Uses of Class
org.metaqtl.Chromosome

Packages that use Chromosome

org.metaqtl
org.metaqtl.adapter
org.metaqtl.algo
org.metaqtl.graph
org.metaqtl.main

Uses of Chromosome in org.metaqtl

Fields in org.metaqtl declared as Chromosome

Chromosome

ChromCluster.ClusterEdge.chrom

Methods in org.metaqtl that return Chromosome

Chromosome[]	ChromCluster.getClusterMembers() This method returns the members of the cluster as an array of Chromosomes.
Chromosome	Chromosome.getSubChromosome(java.lang.String[] markerNames)

Methods in org.metaqtl with parameters of type Chromosome

void	ChromCluster.ClusterGraph.addEdge(Chromosome cur1, Chromosome cur2, CMarkerSequence cms)
static double[]	Chromosome.getDistHeterogeneity(int ncm, int[][] mrkIdx, Chromosome chrom, Chromosome ref)
static int	Chromosome.getFirstCommonMrkIdx(Chromosome chrom, Chromosome chrom2)
static double[]	Chromosome.getRecHeterogeneity(int ncm, int[][] mrkIdx, Chromosome chrom, Chromosome ref)

Constructors in org.metaqtl with parameters of type Chromosome

ChromCluster.ClusterEdge(CMarkerSequence cms, Chromosome chrom)

Uses of Chromosome in org.metaqtl.adapter

Methods in org.metaqtl.adapter that return Chromosome

static Chromosome	ChromosomeAdapter.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[]	ChromosomeAdapter.toChromosomes(IBioGenome map) This methods converts the given map into an array of Chromosome which represents the chromosomes of the input mpe.

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

static MetaQtlAnalysis	MetaQtlAnalysisAdapter.adapt(Chromosome[] chromosomes)
static IBioGenome	ChromosomeAdapter.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.

Uses of Chromosome in org.metaqtl.algo

Fields in org.metaqtl.algo declared as Chromosome

protected Chromosome[]

ClustAlgorithm.chromosomes The chromosome on which the clustering is performed.

Methods in org.metaqtl.algo that return Chromosome

Chromosome[]

QtlProjAlgorithm.getResult()

Methods in org.metaqtl.algo with parameters of type Chromosome

static CMarkerSequence

CMSAlgorithm.run(Chromosome chrom1, Chromosome chrom2) This methods find the common marker sequences between the two given chromosomes.

Uses of Chromosome in org.metaqtl.graph

Fields in org.metaqtl.graph declared as Chromosome

Chromosome

ChromGraph.chromosome The chromosome to draw

Uses of Chromosome in org.metaqtl.main

Methods in org.metaqtl.main that return Chromosome

static Chromosome[]

MetaMain.getChromByNames(Chromosome[] chroms, java.lang.String[] chromNames)

Methods in org.metaqtl.main with parameters of type Chromosome

static Chromosome[]	MetaMain.getChromByNames(Chromosome[] chroms, java.lang.String[] chromNames)
static ChromGraph[]	MetaMain.getChromGraph(Chromosome[] chroms, boolean withQtl, int modeQtl, IBioOntology ontology, MetaQtlAnalysis treeAnalysis)
static QtlPartition	MetaMain.getQtlPartition(Chromosome chromosome, IBioOntology ontology)
static QtlPartition	MetaMain.getQtlPartition(Chromosome chrom, MetaQtlAnalysis analysis, java.lang.String trait, int k, char tclust)