A B C D E F G H I K L M N O P Q R S T U V W X Y Z

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