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

A

A2Xml - Class in org.metaqtl.main

A2Xml() - Constructor for class org.metaqtl.main.A2Xml

absolute() - Method in interface org.thalia.bio.util.ILGroupPosition

absolute() - Method in class org.thalia.bio.util.LGroupPosition

adapt(Chromosome[]) - Static method in class org.metaqtl.adapter.MetaQtlAnalysisAdapter

adapt(EMResult) - Static method in class org.metaqtl.adapter.QtlAdapter

From a result of a EM clustering returns the mixture components as an array of Qtl.

adapt(MetaQtlData) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter

Adapt the given MetaQtlData into a QtlPartition and returns it.

adapt(MetaQtlAnalysis, String, String, int) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter

Adapt the MetaQtlAnalysis analysis for a given value of the number of clusters k and a given trait name code.

adapt(MetaQtlResult, Qtl[], int) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter

addAllele(IBioAllele) - Method in class org.thalia.bio.entity.AlleleContainer

addAllele(IBioAllele) - Method in interface org.thalia.bio.IBioLocus

addAllMap(IBioGenome[]) - Method in class org.metaqtl.MapCluster

addBooleanOption(char, String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a boolean option.

addBooleanOption(String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a boolean option.

addChild(TreeNode) - Method in class org.metaqtl.TreeNode

Add a child to the node.

addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean) - Method in class org.metaqtl.ChromCluster

Add a chromosome to the cluster

addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean) - Method in class org.metaqtl.MapCluster

Add a chromosome to the map cluster framework.

addDoubleOption(char, String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a double option.

addDoubleOption(String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a double option.

addEdge(Chromosome, Chromosome, CMarkerSequence) - Method in class org.metaqtl.ChromCluster.ClusterGraph

addGroup(IBioLGroup) - Method in class org.thalia.bio.entity.GroupContainer

addGroup(IBioLGroup) - Method in interface org.thalia.bio.IBioGenome

addIndividual(IBioIndividual) - Method in class org.thalia.bio.entity.IndividualContainer

addIndividual(IBioIndividual) - Method in interface org.thalia.bio.IBioPopulation

addIntegerOption(char, String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding an integer option.

addIntegerOption(String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding an integer option.

additive - Variable in class org.metaqtl.Qtl.QTLStats

The additive effect of the QTL.

addLocus(IBioLocus) - Method in class org.thalia.bio.entity.LocusContainer

addLocus(IBioLocus) - Method in interface org.thalia.bio.IBioLGroup

addLongOption(char, String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a long integer option.

addLongOption(String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a long integer option.

addMap(IBioGenome, boolean) - Method in class org.metaqtl.MapCluster

Add a map to the cluster.

addOption(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser

Add the specified Option to the list of accepted options

addQtl(Graphics2D, QtlUnit) - Method in class org.metaqtl.graph.QtlLayerBuffer

Try to add a qtl unit to the configuration.

addStringOption(char, String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a string option.

addStringOption(String) - Method in class org.metaqtl.main.CmdLineParser

Convenience method for adding a string option.

addTerm(String, String) - Method in class org.metaqtl.MetaDico

adjTable - Variable in class org.metaqtl.ChromCluster.ClusterGraph

AIC - Static variable in class org.metaqtl.EMCriteria

aic - Variable in class org.metaqtl.EMCriteria

AIC3 - Static variable in class org.metaqtl.EMCriteria

aic3 - Variable in class org.metaqtl.EMCriteria

AIC3_NAME - Static variable in class org.metaqtl.EMCriteria

AIC_NAME - Static variable in class org.metaqtl.EMCriteria

AICc - Static variable in class org.metaqtl.EMCriteria

aicc - Variable in class org.metaqtl.EMCriteria

AICc_NAME - Static variable in class org.metaqtl.EMCriteria

ALIGN_FIRST_COMMON - Static variable in class org.metaqtl.graph.ChromLayer

ALIGN_FIRST_MARKER - Static variable in class org.metaqtl.graph.ChromLayer

alignChromLayers(ChromLayer, ChromLayer, int) - Static method in class org.metaqtl.graph.ChromLayer

ALLELE - Static variable in interface org.thalia.bio.IBioEntityTypes

The integer code for Allele entity

AlleleContainer - Class in org.thalia.bio.entity

Class Description Here

AlleleContainer() - Constructor for class org.thalia.bio.entity.AlleleContainer

AlleleContainer(String, IBioEntity) - Constructor for class org.thalia.bio.entity.AlleleContainer

alleles() - Method in class org.thalia.bio.entity.AlleleContainer

alleles() - Method in interface org.thalia.bio.IBioLocus

AnchoredElement - Class in org.metaqtl.graph

AnchoredElement() - Constructor for class org.metaqtl.graph.AnchoredElement

areMarkersAroundQTL(int, int, int) - Method in class org.metaqtl.Chromosome

Returns true if the QTL position is inside the marker interval which markers indices are mrkIdxL and mrkIdxR.

attach(Object) - Method in class org.metaqtl.graph.ChromLayer

attach(Object) - Method in class org.metaqtl.graph.Layer

Attach the given object to the layer.

attach(Object) - Method in class org.metaqtl.graph.QtlLayer

attach(Object) - Method in class org.metaqtl.graph.QtlPartitionLayer

attach(Object) - Method in class org.metaqtl.graph.QtlTreeLayer

attachQtl(Qtl[]) - Method in class org.metaqtl.Chromosome

attachQTL(IBioLocus[]) - Method in class org.metaqtl.Chromosome

Add

AWE - Static variable in class org.metaqtl.EMCriteria

awe - Variable in class org.metaqtl.EMCriteria

AWE_NAME - Static variable in class org.metaqtl.EMCriteria