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M

m - Variable in class org.metaqtl.MultiFitResult
The number of parameters
m1 - Variable in class org.metaqtl.Qtl
The indice of the left flanking marker.
m2 - Variable in class org.metaqtl.Qtl
The indice of the right flanking marker.
main(String[]) - Static method in class org.metaqtl.main.A2Xml
 
main(String[]) - Static method in class org.metaqtl.main.ConsMap
 
main(String[]) - Static method in class org.metaqtl.main.InfoMap
 
main(String[]) - Static method in class org.metaqtl.main.MapView
 
main(String[]) - Static method in class org.metaqtl.main.MetaDB
 
main(String[]) - Static method in class org.metaqtl.main.MMapView
 
main(String[]) - Static method in class org.metaqtl.main.MQTLView
 
main(String[]) - Static method in class org.metaqtl.main.QTLClust
 
main(String[]) - Static method in class org.metaqtl.main.QTLClustInfo
 
main(String[]) - Static method in class org.metaqtl.main.QTLModel
 
main(String[]) - Static method in class org.metaqtl.main.QTLProj
 
main(String[]) - Static method in class org.metaqtl.main.QTLTree
 
main(String[]) - Static method in class org.metaqtl.main.Xml2A
 
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaCMS
 
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaDraw
 
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaMapDraw
 
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaSimu
 
main(String[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat
 
MAKER_NAME_VSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
 
manageMissingData(int) - Method in class org.metaqtl.MetaQtlData
Manage the missing data.
MapChartFactory - Class in org.thalia.bio.entity.factory
General comments must be added here.
MapChartFactory() - Constructor for class org.thalia.bio.entity.factory.MapChartFactory
 
MapCluster - Class in org.metaqtl
 
MapCluster() - Constructor for class org.metaqtl.MapCluster
Creates a new instance of MapCluster.
MapDBFactory - Class in org.metaqtl.factory
A factory to read the list and the properties of a set of genetic maps.
MapDBFactory() - Constructor for class org.metaqtl.factory.MapDBFactory
 
MapMakerFactory - Class in org.thalia.bio.entity.factory
 
MapMakerFactory() - Constructor for class org.thalia.bio.entity.factory.MapMakerFactory
 
mapName - Variable in class org.metaqtl.Chromosome
The name of the map in which this chromosome is defined.
mapNames - Variable in class org.metaqtl.MetaChrom
The names of the genetic maps.
mapOrigin - Variable in class org.metaqtl.Qtl.QTLProj
The name of the map from which this QTL comes.
MAPPING_CROSS - Static variable in interface org.metaqtl.IBioGenomeProperties
The key for mapping cross.
MAPPING_EXPANSION - Static variable in interface org.metaqtl.IBioGenomeProperties
The key for mapping expansion status.
MAPPING_FUNCTION - Static variable in interface org.metaqtl.IBioGenomeProperties
The key for mapping function.
MAPPING_FUNCTION_HALDANE - Static variable in interface org.metaqtl.IBioGenomeProperties
The code for Haldane mapping function.
MAPPING_FUNCTION_HALDANE - Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for haldane mapping function
MAPPING_FUNCTION_KOSAMBI - Static variable in interface org.metaqtl.IBioGenomeProperties
The code for Kosambi mapping function.
MAPPING_FUNCTION_KOSAMBI - Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for kosambi mapping function
MAPPING_FUNCTION_UNKNOWN - Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for not defined mapping function
MAPPING_UNIT - Static variable in interface org.metaqtl.IBioGenomeProperties
The mapping unit key.
MAPPING_UNIT_CM - Static variable in interface org.metaqtl.IBioGenomeProperties
The code for centi-Morgan unit.
MAPPING_UNIT_CM - Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for centi morgan mapping unit
MAPPING_UNIT_M - Static variable in interface org.metaqtl.IBioGenomeProperties
The code for Morgan unit.
MAPPING_UNIT_M - Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for morgan mapping unit
MAPPING_UNIT_UNKNOWN - Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for unknown mapping unit
MappingFunction - Class in org.metaqtl.util
define all cartogarphies functions
MappingFunction() - Constructor for class org.metaqtl.util.MappingFunction
 
MapRawFactory - Class in org.thalia.bio.entity.factory
 
MapRawFactory() - Constructor for class org.thalia.bio.entity.factory.MapRawFactory
 
mapScale - Variable in class org.metaqtl.Qtl.QTLProj
The scale ratio between the original map and the map on which the QTL has been projected.
MapTabFactory - Class in org.thalia.bio.entity.factory
 
