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

G

G - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion

G_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion

GAMCOF - Static variable in class org.metaqtl.numrec.NumericalUtilities

gammln(double) - Static method in class org.metaqtl.numrec.NumericalUtilities

gammp(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities

gauss(double) - Static method in class org.metaqtl.numrec.NumericalUtilities

This routine returns the value at x of the normal centered gaussian density.

gcf(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities

gen - Variable in class org.metaqtl.Qtl.QTLCross

The number of generations.

gen - Static variable in class org.thalia.bio.util.BioCrossTypes

generalHelp() - Static method in class org.metaqtl.main.MetaMain

generalUsage() - Static method in class org.metaqtl.main.MetaMain

GeneticMap - Class in org.thalia.bio.entity

Class Description Here

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

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

GeneticMap(String) - Constructor for class org.thalia.bio.entity.GeneticMap

GeneticMapBean - Class in org.thalia.bio.entity.bean

Class Description Here

GeneticMapBean() - Constructor for class org.thalia.bio.entity.bean.GeneticMapBean

GeneticMapBeanAdapter - Class in org.thalia.bio.entity.adapter

Class Description Here

GeneticMapBeanAdapter() - Constructor for class org.thalia.bio.entity.adapter.GeneticMapBeanAdapter

GeneticMapProperties - Class in org.metaqtl.util

General comments must be added here.

GeneticMapProperties() - Constructor for class org.metaqtl.util.GeneticMapProperties

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

The integer code for Genome entity

getAdjacentTable() - Method in class org.metaqtl.ChromCluster.ClusterGraph

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

getAllele(String) - Method in interface org.thalia.bio.IBioLocus

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

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

getBestClustering(int) - Method in class org.metaqtl.MetaQtlResult

This methods returns the best models for each criterion defined to select the optimal number of clusters per trait.

getBestModel(int) - Method in class org.metaqtl.MetaQtlAnalysis

This methods returns the best models for each criterion defined to select the optimal number of clusters per chromosome per trait.

getBestResult(EMResult[], int) - Static method in class org.metaqtl.EMCriteria

For the given criterion criterion this methods looks into the array of EMResult and find the model which is optimal.

getBestResult(EMResult[], int, int) - Static method in class org.metaqtl.EMCriteria

getBestResult(EMResult[], String) - Static method in class org.metaqtl.EMCriteria

getBestResult(EMResult[], int, String) - Static method in class org.metaqtl.EMCriteria

getBioAdapter() - Method in class org.thalia.bio.entity.BioEntityCollection

getBioAdapter() - Method in class org.thalia.bio.entity.GeneticMap

getBioAdapter() - Method in class org.thalia.bio.entity.Individual

getBioAdapter() - Method in class org.thalia.bio.entity.LGroup

getBioAdapter() - Method in class org.thalia.bio.entity.Marker

getBioAdapter() - Method in class org.thalia.bio.entity.Ontology

getBioAdapter() - Method in class org.thalia.bio.entity.OntologyTerm

getBioAdapter() - Method in class org.thalia.bio.entity.Population

getBioAdapter() - Method in class org.thalia.bio.entity.QTL

getBioAdapter() - Method in interface org.thalia.bio.IBioAdaptable

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

getCentroid(double[], double[]) - Method in class org.metaqtl.TreeNode

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

getChildrenTerm() - Method in class org.thalia.bio.entity.OntologyTerm

getChildrenTerm() - Method in interface org.thalia.bio.IBioOntologyTerm

Returns the children if the term has chilren, null otherwise.

getChromAxe() - Method in class org.metaqtl.graph.ChromLayer

Return the axe of the chromosome.

getChromAxe() - Method in class org.metaqtl.graph.ChromShape

getChromAxe() - Method in class org.metaqtl.graph.QtlPartitionLayer

getChromByNames(Chromosome[], String[]) - Static method in class org.metaqtl.main.MetaMain

getChromGraph(Chromosome[], boolean, int, IBioOntology, MetaQtlAnalysis) - Static method in class org.metaqtl.main.MetaMain

getChromIdx(String) - Method in class org.metaqtl.MetaQtlAnalysis

getChromNames() - Method in class org.metaqtl.MetaQtlModel

Returns the names of the chromosomes.

getChromosomeName(String) - Method in class org.metaqtl.MapCluster

This method returns the name of the chromosome from the given name.

