mesquite.cont.lib
Class ContinuousAdjustable

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

All Implemented Interfaces:

ItemContainer, AdjustableDistribution, CharacterDistribution, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

ContinuousHistory, GeographicAdjustable

public class ContinuousAdjustable
extends ContinuousDistribution
implements AdjustableDistribution

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

Field Summary

protected DoubleArray	firstItem
protected java.util.Vector	items
protected int	numNodes

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, data, totalCreated

Constructor Summary

ContinuousAdjustable(Taxa taxa, int numNodes)

Method Summary

DoubleArray	addItem(NameReference nr)
DoubleArray	addItem(java.lang.String name)
AdjustableDistribution	adjustSize(Taxa taxa) This readjust procedure can be called to readjust the size of storage of states of a character for nodes.
void	deassignStates() set all states to missing (unassigned)
DoubleArray	establishItem(NameReference nr) Make an item with the passed name.
DoubleArray	establishItem(java.lang.String name)
DoubleArray	getItem(int index)
java.lang.String	getItemName(int index)
int	getItemNumber(NameReference nr)
NameReference	getItemReference(int index)
NameReference	getItemReference(java.lang.String name)
int	getNumItems()
int	getNumNodes() returns number of nodes for which CharacterStates is defined (either terminal taxa, if CharacterDistribution, or all nodes in tree, if CharacterHistory)
int	getNumTaxa() This is the same as getNumNodes.
double	getState(int N)
double	getState(int N, int item)
void	removeItem(int item) Removes item.
void	setCharacterState(int N, CharacterState cs) sets CharacterState at node/taxon it
void	setItemReference(int index, NameReference nr) Sets the name reference for the item number "index".
void	setItems(ContinuousAdjustable s)
void	setItems(java.lang.String[] names)
void	setItemsAs(ItemContainer iCont)
void	setState(int N, double d)
void	setState(int N, int item, double d)
void	tradeStatesBetweenTaxa(int it, int it2) Trade states of nodes it and it2

Methods inherited from class mesquite.cont.lib.ContinuousDistribution

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

Methods inherited from class mesquite.cont.lib.ContinuousStates

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

Methods inherited from class mesquite.lib.characters.CharacterStates

checkIllegalNode, getName, getParentCharacter, getParentData, 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.AdjustableDistribution

setParentCharacter, setParentData

Methods inherited from interface mesquite.lib.characters.CharacterStatesHolder

firstIsGreater, getCharacterDataClass, getCharacterState, getCharacterState, getDefaultModel, getParentCharacter, getParentData, getStateClass, getTaxa, isInapplicable, isUnassigned, isUncertain, logStates, statesEqual, toString, toStringWithDetails

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Renamable

setName

Field Detail

firstItem

protected DoubleArray firstItem

items

protected java.util.Vector items

numNodes

protected int numNodes

Constructor Detail

ContinuousAdjustable

public ContinuousAdjustable(Taxa taxa,
                            int numNodes)

Method Detail

getNumItems

public int getNumItems()

Specified by:

getNumItems in interface ItemContainer

Specified by:

getNumItems 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

Specified by:

getNumTaxa in interface CharacterStatesHolder

getNumNodes

public int getNumNodes()

Description copied from interface: CharacterStatesHolder

returns number of nodes for which CharacterStates is defined (either terminal taxa, if CharacterDistribution, or all nodes in tree, if CharacterHistory)

Specified by:

getNumNodes in interface CharacterStatesHolder

Overrides:

getNumNodes in class ContinuousDistribution

addItem

public DoubleArray addItem(NameReference nr)

establishItem

public DoubleArray establishItem(java.lang.String name)

establishItem

public DoubleArray 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.

addItem

public DoubleArray addItem(java.lang.String name)

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".

setItems

public void setItems(ContinuousAdjustable s)

setItems

public void setItems(java.lang.String[] names)

getItem

public DoubleArray getItem(int index)

getItemName

public java.lang.String getItemName(int index)

Specified by:

getItemName in interface ItemContainer

Specified by:

getItemName 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

deassignStates

public void deassignStates()

Description copied from interface: AdjustableDistribution

set all states to missing (unassigned)

Specified by:

deassignStates in interface AdjustableDistribution

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

setState

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

setState

public void setState(int N,
                     double d)

setCharacterState

public void setCharacterState(int N,
                              CharacterState cs)

Description copied from interface: AdjustableDistribution

sets CharacterState at node/taxon it

Specified by:

setCharacterState in interface AdjustableDistribution

tradeStatesBetweenTaxa

public void tradeStatesBetweenTaxa(int it,
                                   int it2)

Trade states of nodes it and it2

Specified by:

tradeStatesBetweenTaxa in interface AdjustableDistribution

adjustSize

public AdjustableDistribution adjustSize(Taxa taxa)

This readjust procedure can be called to readjust the size of storage of states of a character for nodes.

Specified by:

adjustSize in interface AdjustableDistribution