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A

A2Xml - Class in org.metaqtl.main
A2Xml() - Constructor for class org.metaqtl.main.A2Xml
absolute() - Method in interface org.metaqtl.bio.util.ILGroupPosition
absolute - Variable in class org.metaqtl.bio.util.LGroupPosition
absolute() - Method in class org.metaqtl.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.metaqtl.bio.entity.AlleleContainer
addAllele(IBioAllele) - Method in interface org.metaqtl.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
addEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.BioEntityContainer
addGroup(IBioLGroup) - Method in class org.metaqtl.bio.entity.GroupContainer
addGroup(IBioLGroup) - Method in interface org.metaqtl.bio.IBioGenome
addIndividual(IBioIndividual) - Method in class org.metaqtl.bio.entity.IndividualContainer
addIndividual(IBioIndividual) - Method in interface org.metaqtl.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.metaqtl.bio.entity.LocusContainer
addLocus(IBioLocus) - Method in interface org.metaqtl.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.metaqtl.bio.IBioEntityTypes: The integer code for Allele entity
AlleleContainer - Class in org.metaqtl.bio.entity: Class Description Here
AlleleContainer() - Constructor for class org.metaqtl.bio.entity.AlleleContainer
AlleleContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.AlleleContainer
alleles() - Method in class org.metaqtl.bio.entity.AlleleContainer
alleles() - Method in interface org.metaqtl.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

B

BACKGROUND_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar: The color of the backgroud.
base - Static variable in class org.metaqtl.graph.PaletteColor
BC - Static variable in interface org.metaqtl.bio.IBioCrossTypes
beta(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities: Returns the beta function I(a,b)
betacf(double, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities: Used by betai : Evaluates continued fraction for incomplete beta function by modified Lentz's method.
betai(double, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities: Returns the incomplete beta function Ix(a,b)
BIC - Static variable in class org.metaqtl.EMCriteria
bic - Variable in class org.metaqtl.EMCriteria
BIC_NAME - Static variable in class org.metaqtl.EMCriteria
BioCrossTypes - Class in org.metaqtl.bio.util
BioCrossTypes() - Constructor for class org.metaqtl.bio.util.BioCrossTypes
BioEntity - Class in org.metaqtl.bio.entity: Class Description Here
BioEntity() - Constructor for class org.metaqtl.bio.entity.BioEntity
BioEntity(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.BioEntity
BioEntityAdapter - Class in org.metaqtl.bio.entity.adapter: Class Description Here
BioEntityAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.BioEntityAdapter
BioEntityBean - Class in org.metaqtl.bio.entity.bean: Class Description Here
BioEntityBean() - Constructor for class org.metaqtl.bio.entity.bean.BioEntityBean
BioEntityCollection - Class in org.metaqtl.bio.entity: Class Description Here
BioEntityCollection() - Constructor for class org.metaqtl.bio.entity.BioEntityCollection
BioEntityCollection(int) - Constructor for class org.metaqtl.bio.entity.BioEntityCollection
BioEntityCollectionAdapter - Class in org.metaqtl.bio.entity.adapter: Class Description Here
BioEntityCollectionAdapter() - Constructor for class org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter
BioEntityCollectionBean - Class in org.metaqtl.bio.entity.bean: Class Description Here
BioEntityCollectionBean() - Constructor for class org.metaqtl.bio.entity.bean.BioEntityCollectionBean
BioEntityContainer - Class in org.metaqtl.bio.entity: Class Description Here
BioEntityContainer() - Constructor for class org.metaqtl.bio.entity.BioEntityContainer
BioEntityContainer(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.BioEntityContainer
BioEntityFactory - Class in org.metaqtl.bio.entity.factory: Class Description Here
BioEntityFactory() - Constructor for class org.metaqtl.bio.entity.factory.BioEntityFactory
BioEntityNameComparator - Class in org.metaqtl.bio.util: Class Description Here
BioLocusTypes - Class in org.metaqtl.bio.util
BioLocusTypes() - Constructor for class org.metaqtl.bio.util.BioLocusTypes
BioUtilities - Class in org.metaqtl.bio.util: General comments must be added here.
BioUtilities() - Constructor for class org.metaqtl.bio.util.BioUtilities
BOX_HEIGHT - Static variable in class org.metaqtl.graph.GraphFactory
BOX_WIDTH - Static variable in class org.metaqtl.graph.GraphFactory
build(Graphics2D) - Method in class org.metaqtl.graph.ChromLayer
build(Graphics2D) - Method in class org.metaqtl.graph.Layer: Build the layer.
build(Graphics2D) - Method in class org.metaqtl.graph.QtlLayer
build(Graphics2D) - Method in class org.metaqtl.graph.QtlPartitionLayer
build(Graphics2D) - Method in class org.metaqtl.graph.QtlTreeLayer
buildMetaChrom(ChromCluster) - Method in class org.metaqtl.algo.MetaMapAlgorithm: For a cluster of chromosomes cluster this method builds the consensus chromosome using a Weighted Least Square strategy and returns the result as a MetaChrom object.
buildQtlTree(MetaQtlData) - Method in class org.metaqtl.algo.QtlTreeAlgorithm: For the given data points this method build the tree which represents the hierarchical clustering.
buildShape(Graphics2D, Object) - Method in class org.metaqtl.graph.ChromShape
buildShape(Graphics2D, Object) - Method in class org.metaqtl.graph.GraphShape
buildShape(Graphics2D, Object) - Method in class org.metaqtl.graph.QtlShape: This methods create a new QtlShape from the given graphics context.