getChromWidth() - Method in class org.metaqtl.graph.ChromLayer

getChromWidth() - Method in class org.metaqtl.graph.ChromShape

getClusterByNames(ChromCluster[], String[]) - Static method in class org.metaqtl.main.MetaMain

getClustering(int) - Method in class org.metaqtl.MetaQtlResult

Returns the Qtl clustering result with k clusters.

getClusterMembers() - Method in class org.metaqtl.ChromCluster

This method returns the members of the cluster as an array of Chromosomes.

getClusters() - Method in class org.metaqtl.MapCluster

Returns the chromosome clusters.

getCMrkTotalNumbers() - Method in class org.metaqtl.ChromCluster

getCommonMarkerPaths(ChromLayer) - Method in class org.metaqtl.graph.ChromLayer

getCommonMarkerPoints(ChromLayer) - Method in class org.metaqtl.graph.ChromLayer

getCopy() - Method in class org.metaqtl.Qtl

Returns a copy of the QTL.

getCopy() - Method in class org.metaqtl.Qtl.QTLCross

getCopy() - Method in class org.metaqtl.Qtl.QTLProj

getCopy() - Method in class org.metaqtl.Qtl.QTLStats

getCopy() - Method in class org.metaqtl.Qtl.QTLSupport

getCopy() - Method in class org.metaqtl.Qtl.QTLTrait

getCritDelta(String, int[]) - Method in class org.metaqtl.MetaQtlResult

getCriteria() - Static method in class org.metaqtl.EMCriteria

Returns an iterator on the criteria

getCriteria() - Method in class org.metaqtl.MetaQtlResult

getCriterion(int) - Method in class org.metaqtl.EMCriteria

Get the criterion value according to its integer code.

getCriterion(String) - Method in class org.metaqtl.EMCriteria

getCriterion(int) - Method in class org.metaqtl.EMResult

getCriterion() - Method in class org.metaqtl.MetaQtlModel

getCriterionIdx(String) - Static method in class org.metaqtl.EMCriteria

Returns the integer code for the criterion which matches the given name.

getCritValues(String, int[]) - Method in class org.metaqtl.MetaQtlResult

getCritWeights(String, int[]) - Method in class org.metaqtl.MetaQtlResult

getCrossDesign(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties

This routine returns an object which handle the properties of the offspring which have been used to create the genetic map.

getCrossType() - Method in class org.thalia.bio.entity.CrossPopulation

getCrossType() - Method in interface org.thalia.bio.IBioCross

getCSIdx(int, int) - Method in class org.metaqtl.CMarkerSequence

getDataPoints(int, boolean) - Method in class org.metaqtl.MetaQtlData

For a given trait group indice this methods returns the data points as a matrix of Double X[0..1][0..n-1] where X[0] is the vector of the n position values and X[1] is the vector of the n standard deviations of the positions.

getDF() - Method in interface org.metaqtl.numrec.NumericalUtilities.Function

Returns the derivative of the function.

getDF() - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction

Returns the value of the derivate in x;

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

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

This methods returns the distance between the first marker and the marker with the given indice using the given mapping context.

getDistance(int) - Method in class org.metaqtl.Chromosome

This methods returns the distance between the first marker and the marker with the given indice using the default mapping context.

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

This methods returns the distance between the markers with the given indices assuming that mrkIdxL < mrkIdxR.

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

getDistHeterogeneity(int, int[][], Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome

getEMEps() - Method in class org.metaqtl.algo.QtlClustAlgorithm

getEMRanStartNumber() - Method in class org.metaqtl.algo.QtlClustAlgorithm

getEuclidean() - Method in class org.metaqtl.EMResult

getF() - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction

Returns the value of the function in x.

getFirstCommonMrkIdx(Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome

getFunction() - Method in class org.thalia.bio.entity.Ontology

getFunction() - Method in interface org.thalia.bio.IBioOntology

Returns the function of the ontology

getGeneration() - Method in class org.thalia.bio.entity.Population

getGeneration() - Method in interface org.thalia.bio.IBioCross

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

getGenome() - Method in interface org.thalia.bio.IBioLGroup

getGraph() - Method in class org.metaqtl.ChromCluster

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

getGroup(String) - Method in class org.thalia.bio.entity.GroupContainer

getGroup() - Method in class org.thalia.bio.entity.Locus

getGroup(String) - Method in interface org.thalia.bio.IBioGenome

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

getGroups() - Method in class org.thalia.bio.entity.bean.GeneticMapBean

getHeight() - Method in class org.metaqtl.graph.ChromAxe

getHeight() - Method in class org.metaqtl.graph.ChromLayer

getHeight() - Method in class org.metaqtl.graph.GraphShape

getHeight() - Method in class org.metaqtl.graph.Layer

getHeight() - Method in class org.metaqtl.graph.MetaGraph

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

getHeigth() - Method in class org.metaqtl.graph.QtlShape

getID() - Method in class org.thalia.bio.entity.OntologyTerm

getID() - Method in interface org.thalia.bio.IBioOntologyTerm

Returns the id if the terms.

