org.metaqtl.bio.entity
Class LocusContainer

java.lang.Object
  extended by org.metaqtl.bio.entity.BioEntity
      extended by org.metaqtl.bio.entity.BioEntityContainer
          extended by org.metaqtl.bio.entity.LocusContainer
All Implemented Interfaces:
IBioAdaptable, IBioEntity, IBioLGroup
Direct Known Subclasses:
LGroup

public abstract class LocusContainer
extends BioEntityContainer
implements IBioLGroup

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
 
Constructor Summary
LocusContainer()
           
LocusContainer(java.lang.String name, IBioEntity parent)
           
 
Method Summary
 void addLocus(IBioLocus locus)
           
 IBioGenome getGenome()
           
 IBioLocus getLocus(java.lang.String name)
           
 int getLocusNumber()
           
abstract  int getType()
          There are 2 main class of entities.
 IBioLocus[] loci()
           
 void removeLocus(java.lang.String name)
           
 void setGenome(IBioGenome genome)
           
 void setLoci(IBioLocus[] loci)
           
 
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.IBioEntity
getName, getParent, getProperties, setName, setProperties
 
Methods inherited from interface org.metaqtl.bio.IBioAdaptable
getBioAdapter
 

Constructor Detail

LocusContainer

public LocusContainer()

LocusContainer

public LocusContainer(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 class BioEntity

getGenome

public IBioGenome getGenome()
Specified by:
getGenome in interface IBioLGroup

setGenome

public void setGenome(IBioGenome genome)
Specified by:
setGenome in interface IBioLGroup

loci

public IBioLocus[] loci()
Specified by:
loci in interface IBioLGroup

addLocus

public void addLocus(IBioLocus locus)
Specified by:
addLocus in interface IBioLGroup

getLocus

public IBioLocus getLocus(java.lang.String name)
Specified by:
getLocus in interface IBioLGroup

removeLocus

public void removeLocus(java.lang.String name)
Specified by:
removeLocus in interface IBioLGroup

getLocusNumber

public int getLocusNumber()
Specified by:
getLocusNumber in interface IBioLGroup

setLoci

public void setLoci(IBioLocus[] loci)
Specified by:
setLoci in interface IBioLGroup