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)