getImage(ChromGraph[]) - Static method in class org.metaqtl.graph.GraphFactory

getIndividual(String) - Method in class org.thalia.bio.entity.IndividualContainer

getIndividual(String) - Method in interface org.thalia.bio.IBioPopulation

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

getIndividualNumber() - Method in class org.thalia.bio.entity.Population

getIndividualNumber() - Method in interface org.thalia.bio.IBioPopulation

getInstance() - Static method in class org.thalia.bio.util.BioEntityNameComparator

getInstance() - Static method in class org.thalia.bio.util.LocusPositionComparator

getK() - Method in class org.metaqtl.EMResult

getK(MetaSimuStat.SimuConfig[], String) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getKValues() - Method in class org.metaqtl.MetaQtlResult

getLabelSide() - Method in class org.metaqtl.graph.ChromShape

getLayer(double, double) - Method in class org.metaqtl.graph.QtlLayerBuffer

Returns a QtlLayer which represent the contents of the buffer.

getLeaf(int) - Method in class org.metaqtl.Tree

getLeafHeights() - Method in class org.metaqtl.Tree

getLeafNumber() - Method in class org.metaqtl.Tree

getLeftCSMarker(int, int) - Method in class org.metaqtl.CMarkerSequence

Returns the indices of the marker at the left of the given one.

getLocus() - Method in class org.thalia.bio.entity.bean.LGroupBean

getLocus(String) - Method in class org.thalia.bio.entity.LocusContainer

getLocus() - Method in interface org.thalia.bio.IBioAllele

getLocus(String) - Method in interface org.thalia.bio.IBioLGroup

getLocusAdapter() - Static method in class org.thalia.bio.entity.Locus

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

getLocusNumber() - Method in interface org.thalia.bio.IBioLGroup

getLocusType() - Method in class org.thalia.bio.entity.Marker

getLocusType() - Method in class org.thalia.bio.entity.QTL

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

getMahalanobis(double[]) - Method in class org.metaqtl.EMResult

getMap(IBioGenome[], String) - Static method in class org.metaqtl.main.MetaMain

getMapName() - Method in class org.metaqtl.Chromosome

getMappingCross(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties

getMappingFunction(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties

This methods returns the integer code of the mapping function associated to the given genetic map.

getMappingUnit(IBioGenome) - Static method in class org.metaqtl.util.GeneticMapProperties

getMarkerDico() - Method in class org.metaqtl.ChromCluster

getMarkerDico() - Method in class org.metaqtl.MapCluster

getMarkerIdx(int, int, int) - Method in class org.metaqtl.CMarkerSequence

getMarkerIdxWithName(String) - Method in class org.metaqtl.Chromosome

This method looks if it exists a marker on the chromosome with the given name and returns its indice.

getMarkerIndexByName(String) - Method in class org.metaqtl.ChromCluster

For a given marker name this method returns the marker index of the marker table if found.

getMarkerIntervalNumber() - Method in class org.metaqtl.ChromCluster

This method returns the total number of marker intervals, i.e the sum over chromosomes of the number of marker intervals.

getMarkerName(String) - Method in class org.metaqtl.ChromCluster

This method returns the name of the locus from the given name.

getMarkerName(int) - Method in class org.metaqtl.Chromosome

Returns the names of the marker at the i^th position on the chromosome.

getMarkerNameByIndex(int) - Method in class org.metaqtl.ChromCluster

This method returns the name of the marker according to this indice.

getMarkerNumber() - Method in class org.metaqtl.ChromCluster

This method returns the number of distinct markers implied in this cluster, i.e the size of the marker table.

getMarkerOccurence(int) - Method in class org.metaqtl.ChromCluster

Returns the number of times the marker with the indice i has been seen over the chromosomes of the cluster.

getMetaOccurence(IBioLocus) - Static method in class org.metaqtl.util.LocusProperties

getMetaQtl(String, String, int) - Method in class org.metaqtl.MetaQtlAnalysis

Returns the meta Qtl for the given chromosome indice cidx, the given trait name trait and the given number of clusters k.