MapTabFactory() - Constructor for class org.thalia.bio.entity.factory.MapTabFactory
 
MapView - Class in org.metaqtl.main
 
MapView() - Constructor for class org.metaqtl.main.MapView
 
mapWeight - Variable in class org.metaqtl.Qtl.QTLProj
The cumulated scale weights of the common marke sequences between the original map and the map on which the QTL has been projected.
Marker - Class in org.thalia.bio.entity
Class Description Here
Marker() - Constructor for class org.thalia.bio.entity.Marker
 
Marker(String, IBioEntity) - Constructor for class org.thalia.bio.entity.Marker
 
MARKER - Static variable in interface org.thalia.bio.IBioLocus
 
MARKER_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
 
MARKER_POSITION_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
 
MARKERLOCUS - Static variable in interface org.thalia.bio.IBioEntityTypes
 
mcidx - Variable in class org.metaqtl.CMarkerSequence
The common marker indices on the chromosomes.
merge(GeneticMap) - Method in class org.thalia.bio.entity.GeneticMap
Deprecated.  
mergeGenome(IBioGenome, IBioGenome) - Static method in class org.thalia.bio.util.BioUtilities
This method merges two genomes in a single one : g1 is modified and will contain the result of the merge.
MetaAlgorithm - Class in org.metaqtl.algo
 
MetaAlgorithm() - Constructor for class org.metaqtl.algo.MetaAlgorithm
 
MetaChrom - Class in org.metaqtl
A MetaChrom is the result of the merge of the members of a ChromCluster.
MetaChrom(MultiFitResult, ChromCluster) - Constructor for class org.metaqtl.MetaChrom
Get a new instance of MetaChrom which is initialized by using the result of the merge of the members of a ChromCluster.
MetaCMS - Class in org.thalia.metaqtl.main
 
MetaCMS() - Constructor for class org.thalia.metaqtl.main.MetaCMS
 
MetaDB - Class in org.metaqtl.main
 
MetaDB() - Constructor for class org.metaqtl.main.MetaDB
 
MetaDico - Class in org.metaqtl
This class represents a dictionnary of synonyms.
MetaDico() - Constructor for class org.metaqtl.MetaDico
 
MetaDicoFactory - Class in org.metaqtl.factory
 
MetaDicoFactory() - Constructor for class org.metaqtl.factory.MetaDicoFactory
 
MetaDraw - Class in org.thalia.metaqtl.main
 
MetaDraw() - Constructor for class org.thalia.metaqtl.main.MetaDraw
 
MetaGraph - Class in org.metaqtl.graph
 
MetaGraph() - Constructor for class org.metaqtl.graph.MetaGraph
 
MetaGraphPar - Class in org.metaqtl.graph
 
MetaGraphParFactory - Class in org.metaqtl.factory
 
MetaGraphParFactory() - Constructor for class org.metaqtl.factory.MetaGraphParFactory
 
MetaMain - Class in org.metaqtl.main
 
MetaMain() - Constructor for class org.metaqtl.main.MetaMain
 
MetaMap - Class in org.metaqtl
A MetaMap is a bundle of MetaChrom objects.
MetaMap(int) - Constructor for class org.metaqtl.MetaMap
Creates a new instance of MetaMap which will contain nchr MetaChrom objects.
MetaMapAdapter - Class in org.metaqtl.adapter
This class defines some usefull methods to adapt MetaMap objects into other kinds of objects or the inverse.
MetaMapAdapter() - Constructor for class org.metaqtl.adapter.MetaMapAdapter
 
MetaMapAlgorithm - Class in org.metaqtl.algo
This class is dedicated to the construction of a consensus genetic map from a set of genetic maps based on a Weigthed Least Square approach.
MetaMapAlgorithm(IBioGenome[], IBioGenome, IBioLocus[], MetaDico) - Constructor for class org.metaqtl.algo.MetaMapAlgorithm
 
