Uses of Interface
org.metaqtl.bio.IBioGenome

Packages that use IBioGenome
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 IBioGenome in org.metaqtl
 

Methods in org.metaqtl with parameters of type IBioGenome
 void MapCluster.addAllMap(IBioGenome[] maps)
           
 void MapCluster.addMap(IBioGenome map, boolean skeleton)
          Add a map to the cluster.
 

Uses of IBioGenome in org.metaqtl.adapter
 

Methods in org.metaqtl.adapter that return IBioGenome
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.
static IBioGenome MetaMapAdapter.toIBioGenome(MetaMap metaMap)
          This methos convert a MetaMap object into an object which is consistent with the IBioGenome interface.
 

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

Uses of IBioGenome in org.metaqtl.algo
 

Constructors in org.metaqtl.algo with parameters of type IBioGenome
ClustAlgorithm(IBioGenome map, IBioOntology ontology)
           
ClustAlgorithm(IBioGenome map, java.lang.String name, IBioOntology ontology)
           
MetaMapAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious, MetaDico mrkDico)
           
MetaMapAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious, MetaDico mrkDico)
           
QtlClustAlgorithm(IBioGenome map, IBioOntology ontology)
           
QtlClustAlgorithm(IBioGenome map, java.lang.String chrom, IBioOntology ontology)
           
QtlProjAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious)
          Creates a new instance of QtlProjAlgorithm for the given configuration of projection.
QtlProjAlgorithm(IBioGenome[] maps, IBioGenome skeleton, IBioLocus[] dubious)
          Creates a new instance of QtlProjAlgorithm for the given configuration of projection.
QtlTreeAlgorithm(IBioGenome map, IBioOntology ontology)
           
 

Uses of IBioGenome in org.metaqtl.bio
 

Methods in org.metaqtl.bio that return IBioGenome
 IBioGenome IBioLGroup.getGenome()
           
 

Methods in org.metaqtl.bio with parameters of type IBioGenome
 void IBioLGroup.setGenome(IBioGenome genome)
           
 

Uses of IBioGenome in org.metaqtl.bio.entity
 

Classes in org.metaqtl.bio.entity that implement IBioGenome
 class GeneticMap
          Class Description Here
 class GroupContainer
          Class Description Here
 

Methods in org.metaqtl.bio.entity that return IBioGenome
 IBioGenome LocusContainer.getGenome()
           
 

Methods in org.metaqtl.bio.entity with parameters of type IBioGenome
 void LocusContainer.setGenome(IBioGenome genome)
           
 

Uses of IBioGenome in org.metaqtl.bio.util
 

Methods in org.metaqtl.bio.util with parameters of type IBioGenome
static void BioUtilities.mergeGenome(IBioGenome g1, IBioGenome g2)
          This method merges two genomes in a single one : g1 is modified and will contain the result of the merge.
 

Uses of IBioGenome in org.metaqtl.factory
 

Methods in org.metaqtl.factory that return IBioGenome
static IBioGenome[] MapDBFactory.read(java.io.Reader reader)
          This method reads a file formated as follows : map property1 property2 property3 ...
 

Uses of IBioGenome in org.metaqtl.main
 

Methods in org.metaqtl.main that return IBioGenome
static IBioGenome MetaMain.getMap(IBioGenome[] maps, java.lang.String mapName)
           
protected static IBioGenome MetaMain.getMap(java.lang.String mapFile)
           
protected static IBioGenome[] MetaMain.getMaps(java.lang.String qtlDir)
           
 

Methods in org.metaqtl.main with parameters of type IBioGenome
static IBioGenome MetaMain.getMap(IBioGenome[] maps, java.lang.String mapName)
           
static void MetaMain.removeLocus(IBioGenome[] maps, java.lang.String mrkRmFile)
           
protected static void MetaMain.writeMap(IBioGenome map, java.lang.String outFile)
           
protected static void MetaMain.writeMap(IBioGenome genome, java.lang.String format, java.lang.String outFile)
           
 

Uses of IBioGenome in org.metaqtl.util
 

Methods in org.metaqtl.util with parameters of type IBioGenome
static CrossPopulation GeneticMapProperties.getCrossDesign(IBioGenome map)
          This routine returns an object which handle the properties of the offspring which have been used to create the genetic map.
static CrossPopulation GeneticMapProperties.getMappingCross(IBioGenome map)
           
static int GeneticMapProperties.getMappingFunction(IBioGenome map)
          This methods returns the integer code of the mapping function associated to the given genetic map.
static int GeneticMapProperties.getMappingUnit(IBioGenome map)
           
static boolean GeneticMapProperties.needToBeRescaled(IBioGenome map)
          Returns true if the given map need to be rescaled - due to the mapping extansion for some pedigree designs.
static void GeneticMapProperties.setCrossDesign(IBioGenome map, CrossPopulation crossDesign)
           
static void GeneticMapProperties.setMappingContext(IBioGenome map, int mapping_function, int mapping_unit)