getMetaQtl(int) - Method in class org.metaqtl.MetaQtlResult

getMetaQtls() - Method in class org.metaqtl.Chromosome

getModel(String, String) - Method in class org.metaqtl.MetaQtlModel

getModel(int, int) - Method in class org.metaqtl.MetaQtlModel

getMrkTickPoint2D(int, boolean) - Method in class org.metaqtl.graph.ChromLayer

getMrkTickPoint2D(int, boolean) - Method in class org.metaqtl.graph.ChromShape

getMrkToRm(File) - Static method in class org.metaqtl.main.MetaMain

getMu(int) - Method in class org.metaqtl.EMResult

getMu(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getName() - Method in class org.metaqtl.ChromCluster

Returns the name of the cluster.

getName() - Method in class org.metaqtl.Chromosome

Returns the name of the chromosome.

getName() - Method in class org.metaqtl.Qtl

Returns the name of the QTL.

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

getName() - Method in class org.thalia.bio.entity.bean.BioEntityBean

getName() - Method in class org.thalia.bio.entity.bean.PropertyBean

getName() - Method in class org.thalia.bio.entity.BioEntity

getName() - Method in class org.thalia.bio.entity.BioEntityCollection

getName() - Method in interface org.thalia.bio.IBioEntity

Returns the name of the biological entity

getNodeHeights() - Method in class org.metaqtl.Tree

getNodeNumber() - Method in class org.metaqtl.Tree

getO(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getOption() - Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException

getOptionChar() - Method in exception org.metaqtl.main.CmdLineParser.NotFlagException

getOptionName() - Method in exception org.metaqtl.main.CmdLineParser.UnknownOptionException

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

Equivalent to getOptionValue(o, null).

getOptionValue(CmdLineParser.Option, Object) - Method in class org.metaqtl.main.CmdLineParser

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

getPalette(int) - Static method in class org.metaqtl.graph.PaletteColor

Returns a palete of colors which should be distinct.

getPaletteGradient(int, Color, Color) - Static method in class org.metaqtl.graph.PaletteColor

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

getParent() - Method in class org.thalia.bio.entity.BioEntity

getParent() - Method in class org.thalia.bio.entity.BioEntityCollection

getParent() - Method in interface org.thalia.bio.IBioEntity

Returns the entity that handles this entity.

getParents() - Method in class org.thalia.bio.entity.CrossPopulation

getParents() - Method in class org.thalia.bio.entity.Individual

getParents() - Method in class org.thalia.bio.entity.Population

getParents() - Method in interface org.thalia.bio.IBioCross

getParents() - Method in interface org.thalia.bio.IBioIndividual

Returns the pedigree of the individual

getParentTerm() - Method in class org.thalia.bio.entity.OntologyTerm

getParentTerm() - Method in interface org.thalia.bio.IBioOntologyTerm

Returns the parent of the term.

getPartNames() - Method in class org.metaqtl.QtlPartition

getPedigree() - Method in class org.thalia.bio.entity.Individual

getPi(int) - Method in class org.metaqtl.EMResult

getPopulation() - Method in class org.thalia.bio.entity.Individual

getPopulation() - Method in interface org.thalia.bio.IBioIndividual

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

getPosition() - Method in class org.thalia.bio.entity.Locus

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

getPredict(MetaSimuStat.SimuConfig[], String) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getProba() - Method in class org.metaqtl.Chromosome

getProbaColor(double) - Static method in class org.metaqtl.graph.MetaGraphPar

getProbaColor(double, double) - Static method in class org.metaqtl.graph.MetaGraphPar

getProperties() - Method in class org.thalia.bio.entity.bean.BioEntityBean

getProperties() - Method in class org.thalia.bio.entity.BioEntity

getProperties() - Method in class org.thalia.bio.entity.BioEntityCollection

getProperties() - Method in interface org.thalia.bio.IBioEntity

Gets the properties of the entity.

getQtl(int, int) - Method in class org.metaqtl.MetaQtlData

Returns the j^th QTL in the i^th cluster.

getQtlIdx(int) - Method in class org.metaqtl.MetaQtlData

Returns the indices of the Qtl for the given trait cluster indice i.

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

This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL indice.