MetaMapDraw - Class in org.thalia.metaqtl.main
 
MetaMapDraw() - Constructor for class org.thalia.metaqtl.main.MetaMapDraw
 
MetaMapSummaryFactory - Class in org.metaqtl.factory
A factory to write out the information on a MetaMap.
MetaMapSummaryFactory() - Constructor for class org.metaqtl.factory.MetaMapSummaryFactory
 
metaQtlAnalysis - Variable in class org.metaqtl.Chromosome
The results of a meta-analysis of QTL.
MetaQtlAnalysis - Class in org.metaqtl
A QTL meta analysis consists in a clustering of QTL positions over chromosomes for different group of traits.
MetaQtlAnalysis(int) - Constructor for class org.metaqtl.MetaQtlAnalysis
Creates a new instance of a MetaQtlAnalysis
MetaQtlAnalysisAdapter - Class in org.metaqtl.adapter
 
MetaQtlAnalysisAdapter() - Constructor for class org.metaqtl.adapter.MetaQtlAnalysisAdapter
 
MetaQtlAnalysisFactory - Class in org.metaqtl.factory
A factory to deal with the result of a QTL meta-analysis.
MetaQtlAnalysisFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisFactory
 
MetaQtlAnalysisModelFactory - Class in org.metaqtl.factory
 
MetaQtlAnalysisModelFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisModelFactory
 
MetaQtlAnalysisSummaryFactory - Class in org.metaqtl.factory
A factory to deal with QTL meta-analysis result.
MetaQtlAnalysisSummaryFactory() - Constructor for class org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
 
MetaQtlData - Class in org.metaqtl
QTL meta analysis first requires to gather the QTL according to the group trait they belong and then to format the QTL data into data points to perfom clustering.
MetaQtlData(Qtl[]) - Constructor for class org.metaqtl.MetaQtlData
Create a new instance of MetaQtlData which will represent the given array of Qtl.
MetaQtlModel - Class in org.metaqtl
 
MetaQtlModel() - Constructor for class org.metaqtl.MetaQtlModel
 
MetaQtlModel(int) - Constructor for class org.metaqtl.MetaQtlModel
 
MetaQtlModelFactory - Class in org.metaqtl.factory
 
MetaQtlModelFactory() - Constructor for class org.metaqtl.factory.MetaQtlModelFactory
 
MetaQtlResult - Class in org.metaqtl
A MetaQtlResult is used to store the results of a QTL meta analysis which has been performed for a given trait group on a given chromosome.
MetaQtlResult() - Constructor for class org.metaqtl.MetaQtlResult
 
MetaQtlResult(String, int) - Constructor for class org.metaqtl.MetaQtlResult
 
MetaSimu - Class in org.thalia.metaqtl.main
 
MetaSimu() - Constructor for class org.thalia.metaqtl.main.MetaSimu
 
MetaSimuStat - Class in org.thalia.metaqtl.main
 
MetaSimuStat() - Constructor for class org.thalia.metaqtl.main.MetaSimuStat
 
METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm
A global variable to control the custering method.
mfc - Variable in class org.metaqtl.Chromosome
The mapping function for this chromosome
mir - Variable in class org.metaqtl.EMCriteria
 
MMapView - Class in org.metaqtl.main
 
MMapView() - Constructor for class org.metaqtl.main.MMapView
 
mode - Variable in class org.metaqtl.QtlPartition
The mode of representation
models - Variable in class org.metaqtl.MetaQtlModel
The number of Qtl per chromosome and per trait.
mqtls - Variable in class org.metaqtl.Chromosome
The meta Qtls on this chromosome.
MQTLView - Class in org.metaqtl.main
 
MQTLView() - Constructor for class org.metaqtl.main.MQTLView
 
mr - Variable in class org.metaqtl.Chromosome
The adjacent recombination rate between ordered markers
mrkNames - Variable in class org.metaqtl.Chromosome
The ordered marker names
mrkNames - Variable in class org.metaqtl.MetaChrom
The ordered marker names.
mrkOc - Variable in class org.metaqtl.MetaChrom
The number of occurence per marker oved chromosomes.
mStep(double[], double[], EMResult, double) - Static method in class org.metaqtl.algo.EMAlgorithm
The Maximization step : here this step is straighforward and simple analytical formula are applied to obtain the new parameter estimates.
mu - Variable in class org.metaqtl.EMResult
The means of the clusters.
MultiFitResult - Class in org.metaqtl
This class represents a result of a multilinear regression analysis.
MultiFitResult(int, int) - Constructor for class org.metaqtl.MultiFitResult
Creates a new instance of MultiFitResult with the given number of observations N and parameters M.
mut - Variable in class org.metaqtl.Chromosome
The mapping unit for this chromosome

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