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

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.