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

This methods returns the probability that the QTL be inside the marker interval with the given right and left marker indices and the given QTL.

getQtlNumber() - Method in class org.metaqtl.Chromosome

getQtlNumber() - Method in class org.metaqtl.MetaQtlData

getQtlPartition(Chromosome, IBioOntology) - Static method in class org.metaqtl.main.MetaMain

getQtlPartition(Chromosome, MetaQtlAnalysis, String, int, char) - Static method in class org.metaqtl.main.MetaMain

getQtlPartNames() - Method in class org.metaqtl.graph.QtlPartitionLayer

getQtls() - Method in class org.metaqtl.Chromosome

This method returns a copy of the QTL located on thic chromosome.

getQTLSD(Qtl.QTLSupport, int, int) - Static method in class org.metaqtl.Qtl

Depending on the CI type this methods returns the the standard deviation of the QTL position using the given mapping context.

getQTLSD(double, Qtl.QTLCross, int) - Static method in class org.metaqtl.Qtl

Depending on the r-square parameter and the cross design this method returns the standard deviation of the QTL position for the given mapping context.

getQtlTree() - Method in class org.metaqtl.MetaQtlResult

getRecHeterogeneity(int, int[][], Chromosome, Chromosome) - Static method in class org.metaqtl.Chromosome

getRemainingArgs() - Method in class org.metaqtl.main.CmdLineParser

getResources(IResource, IBioEntity[]) - Static method in class org.thalia.bio.util.ResourceBioEntityQuery

getResult() - Method in class org.metaqtl.algo.ClustAlgorithm

When the algorithm is finished use this method to get the result.

getResult() - Method in class org.metaqtl.algo.MetaMapAlgorithm

getResult() - Method in class org.metaqtl.algo.QtlProjAlgorithm

getResult(String, String) - Method in class org.metaqtl.MetaQtlAnalysis

Returns the result for the given trait name or null if not found.

getResult(String) - Method in class org.metaqtl.MetaQtlAnalysis

Returns the first result for the given chromosome.

getResult(int, String) - Method in class org.metaqtl.MetaQtlAnalysis

Returns the result for the given trait name or null if not found.

getResults(String) - Method in class org.metaqtl.MetaQtlAnalysis

getRightCSMarker(int, int) - Method in class org.metaqtl.CMarkerSequence

getRoot() - Method in class org.metaqtl.Tree

getRoot() - Method in class org.thalia.bio.entity.Ontology

getRoot() - Method in interface org.thalia.bio.IBioOntology

Returns the root of the ontology tree.

getSD(int) - Method in class org.metaqtl.EMResult

getSD1(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getSD2(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getSize() - Method in class org.thalia.bio.entity.Population

Returns the size of the population.

getSize() - Method in interface org.thalia.bio.IBioCross

getSubChromosome(String[]) - Method in class org.metaqtl.Chromosome

getSuboption() - Method in exception org.metaqtl.main.CmdLineParser.UnknownSuboptionException

getSynonymous(String) - Method in class org.metaqtl.MetaDico

getTerm(String) - Method in class org.metaqtl.MetaDico

getTerm(IBioOntologyTerm) - Method in class org.thalia.bio.entity.Ontology

getTerm(String) - Method in class org.thalia.bio.entity.Ontology

getTerm(IBioOntologyTerm) - Method in interface org.thalia.bio.IBioOntology

Returns if exists the term in the ontology which matches the given one.

getTerm(String) - Method in interface org.thalia.bio.IBioOntology

This method looks into the ontology if there is a term with the given name and returns it.

getTerms() - Method in class org.metaqtl.MetaDico

getTraitClusterName(int) - Method in class org.metaqtl.MetaQtlData

getTraitClusterNames() - Method in class org.metaqtl.MetaQtlData

Returns the names of the trait clusters.

getTraitClusterNumber() - Method in class org.metaqtl.MetaQtlData

Returns the number of trait groups for this data set as defined by the clustering method.

getTraitClusterSize(int) - Method in class org.metaqtl.MetaQtlData

Returns the size of the trait cluster i.

getTraitIdx(int, String) - Method in class org.metaqtl.MetaQtlAnalysis

getTraitName() - Method in class org.metaqtl.MetaQtlResult

Returns the name of the trait cluster for this result.

getTraitNames(String) - Method in class org.metaqtl.MetaQtlModel

getTraitNames(int) - Method in class org.metaqtl.MetaQtlModel

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

getType() - Method in class org.thalia.bio.entity.BioEntity

getType() - Method in class org.thalia.bio.entity.BioEntityCollection

getType() - Method in class org.thalia.bio.entity.CrossPopulation

getType() - Method in class org.thalia.bio.entity.GeneticMap

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

getType() - Method in class org.thalia.bio.entity.Individual

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

getType() - Method in class org.thalia.bio.entity.LGroup

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

getType() - Method in class org.thalia.bio.entity.Marker

getType() - Method in class org.thalia.bio.entity.Ontology

getType() - Method in class org.thalia.bio.entity.OntologyTerm

getType() - Method in class org.thalia.bio.entity.Population

getType() - Method in class org.thalia.bio.entity.QTL

getType() - Method in interface org.thalia.bio.IBioEntity

There are 2 main class of entities.

