org.biojavax.ga
Interface Organism

All Superinterfaces:

Changeable

All Known Implementing Classes:

AbstractOrganism, SimpleOrganism

public interface Organism
extends Changeable

A GA 'organism' contains one or more Chromosomes

Since:

1.5

Version:

1.0

Author:

Mark Schreiber

Field Summary

static ChangeType	CHROMOSOMES
static ChangeType	NAME

Method Summary

SymbolList[]	getChromosomes() Gets the organisms 'chromosome' sequences
String	getName() Gets the organisms name
boolean	isHaploid() Is the organism Haploid?
Organism	replicate(String name) Creates a replica of this Organism with a new name.
void	setChromosomes(SymbolList[] chromosomes) Sets the organisms 'chromosome' sequences.
void	setName(String name) Sets the organisms name

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

CHROMOSOMES

static final ChangeType CHROMOSOMES

NAME

static final ChangeType NAME

Method Detail

getChromosomes

SymbolList[] getChromosomes()

Gets the organisms 'chromosome' sequences

Returns:

a SymbolList[]

setChromosomes

void setChromosomes(SymbolList[] chromosomes)
                    throws ChangeVetoException

Sets the organisms 'chromosome' sequences.

Parameters:

chromosomes - a SymbolList[]

Throws:

ChangeVetoException - if the Chromosome collection of the Organism is unchangable

getName

String getName()

Gets the organisms name

Returns:

the name String

setName

void setName(String name)
             throws ChangeVetoException

Sets the organisms name

Parameters:

name - the name of the organism.

Throws:

ChangeVetoException - if the name may not be changed.

replicate

Organism replicate(String name)

Creates a replica of this Organism with a new name.

Parameters:

name - the new name for the sequence.

Returns:

the replicated organism.

isHaploid

boolean isHaploid()

Is the organism Haploid?

Returns:

true if it is.