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S

s_mrkIdxL - Variable in class org.metaqtl.Qtl.QTLProj
The skeleton indice of the left flanking marker.
s_mrkIdxR - Variable in class org.metaqtl.Qtl.QTLProj
The skeleton indice of the right flanking marker.
scale(double) - Method in class org.metaqtl.graph.ChromAxe
Scale the axe in y.
scaleHeight(double) - Method in class org.metaqtl.graph.ChromAxe
 
scaleY(double) - Method in class org.metaqtl.graph.ChromAxe
 
sd - Variable in class org.metaqtl.MetaQtlResult
The QTL position standard deviations.
sd2ci(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
 
sd_mode - Variable in class org.metaqtl.algo.QtlProjAlgorithm
The mode of compuation of the standard deviation of the QTL positions.
sd_position - Variable in class org.metaqtl.Qtl
The standard deviation of the QTL position.
sdd - Variable in class org.metaqtl.MetaChrom
The standard deviation of the position in Morgan.
selfingIndividualInformation(OffspringManager.HaldaneWaddingtonProportion) - Static method in class org.metaqtl.util.OffspringManager
This routine returns the individual means amount of information for the given generation propertions for a self-fertilization design.
selfingRecurrence(OffspringManager.HaldaneWaddingtonProportion, double) - Static method in class org.metaqtl.util.OffspringManager
Given the current proportion C,D,E,F and G and the recombination rate r this routine computes the next generation proportions following the recurrence formula of Haldane and Waddington, 1931, Inbreeding and linkage, Genetics 16:357-374 (see section self-fertilization p358).
SEPARATOR - Static variable in class org.metaqtl.factory.MetaQtlModelFactory
 
set(String, String) - Static method in class org.metaqtl.graph.MetaGraphPar
 
setCentroid(double) - Method in class org.metaqtl.TreeNode
 
setChildren(OntologyTerm[]) - Method in class org.thalia.bio.entity.OntologyTerm
Sets the children of the term.
setChromAxe(ChromAxe) - Method in class org.metaqtl.graph.QtlPartitionLayer
 
setChromAxe(ChromAxe) - Method in class org.metaqtl.graph.QtlTreeLayer
 
setChromName(int, String) - Method in class org.metaqtl.MetaQtlModel
 
setCIMiss(int) - Method in class org.metaqtl.algo.ClustAlgorithm
 
setCIMode(int) - Method in class org.metaqtl.algo.ClustAlgorithm
 
setClusterings(List) - Method in class org.metaqtl.MetaQtlResult
 
setClusterings(EMResult[]) - Method in class org.metaqtl.MetaQtlResult
 
setCriterion(String) - Method in class org.metaqtl.MetaQtlModel
Set the criterion name which was used to obtain this model
setCrossDesign(IBioGenome, CrossPopulation) - Static method in class org.metaqtl.util.GeneticMapProperties
 
setCrossType(int) - Method in class org.thalia.bio.entity.CrossPopulation
 
setDF(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.Function
Sets the derivative of the function at x.
setDubiousMarker(IBioLocus[]) - Method in class org.metaqtl.ChromCluster
This method sets the list of dubious marker.
setDubiousMarker(IBioLocus[]) - Method in class org.metaqtl.MapCluster
This method sets the list of dubious marker.
setEMEps(double) - Method in class org.metaqtl.algo.QtlClustAlgorithm
 
setEMRanStartNumber(int) - Method in class org.metaqtl.algo.QtlClustAlgorithm
 
setFunction(String) - Method in class org.thalia.bio.entity.Ontology
Set the function of the ontology.
setGeneration(int) - Method in class org.thalia.bio.entity.Population
 
setGenome(IBioGenome) - Method in class org.thalia.bio.entity.LocusContainer
 
setGenome(IBioGenome) - Method in interface org.thalia.bio.IBioLGroup
 
setGroup(IBioLGroup) - Method in class org.thalia.bio.entity.AlleleContainer
 
setGroup(IBioLGroup) - Method in class org.thalia.bio.entity.Locus
 
setGroup(IBioLGroup) - Method in interface org.thalia.bio.IBioLocus
 
setGroups(ArrayList) - Method in class org.thalia.bio.entity.bean.GeneticMapBean
 
setID(long) - Method in class org.thalia.bio.entity.OntologyTerm
Sets the indentifient of the term.
setIgnore(boolean) - Method in class org.metaqtl.Qtl
Set the status of the QTL.
setLabelSide(int) - Method in class org.metaqtl.graph.ChromLayer
 
