jebl.evolution.characters

Class DiscreteCharacter

java.lang.Object

jebl.evolution.characters.DiscreteCharacter

All Implemented Interfaces:

Character

public class DiscreteCharacter
extends java.lang.Object
implements Character

Author:

Stephen A. Smith

Constructor Summary

Constructors

Constructor and Description
DiscreteCharacter(java.lang.String name, java.lang.String desc, int numOfStates) Constructs a basic DiscreteCharacter object with no taxa added yet
DiscreteCharacter(java.lang.String name, java.lang.String desc, int numOfStates, java.util.Set<Taxon> taxa) Constructs a basic DiscreteCharacter object with taxa

Method Summary

Methods

Modifier and Type	Method and Description
void	addTaxon(Taxon taxon) add a taxon with this character
java.lang.String	getDesc() return the description of the character
java.lang.String	getName() return the name of the character
double	getNumOfStates()
java.util.Map<java.lang.Integer,java.lang.String>	getStateDesc()
java.lang.String	getStateDesc(int state)
java.util.Set<Taxon>	getTaxa() get a Set of all the taxa for this character
CharacterType	getType() return the CharacterType of the character
java.lang.Object	getValue(Taxon taxon) get a value for a taxon containing the character
boolean	isOrdered()
void	setDesc(java.lang.String desc) set the description of the character
void	setIsOrdered(boolean isOrdered)
void	setName(java.lang.String name) set the name of the character
void	setNumOfStates(int numOfStates)
void	setStateDesc(java.util.Map<java.lang.Integer,java.lang.String> stateDesc)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DiscreteCharacter

public DiscreteCharacter(java.lang.String name,
                 java.lang.String desc,
                 int numOfStates)

Constructs a basic DiscreteCharacter object with no taxa added yet

Parameters:

name - the name of the character

desc - the description of the character

numOfStates - the number of possible states for the character

DiscreteCharacter

public DiscreteCharacter(java.lang.String name,
                 java.lang.String desc,
                 int numOfStates,
                 java.util.Set<Taxon> taxa)

Constructs a basic DiscreteCharacter object with taxa

Parameters:

name - the name of the character

desc - the description of the character

numOfStates - the number of possible states for the character

taxa - the Set containing the taxa with this character

Method Detail

setName

public void setName(java.lang.String name)

Description copied from interface: Character

set the name of the character

Specified by:

setName in interface Character

Parameters:

name - the name of the character

getName

public java.lang.String getName()

Description copied from interface: Character

return the name of the character

Specified by:

getName in interface Character

Returns:

the name of the character

setDesc

public void setDesc(java.lang.String desc)

Description copied from interface: Character

set the description of the character

Specified by:

setDesc in interface Character

Parameters:

desc - the description of the character

getDesc

public java.lang.String getDesc()

Description copied from interface: Character

return the description of the character

Specified by:

getDesc in interface Character

Returns:

the description of the character

getType

public CharacterType getType()

Description copied from interface: Character

return the CharacterType of the character

Specified by:

getType in interface Character

Returns:

the CharacterType of the character

addTaxon

public void addTaxon(Taxon taxon)

Description copied from interface: Character

add a taxon with this character

Specified by:

addTaxon in interface Character

Parameters:

taxon - the taxon to add containing the character

getValue

public java.lang.Object getValue(Taxon taxon)

Description copied from interface: Character

get a value for a taxon containing the character

Specified by:

getValue in interface Character

Parameters:

taxon - the taxon to get the value for

Returns:

the Object value of the character for the given taxon

isOrdered

public boolean isOrdered()

Returns:

whether character is ordered or not

setIsOrdered

public void setIsOrdered(boolean isOrdered)

Parameters:

isOrdered - set whether character is ordered or not

getNumOfStates

public double getNumOfStates()

Returns:

the number of possible states for the character

setNumOfStates

public void setNumOfStates(int numOfStates)

Parameters:

numOfStates - the number of possible states for the characeter

getTaxa

public java.util.Set<Taxon> getTaxa()

Description copied from interface: Character

get a Set of all the taxa for this character

Specified by:

getTaxa in interface Character

Returns:

a Set containing all of the taxa for this character

setStateDesc

public void setStateDesc(java.util.Map<java.lang.Integer,java.lang.String> stateDesc)

Parameters:

stateDesc - a Map of the state descriptions corresponding to the values

getStateDesc

public java.util.Map<java.lang.Integer,java.lang.String> getStateDesc()

Returns:

the Map of the state descriptions corresponding to the values

getStateDesc

public java.lang.String getStateDesc(int state)

Parameters:

state - corresponding to the state

Returns:

state description