C

C - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
c1 - Variable in class org.metaqtl.Qtl: The recombination rate between the QTL position and the left flanking marker.
c2 - Variable in class org.metaqtl.Qtl: The recombination rate between the QTL position and the right flanking marker.
C_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
canAddMoreQtl(double) - Method in class org.metaqtl.graph.QtlLayerBuffer: Retruns true if more Qtl can be added to the configuration, false otherwise.
card - Variable in class org.metaqtl.TreeNode: The number of sequences in the cluster
cartoFunction - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
cartoFunctionHaldane - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
cartoFunctionKey - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
cartoFunctionKosambi - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
ccov - Variable in class org.metaqtl.EMResult: The complete information (just for means).
CENTROID_METHOD - Static variable in class org.metaqtl.algo.HClustAlgorithm: Centroid method
CentroidMethod(double[], double[]) - Static method in class org.metaqtl.algo.HClustAlgorithm: This method performs a hierarchical clustering of the given data points using a centroid method based on the mahalanobis distance.
cg - Variable in class org.metaqtl.Chromosome: The number of generations of the offspring population.
checkProjection(ChromCluster[]) - Method in class org.metaqtl.algo.QtlProjAlgorithm
chi2 - Variable in class org.metaqtl.MetaChrom: The chi-square value of this chromosome.
chi2 - Variable in class org.metaqtl.MultiFitResult: The chi-square of the model.
children - Variable in class org.metaqtl.bio.entity.bean.OntologyTermBean: The children of the term.
children - Variable in class org.metaqtl.TreeNode: Left and right children, or null
CHISQUARE - Static variable in interface org.metaqtl.IBioLGroupProperties: The key for the chisquare value.
chrName - Variable in class org.metaqtl.algo.ClustAlgorithm: The name of the chromosome to study.
chrom - Variable in class org.metaqtl.ChromCluster.ClusterEdge
CHROM_ALIGN_MODE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_DISTANCE_SCALE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_FLANKING_CEX - Static variable in class org.metaqtl.graph.MetaGraphPar: The default cex parameter for flanking regions at the top and the end of the chromosome.
CHROM_NAME_FONT - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_NAME_HSPACE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_STROKE - Static variable in class org.metaqtl.graph.MetaGraphPar: The stroke of the chromosome shape.
CHROM_STROKE_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar: The color of the stroke of the Chromosome shape.
CHROM_TICK_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar: The color of the marker ticks on the chromosome.
CHROM_TICK_STROKE - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_TICK_WIDTH_1 - Static variable in class org.metaqtl.graph.MetaGraphPar: The width of the marker ticks.
CHROM_TICK_WIDTH_2 - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_TICK_WIDTH_3 - Static variable in class org.metaqtl.graph.MetaGraphPar
CHROM_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar: The width of the chromosome.
ChromAxe - Class in org.metaqtl.graph
ChromAxe(double, double, double) - Constructor for class org.metaqtl.graph.ChromAxe
ChromCluster - Class in org.metaqtl: A cluster of chromosomes which share the same name inside a MapCluster framwork.
ChromCluster() - Constructor for class org.metaqtl.ChromCluster: Creates a new instance if ChromCluster.
ChromCluster.ClusterEdge - Class in org.metaqtl
ChromCluster.ClusterEdge(CMarkerSequence, Chromosome) - Constructor for class org.metaqtl.ChromCluster.ClusterEdge
ChromCluster.ClusterGraph - Class in org.metaqtl
ChromCluster.ClusterGraph(ChromCluster) - Constructor for class org.metaqtl.ChromCluster.ClusterGraph
ChromGraph - Class in org.metaqtl.graph: A ChromGraph allows to link together a Chromosome and a QtlPartition in order to be depicted into a graphic.
ChromGraph() - Constructor for class org.metaqtl.graph.ChromGraph
ChromLayer - Class in org.metaqtl.graph
ChromLayer(double, double) - Constructor for class org.metaqtl.graph.ChromLayer
ChromLayer.CMrkTickPath - Class in org.metaqtl.graph
ChromLayer.CMrkTickPath() - Constructor for class org.metaqtl.graph.ChromLayer.CMrkTickPath
ChromLayer.CMrkTickPoint - Class in org.metaqtl.graph
ChromLayer.CMrkTickPoint() - Constructor for class org.metaqtl.graph.ChromLayer.CMrkTickPoint
chromNames - Variable in class org.metaqtl.MetaQtlAnalysis: The names of the chromosomes.
chromNames - Variable in class org.metaqtl.MetaQtlModel: The chromosomes.
Chromosome - Class in org.metaqtl: On a Chromosome there are two types of locus : Marker QTL (Quantitative Trait Loci) inside a mapping context which is defined by both the mapping framework (function and unit) and the population cross design used to build this chromosome.
Chromosome() - Constructor for class org.metaqtl.Chromosome
chromosome - Variable in class org.metaqtl.graph.ChromGraph: The chromosome to draw
ChromosomeAdapter - Class in org.metaqtl.adapter: This class defines some usefull methods to adapt Chromosome objects into other kinds of objects or the inverse.
ChromosomeAdapter() - Constructor for class org.metaqtl.adapter.ChromosomeAdapter
chromosomes - Variable in class org.metaqtl.algo.ClustAlgorithm: The chromosome on which the clustering is performed.
chromosomes - Variable in class org.metaqtl.MetaMap: The meta chromosomes.
ChromShape - Class in org.metaqtl.graph
ChromShape() - Constructor for class org.metaqtl.graph.ChromShape
ci - Variable in class org.metaqtl.Qtl: The QTL confidence interval.
ci2sd(double) - Static method in class org.metaqtl.numrec.NumericalUtilities
ci_height - Variable in class org.metaqtl.graph.QtlShape
CI_MISS_IGNORE - Static variable in interface org.metaqtl.IMetaQtlConstants: MSD Mode : ignore QTL with missing standard deviation.
CI_MISS_IMPUTATION - Static variable in interface org.metaqtl.IMetaQtlConstants: MSD Mode : replace missing standard deviation by the mean of the observed ones.
CI_MODE_AVAILABLE - Static variable in interface org.metaqtl.IMetaQtlConstants: SD Mode : use the available information to compute the standard deviation.
CI_MODE_LOD - Static variable in interface org.metaqtl.IMetaQtlConstants: SD Mode : use only the confidence interval information if defined to compute the standard deviation.
CI_MODE_MAXIMAL - Static variable in interface org.metaqtl.IMetaQtlConstants: SD Mode : compute the standard deviation using both lod support and rsquare information (if available) and then choose the maximal standard-deviation.
CI_MODE_RSQUARE - Static variable in interface org.metaqtl.IMetaQtlConstants: SD Mode : use only the rsquare information if defined to compute the standard deviation.
CI_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer: The default width of the CI of the Qtl
ci_width - Variable in class org.metaqtl.graph.QtlShape
clog - Variable in class org.metaqtl.EMResult: The complete loglikelihood.
close() - Method in class org.metaqtl.bio.util.TabulatedReader: Closes the stream.
close() - Method in class org.metaqtl.bio.util.TabulatedWriter
ClustAlgorithm - Class in org.metaqtl.algo
ClustAlgorithm(IBioGenome, IBioOntology) - Constructor for class org.metaqtl.algo.ClustAlgorithm
ClustAlgorithm(IBioGenome, String, IBioOntology) - Constructor for class org.metaqtl.algo.ClustAlgorithm
cluster - Variable in class org.metaqtl.ChromCluster.ClusterGraph
clusterings - Variable in class org.metaqtl.MetaQtlResult: The meta qtl clusterings.
clusters - Variable in class org.metaqtl.ChromCluster: The list of the cluster members.
CMarkerSequence - Class in org.metaqtl: A Common marker sequence between two ordered set of markers is a sub-set of at least two markers which order is the same between the two sets (may be reverse).
CMarkerSequence(int[][], int) - Constructor for class org.metaqtl.CMarkerSequence: Initiates a new Common marker sequence from the tow arrays of common marker indices mcidx[0..1][0..nmc-1].
CmdLineParser - Class in org.metaqtl.main: Largely GNU-compatible command-line options parser.
CmdLineParser() - Constructor for class org.metaqtl.main.CmdLineParser
CmdLineParser.IllegalOptionValueException - Exception in org.metaqtl.main: Thrown when an illegal or missing value is given by the user for an option that takes a value.
CmdLineParser.IllegalOptionValueException(CmdLineParser.Option, String) - Constructor for exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
CmdLineParser.NotFlagException - Exception in org.metaqtl.main: Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one or more requires a value.
CmdLineParser.NotFlagException(String, char) - Constructor for exception org.metaqtl.main.CmdLineParser.NotFlagException
CmdLineParser.Option - Class in org.metaqtl.main: Representation of a command-line option
CmdLineParser.Option(String, boolean) - Constructor for class org.metaqtl.main.CmdLineParser.Option
CmdLineParser.Option(char, String, boolean) - Constructor for class org.metaqtl.main.CmdLineParser.Option
CmdLineParser.Option.BooleanOption - Class in org.metaqtl.main
CmdLineParser.Option.BooleanOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.BooleanOption
CmdLineParser.Option.BooleanOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.BooleanOption
CmdLineParser.Option.DoubleOption - Class in org.metaqtl.main: An option that expects a floating-point value
CmdLineParser.Option.DoubleOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.DoubleOption
CmdLineParser.Option.DoubleOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.DoubleOption
CmdLineParser.Option.IntegerOption - Class in org.metaqtl.main: An option that expects an integer value
CmdLineParser.Option.IntegerOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.IntegerOption
CmdLineParser.Option.IntegerOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.IntegerOption
CmdLineParser.Option.LongOption - Class in org.metaqtl.main: An option that expects a long integer value
CmdLineParser.Option.LongOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.LongOption
CmdLineParser.Option.LongOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.LongOption
CmdLineParser.Option.StringOption - Class in org.metaqtl.main: An option that expects a string value
CmdLineParser.Option.StringOption(char, String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.StringOption
CmdLineParser.Option.StringOption(String) - Constructor for class org.metaqtl.main.CmdLineParser.Option.StringOption
CmdLineParser.OptionException - Exception in org.metaqtl.main: Base class for exceptions that may be thrown when options are parsed
CmdLineParser.OptionException(String) - Constructor for exception org.metaqtl.main.CmdLineParser.OptionException
CmdLineParser.UnknownOptionException - Exception in org.metaqtl.main: Thrown when the parsed command-line contains an option that is not recognised.
CmdLineParser.UnknownOptionException(String) - Constructor for exception org.metaqtl.main.CmdLineParser.UnknownOptionException
CmdLineParser.UnknownOptionException(String, String) - Constructor for exception org.metaqtl.main.CmdLineParser.UnknownOptionException
CmdLineParser.UnknownSuboptionException - Exception in org.metaqtl.main: Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one is unknown.
CmdLineParser.UnknownSuboptionException(String, char) - Constructor for exception org.metaqtl.main.CmdLineParser.UnknownSuboptionException
cms - Variable in class org.metaqtl.ChromCluster.ClusterEdge
CMSAlgorithm - Class in org.metaqtl.algo: Use this class to find common marker sequences between two chromosomes.
CMSAlgorithm() - Constructor for class org.metaqtl.algo.CMSAlgorithm
COLLECTION - Static variable in interface org.metaqtl.bio.IBioEntityTypes
color2string(Color) - Static method in class org.metaqtl.graph.MetaGraphPar
COMMON_STROKE_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
compare(Object, Object) - Method in class org.metaqtl.bio.util.BioEntityNameComparator
compare(Object, Object) - Method in class org.metaqtl.bio.util.LocusPositionComparator
computeCOV(double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm: Computes the variance-covariance matrix of the mixture component estimates.
computeCriteria() - Method in class org.metaqtl.EMResult: This methos computes the following criteria : AIC AIC3 ICOMP MIR BIC AWE
computeDM(double[], double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm: Computes the matrix of derivatives of the update function.
computeQtlSD(int) - Method in class org.metaqtl.Chromosome: According to the given standard deviation computation mode this method computes for each QTL the value of the standard deviation of the QTL position.
ConsMap - Class in org.metaqtl.main
ConsMap() - Constructor for class org.metaqtl.main.ConsMap
containsKey(String) - Method in class org.metaqtl.bio.util.TabulatedReader: Returns true if the given string is a key of the tabulated file.
copy(EMResult, EMResult) - Static method in class org.metaqtl.EMResult
cov - Variable in class org.metaqtl.MultiFitResult: The variance-covariance matrix of the parameter estimates.
criteria - Variable in class org.metaqtl.EMResult: The model choice criteria.
cross - Variable in class org.metaqtl.Qtl: The QTL cross design.
CROSS_SIZE - Static variable in interface org.metaqtl.IBioGenomeProperties: The cross size key.
CROSS_TYPE - Static variable in interface org.metaqtl.IBioGenomeProperties: The cross type key.
crossLayers - Variable in class org.metaqtl.graph.MetaGraph
CrossPopulation - Class in org.metaqtl.bio.entity: Class Description Here
CrossPopulation() - Constructor for class org.metaqtl.bio.entity.CrossPopulation
CrossPopulation(String, IBioEntity) - Constructor for class org.metaqtl.bio.entity.CrossPopulation
CrossPopulation(String, IBioEntity, int) - Constructor for class org.metaqtl.bio.entity.CrossPopulation
crossToString(int, int) - Static method in class org.metaqtl.bio.util.BioCrossTypes
cs - Variable in class org.metaqtl.Chromosome: The size of the offspring population.
css - Variable in class org.metaqtl.CMarkerSequence: The sizes of the common sequences
ct - Variable in class org.metaqtl.Chromosome: The type of the offspring population.

