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## org.thalia.bio.entity
Class Locus

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

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