org.metaqtl.adapter
Class ChromosomeAdapter

java.lang.Object
  org.metaqtl.adapter.ChromosomeAdapter

public final class ChromosomeAdapter
extends java.lang.Object

This class defines some usefull methods to adapt Chromosome objects into other kinds of objects or the inverse.

Constructor Summary

ChromosomeAdapter()

Method Summary

static Chromosome	toChromosome(IBioLGroup group, IBioCross crossDesign, int mappingFunction, int mappingUnit) This method converts a linkage group into a chromosome of type Chromosome with the given cross design and the given mapping context.
static Chromosome[]	toChromosomes(IBioGenome map) This methods converts the given map into an array of Chromosome which represents the chromosomes of the input mpe.
static IBioGenome	toIBioGenome(Chromosome[] chromosomes, int gout) This routine converts an array of chromosomes into a genetic map with as many chromosomes as the length of the array.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ChromosomeAdapter

public ChromosomeAdapter()

Method Detail

toChromosomes

public static Chromosome[] toChromosomes(IBioGenome map)

This methods converts the given map into an array of Chromosome which represents the chromosomes of the input mpe.

Parameters:

map -

Returns:

an array of Chromosome

toChromosome

public static Chromosome toChromosome(IBioLGroup group,
                                      IBioCross crossDesign,
                                      int mappingFunction,
                                      int mappingUnit)

This method converts a linkage group into a chromosome of type Chromosome with the given cross design and the given mapping context.

Parameters:

group - the linkage group to convert.

crossDesign - the cross design.

mappingFunction - the mapping function.

mappingUnit - the mapping unit.

Returns:

the chromosome

toIBioGenome

public static IBioGenome toIBioGenome(Chromosome[] chromosomes,
                                      int gout)

This routine converts an array of chromosomes into a genetic map with as many chromosomes as the length of the array. The second argument gout takes its values in [0,2] :

• 0 - Both marker and QTL are included.
• 1 - Only marker are included.
• 2 - Only QTL are included.

Use the static attributes MAPPING_UNIT and MAPPING_FUNCTION to change the genetic map mapping unit and function.

Parameters:

chromosomes - the array of Chromosome to convert.

gout - the convertion mode.

Returns:

a genetic map.