D

d - Variable in class org.metaqtl.MetaChrom: The absolute positions of markers in Morgan.
D - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
D_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dataLayers - Variable in class org.metaqtl.graph.MetaGraph
dC - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dD - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dE - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
DEFAULT_HEIGHT - Static variable in class org.metaqtl.graph.MetaGraphPar: The default height.
DEFAULT_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar: The default width.
DEFINITION - Static variable in interface org.metaqtl.bio.IOntologyTermProperties: The definition property of a term in a ontology
dF - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dfridr(NumericalUtilities.Function, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities: Returns the derivative of a function func at a point x by Ridders' method of polynomial extrapolation.
dG - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
DH - Static variable in interface org.metaqtl.bio.IBioCrossTypes
disableLogger() - Method in class org.metaqtl.algo.MetaAlgorithm
dist - Variable in class org.metaqtl.TreeNode: The distance between the node and its parent.
distance(double, int, int) - Static method in class org.metaqtl.util.MappingFunction: Returns the distance from the recombination rate.
distanceUnitCM - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
distanceUnitKey - Static variable in interface org.metaqtl.bio.entity.IGeneticMapProperties
dm - Variable in class org.metaqtl.EMResult: The matrix of convergence rate for the EM-Algorithm (just for means).
DMAX(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities: Returns the max between a and b
DO_SEM - Static variable in class org.metaqtl.algo.EMAlgorithm: If true the best starting point is used to do Supplemental EM (SEM) in order to compute the DM Matrix..
doEM(double[], double[], int, EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm: Apply the EM-Algorithm on the given data set where x is an array of observed value and sd an array of same size than x which stores the standard deviations of the observed values.
DOF - Static variable in interface org.metaqtl.IBioLGroupProperties: The key for the number of degrees of freedom.
dof - Variable in class org.metaqtl.MetaChrom: The number of degrees of freedom.
dof - Variable in class org.metaqtl.MultiFitResult: The number of degrees of freedom.
dominance - Variable in class org.metaqtl.Qtl.QTLStats: The dominance effect of the QTL.
doProjection(ChromCluster[]) - Method in class org.metaqtl.algo.QtlProjAlgorithm
doQtlClustering(MetaQtlData) - Method in class org.metaqtl.algo.QtlClustAlgorithm: For a given data set data performs the clustering on each trait group and returns the results as an array of MetaQtlResult objects.
doTraitGroupClustering() - Method in class org.metaqtl.MetaQtlData: According to the values of the QTLTrait.group attribute of the trait attribute of the qtls this methos clusterize the qtls in trait groups.
doTraitOntologyClustering(IBioOntology) - Method in class org.metaqtl.MetaQtlData: According to the given trait ontology this methods clusterize the QTL in group in such a way that each group represents a trait term in the ontology.
draw(Graphics2D) - Method in class org.metaqtl.graph.ChromLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.ChromShape
draw(Graphics2D) - Method in class org.metaqtl.graph.GraphShape: Draws the shape.
draw(Graphics2D) - Method in class org.metaqtl.graph.Layer: Draws the layer on the given graph context.
draw(Graphics2D, double, double) - Method in class org.metaqtl.graph.MetaGraph
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlPartitionLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlShape
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlTreeLayer
DSWAP(double[], int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities: Swaps elements i and j in a.
DUBIOUS_ORDER - Static variable in interface org.metaqtl.IBioLocusProperties: The key for the marker dubious status.
DubiousLocusFactory - Class in org.metaqtl.factory: A factory to read a list of dubious markers from a file.
DubiousLocusFactory() - Constructor for class org.metaqtl.factory.DubiousLocusFactory