setLabelSide(int) - Method in class org.metaqtl.graph.ChromShape
 
setLoci(IBioLocus[]) - Method in class org.thalia.bio.entity.LocusContainer
 
setLoci(IBioLocus[]) - Method in interface org.thalia.bio.IBioLGroup
 
setLocus(ArrayList) - Method in class org.thalia.bio.entity.bean.LGroupBean
 
setLocus(IBioLocus) - Method in interface org.thalia.bio.IBioAllele
 
setLogger(Writer) - Method in class org.metaqtl.algo.MetaAlgorithm
 
setLogger(OutputStream) - Method in class org.metaqtl.algo.MetaAlgorithm
 
setLogger(Writer) - Method in interface org.metaqtl.IMetaAlgorithm
Give a Writer to the algorithm in order to write out the log info.
setLogger(OutputStream) - Method in interface org.metaqtl.IMetaAlgorithm
Give a OutputStream to the algorithm in order to write out the log info.
setMappingContext(IBioGenome, int, int) - Static method in class org.metaqtl.util.GeneticMapProperties
 
setMarkerDico(MetaDico) - Method in class org.metaqtl.algo.MetaMapAlgorithm
 
setMarkerDico(MetaDico) - Method in class org.metaqtl.ChromCluster
 
setMarkerDico(MetaDico) - Method in class org.metaqtl.MapCluster
 
setMaxClusterNumber(int) - Method in class org.metaqtl.algo.QtlClustAlgorithm
 
setMetaQtls(Qtl[]) - Method in class org.metaqtl.Chromosome
 
setModel(int, int[]) - Method in class org.metaqtl.MetaQtlModel
 
setMrkThresh(int) - Method in class org.metaqtl.ChromCluster
 
setMrkThreshold(int) - Method in class org.metaqtl.algo.MetaMapAlgorithm
 
setName(String) - Method in class org.thalia.bio.entity.bean.BioEntityBean
 
setName(String) - Method in class org.thalia.bio.entity.bean.PropertyBean
 
setName(String) - Method in class org.thalia.bio.entity.BioEntity
 
setName(String) - Method in class org.thalia.bio.entity.BioEntityCollection
 
setName(String) - Method in interface org.thalia.bio.IBioEntity
 
setParameter(String) - Static method in class org.metaqtl.main.MetaMain
 
setParentTerm(IBioOntologyTerm) - Method in class org.thalia.bio.entity.OntologyTerm
Sets the parent of the term.
setPedigree(IBioIndividualTree) - Method in class org.thalia.bio.entity.Individual
 
setPopulation(IBioPopulation) - Method in class org.thalia.bio.entity.Individual
 
setPopulation(IBioPopulation) - Method in interface org.thalia.bio.IBioIndividual
 
setPosition(ILGroupPosition) - Method in class org.thalia.bio.entity.AlleleContainer
 
setPosition(ILGroupPosition) - Method in class org.thalia.bio.entity.Locus
 
setPosition(double) - Method in class org.thalia.bio.entity.Locus
Set the position of the locus on the linkage group in static mode i.e without uncertainty.
setPosition(double, double) - Method in class org.thalia.bio.entity.Locus
Set the position of the locus on the linkage group in estimate mode i.e with uncertainty.
setPosition(ILGroupPosition) - Method in interface org.thalia.bio.IBioLocus
 
setPosition(double) - Method in interface org.thalia.bio.IBioLocus
 
setPosition(double, double) - Method in interface org.thalia.bio.IBioLocus
 
setProba(double[][]) - Method in class org.metaqtl.Chromosome
 
setProperties(ArrayList) - Method in class org.thalia.bio.entity.bean.BioEntityBean
 
setProperties(Properties) - Method in class org.thalia.bio.entity.BioEntity
 
setProperties(Properties) - Method in class org.thalia.bio.entity.BioEntityCollection
 
setProperties(Properties) - Method in interface org.thalia.bio.IBioEntity
Sets the properties of the entity.
setPvalue(double) - Method in class org.metaqtl.algo.QtlProjAlgorithm
 
setQtlIdx(int[]) - Method in class org.metaqtl.MetaQtlResult
Set the indices of the Qtl which are implied in this result.
setRatio(double) - Method in class org.metaqtl.algo.QtlProjAlgorithm
 
