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## Uses of Interface
org.thalia.bio.IBioGenome

Packages that use IBioGenome
org.metaqtl |
org.metaqtl.adapter |
org.metaqtl.algo |
org.metaqtl.factory |
org.metaqtl.main |
org.metaqtl.util |
org.thalia.bio |
org.thalia.bio.entity |
org.thalia.bio.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.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)`

Uses of IBioGenome in org.thalia.bio

Methods in org.thalia.bio that return IBioGenome
`IBioGenome` | `IBioLGroup.getGenome()`

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

Uses of IBioGenome in org.thalia.bio.entity

Classes in org.thalia.bio.entity that implement IBioGenome
`class` | `GeneticMap` Class Description Here
`class` | `GroupContainer` Class Description Here

Methods in org.thalia.bio.entity that return IBioGenome
`IBioGenome` | `LocusContainer.getGenome()`

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

Uses of IBioGenome in org.thalia.bio.util

Methods in org.thalia.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.

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