org.thalia.bio.entity
Class AlleleContainer

java.lang.Object
  org.thalia.bio.entity.BioEntity
      org.thalia.bio.entity.BioEntityContainer
          org.thalia.bio.entity.AlleleContainer

All Implemented Interfaces:

IBioAdaptable, IBioEntity, IBioLocus

Direct Known Subclasses:

Locus

public abstract class AlleleContainer
extends BioEntityContainer
implements IBioLocus

Class Description Here

Author:

Jean-Baptiste Veyrieras

Field Summary

Fields inherited from class org.thalia.bio.entity.BioEntityContainer

entities

Fields inherited from class org.thalia.bio.entity.BioEntity

name, parent, properties

Fields inherited from interface org.thalia.bio.IBioLocus

MARKER, QTL, TypesString

Constructor Summary

AlleleContainer()

AlleleContainer(java.lang.String name, IBioEntity parent)

Method Summary

void	addAllele(IBioAllele allele)
IBioAllele[]	alleles()
IBioAllele	getAllele(java.lang.String name)
int	getAlleleNumber()
IBioLGroup	getGroup()
abstract ILGroupPosition	getPosition()
abstract int	getType() There are 2 main class of entities.
void	removeAllele(java.lang.String name)
void	setGroup(IBioLGroup group)
abstract void	setPosition(ILGroupPosition position)

Methods inherited from class org.thalia.bio.entity.BioEntityContainer

addEntity, entities, entityNumber, getEntity, removeEntity

Methods inherited from class org.thalia.bio.entity.BioEntity

getName, getParent, getProperties, newBioEntity, setName, setProperties

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.thalia.bio.IBioLocus

getLocusType, setPosition, setPosition

Methods inherited from interface org.thalia.bio.IBioEntity

getName, getParent, getProperties, setName, setProperties

Methods inherited from interface org.thalia.bio.IBioAdaptable

getBioAdapter

Constructor Detail

AlleleContainer

public AlleleContainer()

AlleleContainer

public AlleleContainer(java.lang.String name,
                       IBioEntity parent)

Parameters:

name -

parent -

Method Detail

getType

public abstract int getType()

Description copied from interface: IBioEntity

There are 2 main class of entities. The first one deals with population biological entity, i.e population itself and individuals. The second class is a representation of microscopic biological entity from genome container to alleles.

Specified by:

getType in interface IBioEntity

Specified by:

getType in interface IBioLocus

Specified by:

getType in class BioEntity

alleles

public IBioAllele[] alleles()

Specified by:

alleles in interface IBioLocus

addAllele

public void addAllele(IBioAllele allele)

Specified by:

addAllele in interface IBioLocus

removeAllele

public void removeAllele(java.lang.String name)

Specified by:

removeAllele in interface IBioLocus

getAllele

public IBioAllele getAllele(java.lang.String name)

Specified by:

getAllele in interface IBioLocus

getGroup

public IBioLGroup getGroup()

Specified by:

getGroup in interface IBioLocus

setGroup

public void setGroup(IBioLGroup group)

Specified by:

setGroup in interface IBioLocus

getAlleleNumber

public int getAlleleNumber()

Specified by:

getAlleleNumber in interface IBioLocus

getPosition

public abstract ILGroupPosition getPosition()

Specified by:

getPosition in interface IBioLocus

setPosition

public abstract void setPosition(ILGroupPosition position)

Specified by:

setPosition in interface IBioLocus