org.thalia.bio.entity
Class Locus

java.lang.Object
  extended by org.thalia.bio.entity.BioEntity
      extended by org.thalia.bio.entity.BioEntityContainer
          extended by org.thalia.bio.entity.AlleleContainer
              extended by org.thalia.bio.entity.Locus
All Implemented Interfaces:
IBioAdaptable, IBioEntity, IBioLocus
Direct Known Subclasses:
Marker, QTL

public abstract class Locus
extends AlleleContainer
implements IBioLocus


Field Summary
protected  ILGroupPosition position
           
 
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
Locus()
           
Locus(java.lang.String name, IBioEntity parent)
           
 
Method Summary
 IBioLGroup getGroup()
           
static IBioAdapter getLocusAdapter()
           
 ILGroupPosition getPosition()
           
static Locus newLocus(int locusType)
          Returns a new Locus from the given locus type.
static Locus newLocus(java.lang.String string)
          Returns a new Locus from the given locus type.
 void setGroup(IBioLGroup group)
           
 void setPosition(double position)
          Set the position of the locus on the linkage group in static mode i.e without uncertainty.
 void setPosition(double position, double sd)
          Set the position of the locus on the linkage group in estimate mode i.e with uncertainty.
 void setPosition(ILGroupPosition position)
           
 
Methods inherited from class org.thalia.bio.entity.AlleleContainer
addAllele, alleles, getAllele, getAlleleNumber, getType, removeAllele
 
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
addAllele, alleles, getAllele, getAlleleNumber, getLocusType, getType, removeAllele
 
Methods inherited from interface org.thalia.bio.IBioEntity
getName, getParent, getProperties, setName, setProperties
 
Methods inherited from interface org.thalia.bio.IBioAdaptable
getBioAdapter
 

Field Detail

position

protected ILGroupPosition position
Constructor Detail

Locus

public Locus()

Locus

public Locus(java.lang.String name,
             IBioEntity parent)
Parameters:
name -
parent -
Method Detail

newLocus

public static Locus newLocus(int locusType)
Returns a new Locus from the given locus type.

Parameters:
locusType -
Returns:

newLocus

public static Locus newLocus(java.lang.String string)
Returns a new Locus from the given locus type.

Parameters:
string -
Returns:

getLocusAdapter

public static IBioAdapter getLocusAdapter()
Returns:

getGroup

public IBioLGroup getGroup()
Specified by:
getGroup in interface IBioLocus
Overrides:
getGroup in class AlleleContainer

setGroup

public void setGroup(IBioLGroup group)
Specified by:
setGroup in interface IBioLocus
Overrides:
setGroup in class AlleleContainer

getPosition

public ILGroupPosition getPosition()
Specified by:
getPosition in interface IBioLocus
Specified by:
getPosition in class AlleleContainer

setPosition

public void setPosition(ILGroupPosition position)
Specified by:
setPosition in interface IBioLocus
Specified by:
setPosition in class AlleleContainer

setPosition

public void setPosition(double position)
Set the position of the locus on the linkage group in static mode i.e without uncertainty.

Specified by:
setPosition in interface IBioLocus
Parameters:
position - the locus position - absolute.

setPosition

public void setPosition(double position,
                        double sd)
Set the position of the locus on the linkage group in estimate mode i.e with uncertainty.

Specified by:
setPosition in interface IBioLocus
Parameters:
position - the locus position - absolute.