)
void	tradeStatesBetweenTaxa(int ic, int it, int it2) trades the states of character ic between taxa it and it2.
void	transferFrom(int ic, CharacterDistribution s) obtain the states of character ic from the given CharacterDistribution

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, getName, 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.MAdjustableDistribution

setTaxa

Methods inherited from interface mesquite.lib.characters.MCharactersDistribution

adjustHistorySize, getBasisTree, makeBlankAdjustable, makeCharacterData, setBasisTree

Methods inherited from interface mesquite.lib.characters.MCharactersStatesHolder

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

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Field Detail

firstMatrix

protected Double2DArray firstMatrix

matrices

protected java.util.Vector matrices

Constructor Detail

MContinuousAdjustable

public MContinuousAdjustable(Taxa taxa,
                             int numChars,
                             int numTaxa)

MContinuousAdjustable

public MContinuousAdjustable(Taxa taxa)

MContinuousAdjustable

public MContinuousAdjustable()

Method Detail

setAnnotation

public void setAnnotation(java.lang.String s,
                          boolean notify)

Specified by:

setAnnotation in interface Annotatable

getAnnotation

public java.lang.String getAnnotation()

Specified by:

getAnnotation in interface Annotatable

setParentData

public void setParentData(CharacterData cd)

sets the parent CharacterData from which this CharacterDistribution is derived or related

Specified by:

setParentData in interface MAdjustableDistribution

setSize

public void setSize(int numChars,
                    int numTaxa)

Description copied from interface: MAdjustableDistribution

Set the size of the matrix

Specified by:

setSize in interface MAdjustableDistribution

addItem

public Double2DArray addItem(NameReference nr)

addItem

public Double2DArray addItem(java.lang.String name)

establishItem

public Double2DArray establishItem(java.lang.String name)

establishItem

public Double2DArray establishItem(NameReference nr)

Make an item with the passed name. If the an item already made is not yet named, then this will simply use this item and give it a new name. Otherwise, a new matrix is made for a new item, and the name is attached to it.

getNumberOfItems

public int getNumberOfItems()

Specified by:

getNumberOfItems in class MContinuousStates

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

setItemsAs

public void setItemsAs(ItemContainer iCont)

removeItem

public void removeItem(int item)

Removes item.

setItemReference

public void setItemReference(int index,
                             NameReference nr)

Sets the name reference for the item number "index".

deassignStates

public void deassignStates()

Description copied from interface: MAdjustableDistribution

assign missing data (unassigned) to all of the characters

Specified by:

deassignStates in interface MAdjustableDistribution

transferFrom

public void transferFrom(int ic,
                         CharacterDistribution s)

obtain the states of character ic from the given CharacterDistribution

Specified by:

transferFrom in interface MAdjustableDistribution

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

setStates

public void setStates(java.util.Vector matrices)

setStates

public void setStates(Double2DArray matrix)

setState

public void setState(int ic,
                     int N,
                     int item,
                     double d)

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

setState

public void setState(int ic,
                     int N,
                     double d)

setCharacterState

public void setCharacterState(CharacterState cs,
                              int ic,
                              int it)

sets the state of character ic in taxon it from CharacterState cs. If incoming CharacterState has more items or items with names not seen in this ContinuousData, then new items are created in the ContinuousData

Specified by:

setCharacterState in interface MAdjustableDistribution

tradeStatesBetweenTaxa

public void tradeStatesBetweenTaxa(int ic,
                                   int it,
                                   int it2)

Description copied from interface: MAdjustableDistribution

trades the states of character ic between taxa it and it2. Used for reshuffling.

Specified by:

tradeStatesBetweenTaxa in interface MAdjustableDistribution

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

Specified by:

getNumTaxa in interface MCharactersStatesHolder

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()

Specified by:

getNumChars in interface MCharactersStatesHolder