E

E - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
E_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
edist - Variable in class org.metaqtl.EMResult: The euclidean distance between the current and the previous vector of parameters (mu + pi)
EM_CONTINUE - Static variable in class org.metaqtl.algo.EMAlgorithm: The EM convergence status : continue
EM_ERR - Static variable in class org.metaqtl.algo.EMAlgorithm: The EM convergence tolerance.
EM_FAILURE - Static variable in class org.metaqtl.algo.EMAlgorithm: The EM convergence status : failure
EM_ITER_MAX - Static variable in class org.metaqtl.algo.EMAlgorithm: The EM maximum number of iterations.
EM_MIN_DISTANCE - Static variable in class org.metaqtl.algo.EMAlgorithm: The minimal mahalanobis distance between components.
EM_OK - Static variable in class org.metaqtl.algo.EMAlgorithm: The EM convergence status : success
EM_START - Static variable in class org.metaqtl.algo.EMAlgorithm: The number of replicates for a run of the EM-algorithm.
EMAlgorithm - Class in org.metaqtl.algo: This class defines methods to perform the EM-algorithm for univariate mixture of gaussians with known variances.
EMAlgorithm() - Constructor for class org.metaqtl.algo.EMAlgorithm
EMCriteria - Class in org.metaqtl
EMCriteria() - Constructor for class org.metaqtl.EMCriteria
EMPTY_BIOALLELE_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
EMPTY_BIOENTITY_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
EMPTY_BIOLGROUP_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
EMPTY_BIOLOCUS_ARRAY - Static variable in interface org.metaqtl.bio.entity.IBioConstants
emRate(EMResult, double[], double[]) - Static method in class org.metaqtl.algo.EMAlgorithm: Compute the euclidean distance between the new parameters and the old ones to obtain a simple approximation of the EM convergence rate.
EMResult - Class in org.metaqtl
EMResult() - Constructor for class org.metaqtl.EMResult
EMResult(int, int) - Constructor for class org.metaqtl.EMResult
EMResultFactory - Class in org.metaqtl.factory
EMResultFactory() - Constructor for class org.metaqtl.factory.EMResultFactory
entities - Variable in class org.metaqtl.bio.entity.bean.BioEntityCollectionBean
entities - Variable in class org.metaqtl.bio.entity.BioEntityContainer
entities() - Method in class org.metaqtl.bio.entity.BioEntityContainer
entityNumber() - Method in class org.metaqtl.bio.entity.BioEntityContainer
eStep(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm: The Expectation step : it just consists in updating the Z matrix, i.e the cluster membership probabilities.
ESTIMATED - Static variable in interface org.metaqtl.bio.util.ILGroupPosition
EstimatedLocusPosition - Class in org.metaqtl.bio.util: Class Description Here
EstimatedLocusPosition(double, double) - Constructor for class org.metaqtl.bio.util.EstimatedLocusPosition
extractLocus(IBioLocus[], int) - Static method in class org.metaqtl.bio.util.BioLocusTypes: This returns extracts in the given array of loci the locus which type matches the given one.

F

F - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
F_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
fisherVariance(double, int, int, int) - Static method in class org.metaqtl.util.OffspringManager: Returns the inverse of the Fisher Information depending on the type of cross for a given recombination rate and a given population size.
fixCluster() - Method in class org.metaqtl.ChromCluster: This methods frozes the index of the distinct markers over all the members of the cluster.
font2string(Font) - Static method in class org.metaqtl.graph.MetaGraphPar
formatDouble(double) - Static method in class org.metaqtl.bio.util.NumberFormat
frames - Variable in class org.metaqtl.CMarkerSequence: The frame of the common marker sequences
from - Variable in class org.metaqtl.graph.QtlUnit
from - Variable in class org.metaqtl.Qtl.QTLSupport: The position from the first marker to the left border of the IC.
fromEntity(IBioEntity, BioEntityBean) - Static method in class org.metaqtl.bio.entity.adapter.BioEntityAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.GeneticMapBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.LGroupBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.LocusBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
fromEntity(IBioEntity) - Method in class org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
fromEntity(IBioEntity) - Method in interface org.metaqtl.bio.IBioAdapter: Convert the given compliant object to a bio entity object.
fromQTL(Qtl) - Static method in class org.metaqtl.adapter.QtlAdapter: This method converts a Qtl into an object which class implements the IBioLocus interface.
func(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.Function: Returns the value of the function in x.
funcd(double) - Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction: Compute both the value and the derivate of the function in x.
function - Variable in class org.metaqtl.bio.entity.bean.OntologyBean: The function of the ontology.




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 - 
Static variable in class org.metaqtl.bio.util.BioCrossTypes
 
gen - 
Variable in class org.metaqtl.Qtl.QTLCross
The number of generations.
generalHelp() - 
Static method in class org.metaqtl.main.MetaMain
 
generalUsage() - 
Static method in class org.metaqtl.main.MetaMain
 
generation - 
Variable in class org.metaqtl.bio.entity.Population
 
GeneticMap - Class in org.metaqtl.bio.entity
Class Description Here
GeneticMap() - 
Constructor for class org.metaqtl.bio.entity.GeneticMap
 
GeneticMap(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.GeneticMap
 
GeneticMap(String) - 
Constructor for class org.metaqtl.bio.entity.GeneticMap
 
GeneticMapBean - Class in org.metaqtl.bio.entity.bean
Class Description Here
GeneticMapBean() - 
Constructor for class org.metaqtl.bio.entity.bean.GeneticMapBean
 
GeneticMapBeanAdapter - Class in org.metaqtl.bio.entity.adapter
Class Description Here
GeneticMapBeanAdapter() - 
Constructor for class org.metaqtl.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.metaqtl.bio.IBioEntityTypes
The integer code for Genome entity
get(String) - 
Method in class org.metaqtl.bio.util.TabulatedReader
Returns the value of the field which belongs to the given key.
getAdjacentTable() - 
Method in class org.metaqtl.ChromCluster.ClusterGraph
 
getAllele(String) - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
getAllele(String) - 
Method in interface org.metaqtl.bio.IBioLocus
 
getAlleleNumber() - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
getAlleleNumber() - 
Method in interface org.metaqtl.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.metaqtl.bio.entity.BioEntityCollection
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.GeneticMap
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.Individual
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.LGroup
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.Marker
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.Ontology
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.OntologyTerm
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.Population
 
getBioAdapter() - 
Method in class org.metaqtl.bio.entity.QTL
 
getBioAdapter() - 
Method in interface org.metaqtl.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.metaqtl.bio.entity.OntologyTerm
 
getChildrenTerm() - 
Method in interface org.metaqtl.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
 
getCluster(String) - 
Static method in class org.metaqtl.main.MetaMain
 
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.metaqtl.bio.entity.CrossPopulation
 
getCrossType() - 
Method in interface org.metaqtl.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;
getDico(String) - 
Static method in class org.metaqtl.main.MetaMain
 
