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
 

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