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

getType() - Method in class org.thalia.bio.util.EstimatedLocusPosition

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

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

getType() - Method in class org.thalia.bio.util.StaticLocusPosition

getUSD(EMResult, int, int, String) - Method in class org.metaqtl.MetaQtlResult

getValue() - Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException

getValue(String, Locale) - Method in class org.metaqtl.main.CmdLineParser.Option

getValue() - Method in class org.thalia.bio.entity.bean.PropertyBean

getVLabels() - Method in class org.metaqtl.ChromCluster.ClusterGraph

getWidth() - Method in class org.metaqtl.graph.ChromLayer

getWidth() - Method in class org.metaqtl.graph.GraphShape

getWidth() - Method in class org.metaqtl.graph.Layer

getWidth() - Method in class org.metaqtl.graph.MetaGraph

getWidth() - Method in class org.metaqtl.graph.QtlShape

getWorkAmount() - Method in class org.metaqtl.algo.MetaAlgorithm

getWorkAmount() - Method in interface org.metaqtl.IMetaAlgorithm

Returns the amount of the work to do.

getWorkProgress() - Method in class org.metaqtl.algo.MetaAlgorithm

getWorkProgress() - Method in interface org.metaqtl.IMetaAlgorithm

Returns the amount of work which have already been done.

getX() - Method in class org.metaqtl.graph.AnchoredElement

getX() - Method in class org.metaqtl.graph.ChromAxe

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

getX(MetaSimuStat.SimuConfig[]) - Static method in class org.thalia.metaqtl.main.MetaSimuStat

getXBestPred() - Method in class org.metaqtl.EMResult

getXChrom() - Method in class org.metaqtl.graph.ChromShape

getXPred() - Method in class org.metaqtl.EMResult

getXPredIdx(int) - Method in class org.metaqtl.EMResult

getY() - Method in class org.metaqtl.graph.AnchoredElement

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

getYDistance(QtlShape, QtlShape) - Static method in class org.metaqtl.graph.QtlShape

Computes the distance between two Qtl shapes assuming along the same axe Y (i.e the shapes have same X).

getYMax() - Method in class org.metaqtl.graph.ChromAxe

getYMax() - Method in class org.metaqtl.graph.ChromLayer

getYMax() - Method in class org.metaqtl.graph.ChromShape

getYMax() - Method in class org.metaqtl.graph.GraphShape

getYMax() - Method in class org.metaqtl.graph.Layer

getYMax() - Method in class org.metaqtl.graph.QtlLayer

getYMax() - Method in class org.metaqtl.graph.QtlPartitionLayer

getYMax() - Method in class org.metaqtl.graph.QtlShape

getYMax() - Method in class org.metaqtl.graph.QtlTreeLayer

getYMin() - Method in class org.metaqtl.graph.ChromAxe

getYMin() - Method in class org.metaqtl.graph.ChromLayer

getYMin() - Method in class org.metaqtl.graph.ChromShape

getYMin() - Method in class org.metaqtl.graph.GraphShape

getYMin() - Method in class org.metaqtl.graph.Layer

getYMin() - Method in class org.metaqtl.graph.QtlLayer

getYMin() - Method in class org.metaqtl.graph.QtlPartitionLayer

getYMin() - Method in class org.metaqtl.graph.QtlShape

getYMin() - Method in class org.metaqtl.graph.QtlTreeLayer

getZ(int) - Method in class org.metaqtl.EMResult

GraphFactory - Class in org.metaqtl.graph

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

GraphShape - Class in org.metaqtl.graph

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

group - Variable in class org.metaqtl.Qtl.QTLTrait

The name of the group to which the trait belongs.

GroupContainer - Class in org.thalia.bio.entity

Class Description Here

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

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

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

groupNumber() - Method in interface org.thalia.bio.IBioGenome

groups - Variable in class org.thalia.bio.entity.bean.GeneticMapBean

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

groups() - Method in interface org.thalia.bio.IBioGenome

gser(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities