org.metaqtl.bio.entity
Class Locus

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

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.metaqtl.bio.entity.AlleleContainer

addAllele, alleles, getAllele, getAlleleNumber, getType, removeAllele

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

addAllele, alleles, getAllele, getAlleleNumber, getLocusType, getType, removeAllele

Methods inherited from interface org.metaqtl.bio.IBioEntity

getName, getParent, getProperties, setName, setProperties

Methods inherited from interface org.metaqtl.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.