Uses of Interface
org.metaqtl.bio.IBioLocus

Packages that use IBioLocus

org.metaqtl
org.metaqtl.adapter
org.metaqtl.algo
org.metaqtl.bio
org.metaqtl.bio.entity
org.metaqtl.bio.util
org.metaqtl.factory
org.metaqtl.main
org.metaqtl.util

Uses of IBioLocus in org.metaqtl

Methods in org.metaqtl with parameters of type IBioLocus

void	Chromosome.attachQTL(IBioLocus[] qtls) Add
boolean	ChromCluster.isDubiousLocus(IBioLocus locus) If a list of dubious markers has been set before then this routine checks if the given locus is not included into this list.
void	ChromCluster.setDubiousMarker(IBioLocus[] dubious) This method sets the list of dubious marker.
void	MapCluster.setDubiousMarker(IBioLocus[] dubious) This method sets the list of dubious marker.

Uses of IBioLocus in org.metaqtl.adapter

Methods in org.metaqtl.adapter that return IBioLocus

static IBioLocus

QtlAdapter.fromQTL(Qtl qtl) This method converts a Qtl into an object which class implements the IBioLocus interface.

Methods in org.metaqtl.adapter with parameters of type IBioLocus

static Qtl

QtlAdapter.toQTL(IBioLocus locus) This method converts an object which class implements the IBioLocus interface into a Qtl.

Uses of IBioLocus in org.metaqtl.algo

Constructors in org.metaqtl.algo with parameters of type IBioLocus

MetaMapAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious, MetaDico mrkDico)

QtlProjAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious)
Creates a new instance of QtlProjAlgorithm for the given configuration of projection.

Uses of IBioLocus in org.metaqtl.bio

Methods in org.metaqtl.bio that return IBioLocus

IBioLocus	IBioAllele.getLocus()
IBioLocus	IBioLGroup.getLocus(java.lang.String name)
IBioLocus[]	IBioLGroup.loci()

Methods in org.metaqtl.bio with parameters of type IBioLocus

void	IBioLGroup.addLocus(IBioLocus locus)
void	IBioLGroup.setLoci(IBioLocus[] loci)
void	IBioAllele.setLocus(IBioLocus locus)

Uses of IBioLocus in org.metaqtl.bio.entity

Classes in org.metaqtl.bio.entity that implement IBioLocus

class	AlleleContainer Class Description Here
class	Locus
class	Marker Class Description Here
class	QTL Class Description Here

Fields in org.metaqtl.bio.entity declared as IBioLocus

static IBioLocus[]

IBioConstants.EMPTY_BIOLOCUS_ARRAY

Methods in org.metaqtl.bio.entity that return IBioLocus

IBioLocus	LocusContainer.getLocus(java.lang.String name)
IBioLocus[]	LocusContainer.loci()

Methods in org.metaqtl.bio.entity with parameters of type IBioLocus

void	LocusContainer.addLocus(IBioLocus locus)
void	LocusContainer.setLoci(IBioLocus[] loci)

Uses of IBioLocus in org.metaqtl.bio.util

Methods in org.metaqtl.bio.util that return IBioLocus

static IBioLocus[]	BioLocusTypes.extractLocus(IBioLocus[] loci, int type) This returns extracts in the given array of loci the locus which type matches the given one.
static IBioLocus[]	BioUtilities.sortLociByPosition(IBioLocus[] loci) Sort tab with loci

Methods in org.metaqtl.bio.util with parameters of type IBioLocus

static IBioLocus[]	BioLocusTypes.extractLocus(IBioLocus[] loci, int type) This returns extracts in the given array of loci the locus which type matches the given one.
static IBioLocus[]	BioUtilities.sortLociByPosition(IBioLocus[] loci) Sort tab with loci

Uses of IBioLocus in org.metaqtl.factory

Methods in org.metaqtl.factory that return IBioLocus

static IBioLocus[]

DubiousLocusFactory.read(java.io.Reader reader) This routine reads the list of dubious markers from the given file location and returns if succeed an array of IBioLocus objects.

Uses of IBioLocus in org.metaqtl.main

Methods in org.metaqtl.main that return IBioLocus

protected static IBioLocus[]

MetaMain.getDubious(java.lang.String dubFile)

Uses of IBioLocus in org.metaqtl.util

Methods in org.metaqtl.util with parameters of type IBioLocus

static int	LocusProperties.getMetaOccurence(IBioLocus locus)
static boolean	LocusProperties.isDubiousOrderLocus(IBioLocus locus) Returns true if the given locus has a property order.dubious set to one, false otherwise