setRoot(IBioOntologyTerm) - Method in class org.thalia.bio.entity.Ontology
 
setRoot(OntologyTerm) - Method in class org.thalia.bio.entity.Ontology
 
setRoot(IBioOntologyTerm) - Method in interface org.thalia.bio.IBioOntology
Sets the root of the ontology.
setSD(Double[]) - Method in class org.metaqtl.MetaQtlResult
Set the standard deviations of the Qtl.
setSize(int) - Method in class org.thalia.bio.entity.Population
Set the population size.
setTerm(String, List) - Method in class org.metaqtl.MetaDico
 
setTraitNames(int, String[]) - Method in class org.metaqtl.MetaQtlModel
 
setTree(Tree) - Method in class org.metaqtl.MetaQtlResult
 
setTree(Tree) - Method in class org.metaqtl.QtlPartition
 
setTreeMethod(int) - Method in class org.metaqtl.algo.QtlTreeAlgorithm
 
setValue(String) - Method in class org.thalia.bio.entity.bean.PropertyBean
 
setX(double) - Method in class org.metaqtl.graph.AnchoredElement
 
setX(double) - Method in class org.metaqtl.graph.ChromAxe
 
setX(Double[]) - Method in class org.metaqtl.MetaQtlResult
Set the observed positions of the Qtl.
setX(double) - Method in class org.metaqtl.TreeNode
 
setY(double) - Method in class org.metaqtl.graph.AnchoredElement
 
setY(double) - Method in class org.metaqtl.TreeNode
 
setYMax(double) - Method in class org.metaqtl.graph.ChromAxe
 
setYMin(double) - Method in class org.metaqtl.graph.ChromAxe
 
SF - Static variable in interface org.thalia.bio.IBioCrossTypes
 
shareFlanking - Variable in class org.metaqtl.Qtl.QTLProj
True if the two maps share a common marker sequence around the QTL.
shortForm() - Method in class org.metaqtl.main.CmdLineParser.Option
 
SIGN(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
Returns abs(a) if b > 0, -abs(a) otherwise.
SINGLE_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
 
SINGLE_COMMON_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
 
size - Variable in class org.metaqtl.Qtl.QTLCross
The number of individuals.
skeleton - Variable in class org.metaqtl.Chromosome
The skeleton status for this member
sortCluster() - Method in class org.metaqtl.EMResult
Sort the components in increasing order.
sortLociByPosition(IBioLocus[]) - Static method in class org.thalia.bio.util.BioUtilities
Sort tab with loci
SQR(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
Returns a^2
standardError() - Method in interface org.thalia.bio.util.ILGroupPosition
 
standardError() - Method in class org.thalia.bio.util.LGroupPosition
 
STATIC - Static variable in interface org.thalia.bio.util.ILGroupPosition
 
StaticLocusPosition - Class in org.thalia.bio.util
Class Description Here
StaticLocusPosition(double) - Constructor for class org.thalia.bio.util.StaticLocusPosition
 
stats - Variable in class org.metaqtl.Qtl
The QTL statistics
stderr - Variable in class org.thalia.bio.entity.bean.LocusBean
 
string2color(String) - Static method in class org.metaqtl.graph.MetaGraphPar
 
string2font(String) - Static method in class org.metaqtl.graph.MetaGraphPar
 
summarize(OutputStream) - Method in class org.metaqtl.ChromCluster.ClusterGraph
 
SVDAlgorithm - Class in org.metaqtl.algo
This class defines methods to solve usual linear algebra problems by using Singular Value Decomposition (SVD) strategy.
SVDAlgorithm() - Constructor for class org.metaqtl.algo.SVDAlgorithm
 
SVDBackSub(double[][], double[], double[][], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
Solves A.X=B for a vector X, where A is specified by the matrix U,V and the vector w as returned by the SVDecomposition() method.
SVDecomposition(double[][], double[][], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
Given a matrix A, this routine computes its singular value decomposition A = U.W.V' .
SVDMFit(double[][], double[], double[], int, int) - Static method in class org.metaqtl.algo.SVDAlgorithm
Given a set of data points y[1..m] with indiviudal weights w[1..m], use chi2 minimization to determine the coefficients a[1..n] of the fitting function y = X*a.
swap - Variable in class org.metaqtl.Qtl.QTLProj
True if the flanking marker order are inversed between the skeleton and the original map.
synchChromGraphs(ChromGraph[], Set) - Static method in class org.metaqtl.main.MetaMain
 
SYNONYMS - Static variable in interface org.thalia.bio.IOntologyTermProperties
The synonyms property for a term in a ontology.

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