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Packages that use IBioGenome | |
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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 |
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Methods in org.metaqtl with parameters of type IBioGenome | |
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void |
MapCluster.addAllMap(IBioGenome[] maps)
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void |
MapCluster.addMap(IBioGenome map,
boolean skeleton)
Add a map to the cluster. |
Uses of IBioGenome in org.metaqtl.adapter |
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Methods in org.metaqtl.adapter that return IBioGenome | |
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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 | |
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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 |
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Constructors in org.metaqtl.algo with parameters of type IBioGenome | |
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ClustAlgorithm(IBioGenome map,
IBioOntology ontology)
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ClustAlgorithm(IBioGenome map,
java.lang.String name,
IBioOntology ontology)
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MetaMapAlgorithm(IBioGenome[] maps,
IBioGenome skeleton,
IBioLocus[] dubious,
MetaDico mrkDico)
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MetaMapAlgorithm(IBioGenome[] maps,
IBioGenome skeleton,
IBioLocus[] dubious,
MetaDico mrkDico)
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QtlClustAlgorithm(IBioGenome map,
IBioOntology ontology)
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QtlClustAlgorithm(IBioGenome map,
java.lang.String chrom,
IBioOntology ontology)
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QtlProjAlgorithm(IBioGenome[] maps,
IBioGenome skeleton,
IBioLocus[] dubious)
Creates a new instance of QtlProjAlgorithm for
the given configuration of projection. |
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QtlProjAlgorithm(IBioGenome[] maps,
IBioGenome skeleton,
IBioLocus[] dubious)
Creates a new instance of QtlProjAlgorithm for
the given configuration of projection. |
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QtlTreeAlgorithm(IBioGenome map,
IBioOntology ontology)
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Uses of IBioGenome in org.metaqtl.bio |
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Methods in org.metaqtl.bio that return IBioGenome | |
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IBioGenome |
IBioLGroup.getGenome()
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Methods in org.metaqtl.bio with parameters of type IBioGenome | |
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void |
IBioLGroup.setGenome(IBioGenome genome)
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Uses of IBioGenome in org.metaqtl.bio.entity |
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Classes in org.metaqtl.bio.entity that implement IBioGenome | |
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class |
GeneticMap
Class Description Here |
class |
GroupContainer
Class Description Here |
Methods in org.metaqtl.bio.entity that return IBioGenome | |
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IBioGenome |
LocusContainer.getGenome()
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Methods in org.metaqtl.bio.entity with parameters of type IBioGenome | |
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void |
LocusContainer.setGenome(IBioGenome genome)
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Uses of IBioGenome in org.metaqtl.bio.util |
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Methods in org.metaqtl.bio.util with parameters of type IBioGenome | |
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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 |
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Methods in org.metaqtl.factory that return IBioGenome | |
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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 |
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Methods in org.metaqtl.main that return IBioGenome | |
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static IBioGenome |
MetaMain.getMap(IBioGenome[] maps,
java.lang.String mapName)
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protected static IBioGenome |
MetaMain.getMap(java.lang.String mapFile)
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protected static IBioGenome[] |
MetaMain.getMaps(java.lang.String qtlDir)
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Methods in org.metaqtl.main with parameters of type IBioGenome | |
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static IBioGenome |
MetaMain.getMap(IBioGenome[] maps,
java.lang.String mapName)
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static void |
MetaMain.removeLocus(IBioGenome[] maps,
java.lang.String mrkRmFile)
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protected static void |
MetaMain.writeMap(IBioGenome map,
java.lang.String outFile)
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protected static void |
MetaMain.writeMap(IBioGenome genome,
java.lang.String format,
java.lang.String outFile)
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Uses of IBioGenome in org.metaqtl.util |
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Methods in org.metaqtl.util with parameters of type IBioGenome | |
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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)
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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)
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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)
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static void |
GeneticMapProperties.setMappingContext(IBioGenome map,
int mapping_function,
int mapping_unit)
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