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
 
getDubious(String) - 
Static method in class org.metaqtl.main.MetaMain
 
getEMEps() - 
Method in class org.metaqtl.algo.QtlClustAlgorithm
 
getEMRanStartNumber() - 
Method in class org.metaqtl.algo.QtlClustAlgorithm
 
getEntity(String) - 
Method in class org.metaqtl.bio.entity.BioEntityContainer
 
getEntityBeanClass() - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
 
getEntityBeanClass() - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
getEntityBeanClass() - 
Method in class org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
 
getEntityBeanClass() - 
Method in class org.metaqtl.bio.entity.factory.XmlOntologyFactory
 
getEntityType() - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
 
getEntityType() - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
getEntityType() - 
Method in class org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
 
getEntityType() - 
Method in class org.metaqtl.bio.entity.factory.XmlOntologyFactory
 
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.metaqtl.bio.entity.Ontology
 
getFunction() - 
Method in interface org.metaqtl.bio.IBioOntology
Returns the function of the ontology
getGeneration() - 
Method in class org.metaqtl.bio.entity.Population
 
getGeneration() - 
Method in interface org.metaqtl.bio.IBioCross
 
getGenome() - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
getGenome() - 
Method in interface org.metaqtl.bio.IBioLGroup
 
getGraph() - 
Method in class org.metaqtl.ChromCluster
 
getGroup() - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
getGroup(String) - 
Method in class org.metaqtl.bio.entity.GroupContainer
 
getGroup() - 
Method in class org.metaqtl.bio.entity.Locus
 
getGroup(String) - 
Method in interface org.metaqtl.bio.IBioGenome
 
getGroup() - 
Method in interface org.metaqtl.bio.IBioLocus
 
getGroups() - 
Method in class org.metaqtl.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.metaqtl.bio.entity.OntologyTerm
 
getID() - 
Method in interface org.metaqtl.bio.IBioOntologyTerm
Returns the id if the terms.
getImage(ChromGraph[]) - 
Static method in class org.metaqtl.graph.GraphFactory
 
getIndividual(String) - 
Method in class org.metaqtl.bio.entity.IndividualContainer
 
getIndividual(String) - 
Method in interface org.metaqtl.bio.IBioPopulation
 
getIndividualNumber() - 
Method in class org.metaqtl.bio.entity.IndividualContainer
 
getIndividualNumber() - 
Method in class org.metaqtl.bio.entity.Population
 
getIndividualNumber() - 
Method in interface org.metaqtl.bio.IBioPopulation
 
getInstance() - 
Static method in class org.metaqtl.bio.util.BioEntityNameComparator
 
getInstance() - 
Static method in class org.metaqtl.bio.util.LocusPositionComparator
 
getK() - 
Method in class org.metaqtl.EMResult
 
getKeys() - 
Method in class org.metaqtl.bio.util.TabulatedReader
Returns the set of the keys.
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.metaqtl.bio.entity.bean.LGroupBean
 
getLocus(String) - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
getLocus() - 
Method in interface org.metaqtl.bio.IBioAllele
 
getLocus(String) - 
Method in interface org.metaqtl.bio.IBioLGroup
 
getLocusAdapter() - 
Static method in class org.metaqtl.bio.entity.Locus
 
getLocusNumber() - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
getLocusNumber() - 
Method in interface org.metaqtl.bio.IBioLGroup
 
getLocusType() - 
Method in class org.metaqtl.bio.entity.Marker
 
getLocusType() - 
Method in class org.metaqtl.bio.entity.QTL
 
getLocusType() - 
Method in interface org.metaqtl.bio.IBioLocus
 
getLogger() - 
Method in class org.metaqtl.algo.MetaAlgorithm
Returns the logger for this algorithm as a 
 PrintStream.
getMahalanobis(double[]) - 
Method in class org.metaqtl.EMResult
 
getMap(String) - 
Static method in class org.metaqtl.main.MetaMain
 
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
 
getMaps(String) - 
Static method in class org.metaqtl.main.MetaMain
 
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
 
getName() - 
Method in class org.metaqtl.bio.entity.bean.BioEntityBean
 
getName() - 
Method in class org.metaqtl.bio.entity.bean.PropertyBean
 
getName() - 
Method in class org.metaqtl.bio.entity.BioEntity
 
getName() - 
Method in class org.metaqtl.bio.entity.BioEntityCollection
 
getName() - 
Method in interface org.metaqtl.bio.IBioEntity
Returns the name of the biological entity
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
 
getNodeHeights() - 
Method in class org.metaqtl.Tree
 
getNodeNumber() - 
Method in class org.metaqtl.Tree
 
getOntology(String, char) - 
Static method in class org.metaqtl.main.MetaMain
 
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.bio.entity.BioEntity
 
getParent() - 
Method in class org.metaqtl.bio.entity.BioEntityCollection
 
getParent() - 
Method in interface org.metaqtl.bio.IBioEntity
Returns the entity that handles this entity.
getParent() - 
Method in class org.metaqtl.TreeNode
 
getParents() - 
Method in class org.metaqtl.bio.entity.CrossPopulation
 
getParents() - 
Method in class org.metaqtl.bio.entity.Individual
 
getParents() - 
Method in class org.metaqtl.bio.entity.Population
 
getParents() - 
Method in interface org.metaqtl.bio.IBioCross
 
getParents() - 
Method in interface org.metaqtl.bio.IBioIndividual
Returns the pedigree of the individual
getParentTerm() - 
Method in class org.metaqtl.bio.entity.OntologyTerm
 
getParentTerm() - 
Method in interface org.metaqtl.bio.IBioOntologyTerm
Returns the parent of the term.
getPartNames() - 
Method in class org.metaqtl.QtlPartition
 
getPedigree() - 
Method in class org.metaqtl.bio.entity.Individual
 
getPi(int) - 
Method in class org.metaqtl.EMResult
 
getPopulation() - 
Method in class org.metaqtl.bio.entity.Individual
 
getPopulation() - 
Method in interface org.metaqtl.bio.IBioIndividual
 
getPosition() - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
getPosition() - 
Method in class org.metaqtl.bio.entity.Locus
 
getPosition() - 
Method in interface org.metaqtl.bio.IBioLocus
 
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.metaqtl.bio.entity.bean.BioEntityBean
 
getProperties() - 
Method in class org.metaqtl.bio.entity.BioEntity
 
getProperties() - 
Method in class org.metaqtl.bio.entity.BioEntityCollection
 
getProperties() - 
Method in interface org.metaqtl.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
 
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) - 
Static method in class org.metaqtl.main.MetaMain
 
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.bio.entity.Ontology
 
getRoot() - 
Method in interface org.metaqtl.bio.IBioOntology
Returns the root of the ontology tree.
getRoot() - 
Method in class org.metaqtl.Tree
 
getSD(int) - 
Method in class org.metaqtl.EMResult
 
getSize() - 
Method in class org.metaqtl.bio.entity.Population
Returns the size of the population.
getSize() - 
Method in interface org.metaqtl.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(IBioOntologyTerm) - 
Method in class org.metaqtl.bio.entity.Ontology
 
getTerm(String) - 
Method in class org.metaqtl.bio.entity.Ontology
 
getTerm(IBioOntologyTerm) - 
Method in interface org.metaqtl.bio.IBioOntology
Returns if exists the term in the ontology which 
 matches the given one.
getTerm(String) - 
Method in interface org.metaqtl.bio.IBioOntology
This method looks into the ontology if there is 
 a term with the given name and returns it.
getTerm(String) - 
Method in class org.metaqtl.MetaDico
 
getTerms() - 
Method in class org.metaqtl.MetaDico
 
getToken() - 
Method in class org.metaqtl.bio.util.TabulatedReader
 
getToken() - 
Method in class org.metaqtl.bio.util.TabulatedWriter
 
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.metaqtl.bio.entity.AlleleContainer
 
