org.metaqtl.bio.entity
Class AlleleContainer

java.lang.Object
  extended by org.metaqtl.bio.entity.BioEntity
      extended by org.metaqtl.bio.entity.BioEntityContainer
          extended by org.metaqtl.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.metaqtl.bio.entity.BioEntityContainer
entities
 
Fields inherited from class org.metaqtl.bio.entity.BioEntity
name, parent, properties
 
Fields inherited from interface org.metaqtl.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.metaqtl.bio.entity.BioEntityContainer
addEntity, entities, entityNumber, getEntity, removeEntity
 
Methods inherited from class org.metaqtl.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.metaqtl.bio.IBioLocus
getLocusType, setPosition, setPosition
 
Methods inherited from interface org.metaqtl.bio.IBioEntity
getName, getParent, getProperties, setName, setProperties
 
Methods inherited from interface org.metaqtl.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