mesquite.cont.lib
Class ContinuousStates

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

All Implemented Interfaces:

ItemContainer, CharacterStatesHolder, Listable, Renamable, WithStringDetails

Direct Known Subclasses:

ContinuousDistribution, GeographicStates

public abstract class ContinuousStates
extends CharacterStates
implements ItemContainer

Contains an array of continuous character states for one character, at each of the taxa or nodes See notes under ContinuousData regarding items

Field Summary

Fields inherited from class mesquite.lib.characters.CharacterStates

characterNumber, data, totalCreated

Constructor Summary

ContinuousStates(Taxa taxa)

Method Summary

boolean	firstIsGreater(int N, int M) Is the first state greater than second? This uses only the first item!
java.lang.Class	getCharacterDataClass() returns the corresponding CharacterData subclass
CharacterState	getCharacterState() returns blank CharacterState object
CharacterState	getCharacterState(CharacterState cs, int N) get CharacterState at node N
java.lang.String	getDataTypeName() returns the name of the type of data stored
CharacterModel	getDefaultModel(MesquiteProject file, java.lang.String paradigm) passed the file, finds the default character model.
abstract java.lang.String	getItemName(int index)
abstract int	getItemNumber(NameReference nr)
abstract NameReference	getItemReference(int index)
abstract NameReference	getItemReference(java.lang.String name)
abstract int	getNumItems()
abstract double	getState(int N)
abstract double	getState(int N, int item)
java.lang.Class	getStateClass() Indicates the type of character stored
boolean	isInapplicable(int N) returns whether the character is inapplicable at node/taxon N
boolean	isUnassigned(int N) returns whether the state of character is missing in node/taxon N
boolean	isUncertain(int N) returns whether the state of character has uncertainty in node/taxon N
void	logStates() output to log a list of the states.
boolean	statesEqual(int N, int M) returns whether states at nodes n and m are equal
java.lang.String	toString(int node, java.lang.String lineEnding) get string describing character states at terminal taxon.
int	userQueryItem(java.lang.String message, MesquiteModule module)

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.CharacterStatesHolder

getNumNodes, getNumTaxa

Constructor Detail

ContinuousStates

public ContinuousStates(Taxa taxa)

Method Detail

getCharacterState

public CharacterState getCharacterState()

returns blank CharacterState object

Specified by:

getCharacterState in interface CharacterStatesHolder

getStateClass

public java.lang.Class getStateClass()

Indicates the type of character stored

Specified by:

getStateClass in interface CharacterStatesHolder

getCharacterDataClass

public java.lang.Class getCharacterDataClass()

returns the corresponding CharacterData subclass

Specified by:

getCharacterDataClass in interface CharacterStatesHolder

getDataTypeName

public java.lang.String getDataTypeName()

returns the name of the type of data stored

getNumItems

public abstract int getNumItems()

Specified by:

getNumItems in interface ItemContainer

getItemName

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

Specified by:

getItemName in interface ItemContainer

getItemReference

public abstract NameReference getItemReference(java.lang.String name)

Specified by:

getItemReference in interface ItemContainer

getItemReference

public abstract NameReference getItemReference(int index)

Specified by:

getItemReference in interface ItemContainer

getItemNumber

public abstract int getItemNumber(NameReference nr)

Specified by:

getItemNumber in interface ItemContainer

getDefaultModel

public CharacterModel getDefaultModel(MesquiteProject file,
                                      java.lang.String paradigm)

Description copied from interface: CharacterStatesHolder

passed the file, finds the default character model. This is not done well yet. Should be passed the paradigm. Is passed the so the CharacterModel object can be looked up

Specified by:

getDefaultModel in interface CharacterStatesHolder

logStates

public void logStates()

Description copied from interface: CharacterStatesHolder

output to log a list of the states. for debugging purposes

Specified by:

logStates in interface CharacterStatesHolder

getState

public abstract double getState(int N,
                                int item)

getState

public abstract double getState(int N)

isInapplicable

public boolean isInapplicable(int N)

Description copied from interface: CharacterStatesHolder

returns whether the character is inapplicable at node/taxon N

Specified by:

isInapplicable in interface CharacterStatesHolder

isUnassigned

public boolean isUnassigned(int N)

Description copied from interface: CharacterStatesHolder

returns whether the state of character is missing in node/taxon N

Specified by:

isUnassigned in interface CharacterStatesHolder

isUncertain

public boolean isUncertain(int N)

returns whether the state of character has uncertainty in node/taxon N

Specified by:

isUncertain in interface CharacterStatesHolder

userQueryItem

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

getCharacterState

public CharacterState getCharacterState(CharacterState cs,
                                        int N)

Description copied from interface: CharacterStatesHolder

get CharacterState at node N

Specified by:

getCharacterState in interface CharacterStatesHolder

firstIsGreater

public boolean firstIsGreater(int N,
                              int M)

Is the first state greater than second? This uses only the first item!

Specified by:

firstIsGreater in interface CharacterStatesHolder

statesEqual

public boolean statesEqual(int N,
                           int M)

Description copied from interface: CharacterStatesHolder

returns whether states at nodes n and m are equal

Specified by:

statesEqual in interface CharacterStatesHolder

toString

public java.lang.String toString(int node,
                                 java.lang.String lineEnding)

Description copied from interface: CharacterStatesHolder

get string describing character states at terminal taxon.

Specified by:

toString in interface CharacterStatesHolder