getType() - 
Method in class org.metaqtl.bio.entity.BioEntity
 
getType() - 
Method in class org.metaqtl.bio.entity.BioEntityCollection
 
getType() - 
Method in class org.metaqtl.bio.entity.CrossPopulation
 
getType() - 
Method in class org.metaqtl.bio.entity.GeneticMap
 
getType() - 
Method in class org.metaqtl.bio.entity.GroupContainer
 
getType() - 
Method in class org.metaqtl.bio.entity.Individual
 
getType() - 
Method in class org.metaqtl.bio.entity.IndividualContainer
 
getType() - 
Method in class org.metaqtl.bio.entity.LGroup
 
getType() - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
getType() - 
Method in class org.metaqtl.bio.entity.Marker
 
getType() - 
Method in class org.metaqtl.bio.entity.Ontology
 
getType() - 
Method in class org.metaqtl.bio.entity.OntologyTerm
 
getType() - 
Method in class org.metaqtl.bio.entity.Population
 
getType() - 
Method in class org.metaqtl.bio.entity.QTL
 
getType() - 
Method in interface org.metaqtl.bio.IBioEntity
There are 2 main class of entities.
getType() - 
Method in interface org.metaqtl.bio.IBioLocus
 
getType() - 
Method in class org.metaqtl.bio.util.EstimatedLocusPosition
 
getType() - 
Method in interface org.metaqtl.bio.util.ILGroupPosition
 
getType() - 
Method in class org.metaqtl.bio.util.LGroupPosition
 
getType() - 
Method in class org.metaqtl.bio.util.StaticLocusPosition
 
getUSD(EMResult, int, int, String) - 
Method in class org.metaqtl.MetaQtlResult
 
getValue() - 
Method in class org.metaqtl.bio.entity.bean.PropertyBean
 
getValue() - 
Method in exception org.metaqtl.main.CmdLineParser.IllegalOptionValueException
 
getValue(String, Locale) - 
Method in class org.metaqtl.main.CmdLineParser.Option
 
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
 
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.metaqtl.bio.entity
Class Description Here
GroupContainer() - 
Constructor for class org.metaqtl.bio.entity.GroupContainer
 
GroupContainer(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.GroupContainer
 
groupNumber() - 
Method in class org.metaqtl.bio.entity.GroupContainer
 
groupNumber() - 
Method in interface org.metaqtl.bio.IBioGenome
 
groups - 
Variable in class org.metaqtl.bio.entity.bean.GeneticMapBean
 
groups() - 
Method in class org.metaqtl.bio.entity.GroupContainer
 
groups() - 
Method in interface org.metaqtl.bio.IBioGenome
 
gser(double, double) - 
Static method in class org.metaqtl.numrec.NumericalUtilities
 



H

hasChildren() - 
Method in class org.metaqtl.bio.entity.OntologyTerm
 
hasChildren() - 
Method in interface org.metaqtl.bio.IBioOntologyTerm
Returns true if the term has children, false
 otherwise.
hasNext() - 
Method in class org.metaqtl.bio.util.TabulatedReader
Returns true if there is still a line to read.
hasProba() - 
Method in class org.metaqtl.graph.ChromLayer
 
hasQTL() - 
Method in class org.metaqtl.Chromosome
This method tests if the chromosome have a 
 set of QTL defined.
haveSameFrame(int, int) - 
Method in class org.metaqtl.CMarkerSequence
 
HClustAlgorithm - Class in org.metaqtl.algo
This class implements stantard agglomerative hierarchical
 clustering methods.
HClustAlgorithm() - 
Constructor for class org.metaqtl.algo.HClustAlgorithm
 
HEADER - 
Static variable in class org.metaqtl.bio.entity.factory.OntologyTabFactory
 
HEIGHT - 
Static variable in class org.metaqtl.graph.GraphFactory
 
height - 
Variable in class org.metaqtl.graph.GraphShape
 
height - 
Variable in class org.metaqtl.graph.Layer
The height of the layer.
height - 
Variable in class org.metaqtl.TreeNode
The distance between the node and the root of the tree (if defined).
help - 
Variable in class org.metaqtl.main.MetaMain
 
HORIZONTAL_MODE - 
Static variable in class org.metaqtl.QtlPartition
 



I

IBioAdaptable - Interface in org.metaqtl.bio
 
IBioAdapter - Interface in org.metaqtl.bio
 
IBioAllele - Interface in org.metaqtl.bio
Class Description Here
IBioConstants - Interface in org.metaqtl.bio.entity
Class Description Here
IBioCross - Interface in org.metaqtl.bio
Class Description Here
IBioCrossTypes - Interface in org.metaqtl.bio
Class Description Here
IBioEntity - Interface in org.metaqtl.bio
Class Description Here
IBioEntityTypes - Interface in org.metaqtl.bio
Class Description Here
IBioGenome - Interface in org.metaqtl.bio
 
IBioGenomeProperties - Interface in org.metaqtl
This interface defines both the keys and the 
 default values of properties which
 can be handled by a org.thalia.bio.entity.IBioGenome.
IBioIndividual - Interface in org.metaqtl.bio
Class Description Here
IBioIndividualTree - Interface in org.metaqtl.bio
Class Description Here
IBioLGroup - Interface in org.metaqtl.bio
 
IBioLGroupProperties - Interface in org.metaqtl
This interface defines the key of properties which can
 be handled by a org.thalia.bio.entity.IBioLGroup.
IBioLocus - Interface in org.metaqtl.bio
 
IBioLocusProperties - Interface in org.metaqtl
This interface defines the key of the properties which
 can be handled by a org.thalia.bio.entity.IBioLocus.
IBioOntology - Interface in org.metaqtl.bio
This interface defines some rules to handle a ontology.
IBioOntologyTerm - Interface in org.metaqtl.bio
This class defines a term of an ontology.
IBioPopulation - Interface in org.metaqtl.bio
Class Description Here
ic1 - 
Variable in class org.metaqtl.Qtl.QTLSupport
The recombination rate between the QTL position
 and the left border of the IC.
ic2 - 
Variable in class org.metaqtl.Qtl.QTLSupport
The recombination rate between the QTL position
 and the right border of the IC.
ICOMP - 
Static variable in class org.metaqtl.EMCriteria
 
icomp - 
Variable in class org.metaqtl.EMCriteria
 
ICOMP_NAME - 
Static variable in class org.metaqtl.EMCriteria
 
id - 
Variable in class org.metaqtl.bio.entity.bean.OntologyTermBean
The id of the term.
id - 
Variable in class org.metaqtl.Qtl
The id of the Qtl
idx - 
Variable in class org.metaqtl.TreeNode
?
 The identifiant of the cluster.
idx1 - 
Variable in class org.metaqtl.CMarkerSequence
The indices of the markers on the first
 chromosome for the common sequences.
idx2 - 
Variable in class org.metaqtl.CMarkerSequence
The indices of the marker on the second
 chromosome for the common sequences.
IGeneticMapProperties - Interface in org.metaqtl.bio.entity
Class Description Here
ILGroupPosition - Interface in org.metaqtl.bio.util
Class Description Here
IMetaAlgorithm - Interface in org.metaqtl
This interface defines some methods which are common
 to data analysis algorithms.
IMetaQtlConstants - Interface in org.metaqtl
This interface defines some global constants which are used
 by several classes of the package.
IMIN(int, int) - 
Static method in class org.metaqtl.numrec.NumericalUtilities
Returns the min between a and b
incms - 
Variable in class org.metaqtl.CMarkerSequence
 
indexx(int, double[], int[]) - 
Static method in class org.metaqtl.numrec.NumericalUtilities
Sort the given array of double arrin[1..n] without destroying it and
 returns the sorted indices of the array elements into indx[1..n].
Individual - Class in org.metaqtl.bio.entity
Class Description Here
Individual() - 
Constructor for class org.metaqtl.bio.entity.Individual
 
