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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
 

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