Individual(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.Individual
 
INDIVIDUAL - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
The integer code for an individual entity
IndividualContainer - Class in org.metaqtl.bio.entity
Class Description Here
IndividualContainer() - 
Constructor for class org.metaqtl.bio.entity.IndividualContainer
 
IndividualContainer(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.IndividualContainer
 
individuals() - 
Method in class org.metaqtl.bio.entity.IndividualContainer
 
individuals() - 
Method in interface org.metaqtl.bio.IBioPopulation
 
InfoMap - Class in org.metaqtl.main
 
InfoMap() - 
Constructor for class org.metaqtl.main.InfoMap
 
init(Graphics2D, ChromGraph[]) - 
Method in class org.metaqtl.graph.MetaGraph
 
initCmdLineParser() - 
Method in class org.metaqtl.main.MetaMain
 
initEM(double[], double[], EMResult, Random) - 
Static method in class org.metaqtl.algo.EMAlgorithm
Initializes the EM algorithm by randomly assigning observations to
 the clusters and do one M-Step to compute the first values of the 
 parameters.
initNodeIdx() - 
Method in class org.metaqtl.Tree
 
initPalettes() - 
Static method in class org.metaqtl.graph.MetaGraphPar
 
initProbaPalette() - 
Static method in class org.metaqtl.graph.MetaGraphPar
 
initQTLPalette() - 
Static method in class org.metaqtl.graph.MetaGraphPar
 
initQTLPalette(int) - 
Static method in class org.metaqtl.graph.MetaGraphPar
 
initReverse() - 
Method in class org.metaqtl.Tree
 
intScale - 
Variable in class org.metaqtl.Qtl.QTLProj
The scale ratio between the original flanking
 marker interval and the one on the map used
 for projection.
IOntologyTermProperties - Interface in org.metaqtl.bio
 
IRISe - 
Static variable in interface org.metaqtl.bio.IBioCrossTypes
 
IRISi - 
Static variable in interface org.metaqtl.bio.IBioCrossTypes
 
isConnected(int) - 
Method in class org.metaqtl.ChromCluster.ClusterGraph
Test if the graph is connected
isConnected(int) - 
Method in class org.metaqtl.ChromCluster
Tests if the cluster of chromosome is connected using a graph
 approach.
isDubiousLocus(IBioLocus) - 
Method in class org.metaqtl.ChromCluster
If a list of dubious markers has been set before
 then this routine checks if the given locus is
 not included into this list.
isDubiousOrderLocus(IBioLocus) - 
Static method in class org.metaqtl.util.LocusProperties
Returns true if the given locus has a property order.dubious
 set to one, false otherwise
isIgnore() - 
Method in class org.metaqtl.Qtl
This methods returns true if the QTL must be ignored.
isLoggerEnable() - 
Method in class org.metaqtl.algo.MetaAlgorithm
 
ISWAP(int[], int, int) - 
Static method in class org.metaqtl.numrec.NumericalUtilities
Swaps elements i and j in a.
iterate(double[], double[], EMResult) - 
Static method in class org.metaqtl.algo.EMAlgorithm
This method performs one iteration of the EM-algorithm.



K

k - 
Variable in class org.metaqtl.EMResult
The number of clusters.



L

label - 
Variable in class org.metaqtl.TreeNode
The label of the cluster
Layer - Class in org.metaqtl.graph
 
Layer(double, double) - 
Constructor for class org.metaqtl.graph.Layer
Creates a layer without any width and heigth
 constraints which upper left corner will be
 located at the point (x,y).
LAYER_HSPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The horizontal space between layers.
LAYER_VSPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The vertical space between layers.
leaf - 
Variable in class org.metaqtl.TreeNode
The status of the node.
LEFT_LABEL - 
Static variable in class org.metaqtl.graph.ChromLayer
 
LEFT_LABEL - 
Static variable in class org.metaqtl.graph.ChromShape
 
LEGEND_BOX_CEX - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_FONT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_GRAD_HEIGHT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_GRAD_WIDTH - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_HSPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_PART_HEIGHT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_PART_WIDTH - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
LEGEND_SCALE_UNIT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
legendLayer - 
Variable in class org.metaqtl.graph.MetaGraph
 
LGroup - Class in org.metaqtl.bio.entity
Class Description Here
LGroup() - 
Constructor for class org.metaqtl.bio.entity.LGroup
 
LGroup(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.LGroup
 
LGROUP - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
The integer code for Linkage Group entity
LGroupBean - Class in org.metaqtl.bio.entity.bean
Class Description Here
LGroupBean() - 
Constructor for class org.metaqtl.bio.entity.bean.LGroupBean
 
LGroupBeanAdapter - Class in org.metaqtl.bio.entity.adapter
Class Description Here
LGroupBeanAdapter() - 
Constructor for class org.metaqtl.bio.entity.adapter.LGroupBeanAdapter
 
LGroupPosition - Class in org.metaqtl.bio.util
Class Description Here
LGroupPosition(double) - 
Constructor for class org.metaqtl.bio.util.LGroupPosition
 
LGroupPosition(double, double) - 
Constructor for class org.metaqtl.bio.util.LGroupPosition
 
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
 
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
 
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.MapChartFactory
TODO (non-Javadoc)
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapChartFactory
TODO (non-Javadoc)
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
 
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
 
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapRawFactory
 
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.MapRawFactory
 
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.MapTabFactory
 
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapTabFactory
 
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
 
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory

         Term_id        : the term identifient.
load(InputStream) - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
load(Reader) - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
loci() - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
loci() - 
Method in interface org.metaqtl.bio.IBioLGroup
 
locus - 
Variable in class org.metaqtl.bio.entity.bean.LGroupBean
 
Locus - Class in org.metaqtl.bio.entity
 
Locus() - 
Constructor for class org.metaqtl.bio.entity.Locus
 
Locus(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.Locus
 
LOCUS - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
The integer code for Locus entity
LocusBean - Class in org.metaqtl.bio.entity.bean
Class Description Here
LocusBean() - 
Constructor for class org.metaqtl.bio.entity.bean.LocusBean
 
LocusBeanAdapter - Class in org.metaqtl.bio.entity.adapter
Class Description Here
LocusBeanAdapter() - 
Constructor for class org.metaqtl.bio.entity.adapter.LocusBeanAdapter
 
LocusContainer - Class in org.metaqtl.bio.entity
Class Description Here
LocusContainer() - 
Constructor for class org.metaqtl.bio.entity.LocusContainer
 
LocusContainer(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.LocusContainer
 
locusNames - 
Variable in class org.metaqtl.ChromCluster
Ths locus name index table
LocusPositionComparator - Class in org.metaqtl.bio.util
Class Description Here
LocusProperties - Class in org.metaqtl.util
 
LocusProperties() - 
Constructor for class org.metaqtl.util.LocusProperties
 
lod - 
Variable in class org.metaqtl.Qtl.QTLStats
The lod score of the QTL.
lodDecrease - 
Variable in class org.metaqtl.Qtl.QTLSupport
The value of the LOD decrease used to obtain the CI.
logger - 
Variable in class org.metaqtl.algo.MetaAlgorithm
The logger.
loggerUp - 
Variable in class org.metaqtl.algo.MetaAlgorithm
The logger status.
longForm() - 
Method in class org.metaqtl.main.CmdLineParser.Option
 



M

m - 
Variable in class org.metaqtl.MultiFitResult
The number of parameters
m1 - 
Variable in class org.metaqtl.Qtl
The indice of the left flanking marker.
m2 - 
Variable in class org.metaqtl.Qtl
The indice of the right flanking marker.
main(String[]) - 
Static method in class org.metaqtl.main.A2Xml
 
main(String[]) - 
Static method in class org.metaqtl.main.ConsMap
 
main(String[]) - 
Static method in class org.metaqtl.main.InfoMap
 
main(String[]) - 
Static method in class org.metaqtl.main.MapView
 
main(String[]) - 
Static method in class org.metaqtl.main.MetaDB
 
main(String[]) - 
Static method in class org.metaqtl.main.MMapView
 
main(String[]) - 
Static method in class org.metaqtl.main.MQTLView
 
main(String[]) - 
Static method in class org.metaqtl.main.QTLClust
 
main(String[]) - 
Static method in class org.metaqtl.main.QTLClustInfo
 
main(String[]) - 
Static method in class org.metaqtl.main.QTLModel
 
main(String[]) - 
Static method in class org.metaqtl.main.QTLProj
 
main(String[]) - 
Static method in class org.metaqtl.main.QTLTree
 
main(String[]) - 
Static method in class org.metaqtl.main.Xml2A
 
MAKER_NAME_VSPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
manageMissingData(int) - 
Method in class org.metaqtl.MetaQtlData
Manage the missing data.
MapChartFactory - Class in org.metaqtl.bio.entity.factory
General comments must be added here.
MapChartFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.MapChartFactory
 
MapCluster - Class in org.metaqtl
 
MapCluster() - 
Constructor for class org.metaqtl.MapCluster
Creates a new instance of MapCluster.
MapDBFactory - Class in org.metaqtl.factory
A factory to read the list and the properties of a set
 of genetic maps.
MapDBFactory() - 
Constructor for class org.metaqtl.factory.MapDBFactory
 
MapMakerFactory - Class in org.metaqtl.bio.entity.factory
 
MapMakerFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.MapMakerFactory
 
mapName - 
Variable in class org.metaqtl.Chromosome
The name of the map in which this chromosome
 is defined.
mapNames - 
Variable in class org.metaqtl.MetaChrom
The names of the genetic maps.
mapOrigin - 
Variable in class org.metaqtl.Qtl.QTLProj
The name of the map from which
 this QTL comes.
MAPPING_CROSS - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The key for mapping cross.
MAPPING_EXPANSION - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The key for mapping expansion status.
MAPPING_FUNCTION - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The key for mapping function.
MAPPING_FUNCTION_HALDANE - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The code for Haldane mapping function.
MAPPING_FUNCTION_HALDANE - 
Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for haldane mapping function
MAPPING_FUNCTION_KOSAMBI - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The code for Kosambi mapping function.
MAPPING_FUNCTION_KOSAMBI - 
Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for kosambi mapping function
MAPPING_FUNCTION_UNKNOWN - 
Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for not defined mapping function
MAPPING_UNIT - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The mapping unit key.
MAPPING_UNIT_CM - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The code for centi-Morgan unit.
MAPPING_UNIT_CM - 
Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for centi morgan mapping unit
MAPPING_UNIT_M - 
Static variable in interface org.metaqtl.IBioGenomeProperties
The code for Morgan unit.
MAPPING_UNIT_M - 
Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for morgan mapping unit
MAPPING_UNIT_UNKNOWN - 
Static variable in interface org.metaqtl.IMetaQtlConstants
Integer code for unknown mapping unit
MappingFunction - Class in org.metaqtl.util
define all cartogarphies functions
MappingFunction() - 
Constructor for class org.metaqtl.util.MappingFunction
 
MapRawFactory - Class in org.metaqtl.bio.entity.factory
 
MapRawFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.MapRawFactory
 
mapScale - 
Variable in class org.metaqtl.Qtl.QTLProj
The scale ratio between the original
 map and the map on which the QTL has
 been projected.
MapTabFactory - Class in org.metaqtl.bio.entity.factory
 
MapTabFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.MapTabFactory
 
MapView - Class in org.metaqtl.main
 
MapView() - 
Constructor for class org.metaqtl.main.MapView
 
mapWeight - 
Variable in class org.metaqtl.Qtl.QTLProj
The cumulated scale weights of the common
 marke sequences between the original map
 and the map on which the QTL has been projected.
Marker - Class in org.metaqtl.bio.entity
Class Description Here
Marker() - 
Constructor for class org.metaqtl.bio.entity.Marker
 
Marker(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.Marker
 
MARKER - 
Static variable in interface org.metaqtl.bio.IBioLocus
 
MARKER_NAME_FONT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
MARKER_POSITION_FONT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
MARKERLOCUS - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
 
mcidx - 
Variable in class org.metaqtl.CMarkerSequence
The common marker indices on the chromosomes.
merge(GeneticMap) - 
Method in class org.metaqtl.bio.entity.GeneticMap
Deprecated.  
mergeGenome(IBioGenome, IBioGenome) - 
Static method in class org.metaqtl.bio.util.BioUtilities
This method merges two genomes in a single one : g1 is
 modified and will contain the result of the merge.
MetaAlgorithm - Class in org.metaqtl.algo
 
MetaAlgorithm() - 
Constructor for class org.metaqtl.algo.MetaAlgorithm
 
MetaChrom - Class in org.metaqtl
A MetaChrom is the result of the merge of the members of a
 ChromCluster.
MetaChrom(MultiFitResult, ChromCluster) - 
Constructor for class org.metaqtl.MetaChrom
Get a new instance of MetaChrom which is 
 initialized by using the result
 of the merge of the members of a ChromCluster.
MetaDB - Class in org.metaqtl.main
 
MetaDB() - 
Constructor for class org.metaqtl.main.MetaDB
 
MetaDico - Class in org.metaqtl
This class represents a dictionnary of synonyms.
MetaDico() - 
Constructor for class org.metaqtl.MetaDico
 
MetaDicoFactory - Class in org.metaqtl.factory
 
MetaDicoFactory() - 
Constructor for class org.metaqtl.factory.MetaDicoFactory
 
MetaGraph - Class in org.metaqtl.graph
 
MetaGraph() - 
Constructor for class org.metaqtl.graph.MetaGraph
 
MetaGraphPar - Class in org.metaqtl.graph
 
MetaGraphParFactory - Class in org.metaqtl.factory
 
MetaGraphParFactory() - 
Constructor for class org.metaqtl.factory.MetaGraphParFactory
 
MetaMain - Class in org.metaqtl.main
 
MetaMain() - 
Constructor for class org.metaqtl.main.MetaMain
 
MetaMap - Class in org.metaqtl
A MetaMap is a bundle of MetaChrom objects.
MetaMap(int) - 
Constructor for class org.metaqtl.MetaMap
Creates a new instance of MetaMap
 which will contain nchr MetaChrom
 objects.
MetaMapAdapter - Class in org.metaqtl.adapter
This class defines some usefull methods to adapt MetaMap
 objects into other kinds of objects or the inverse.
MetaMapAdapter() - 
Constructor for class org.metaqtl.adapter.MetaMapAdapter
 
MetaMapAlgorithm - Class in org.metaqtl.algo
This class is dedicated to the construction of a consensus
 genetic map from a set of genetic maps based on a Weigthed
 Least Square approach.
MetaMapAlgorithm(IBioGenome[], IBioGenome, IBioLocus[], MetaDico) - 
Constructor for class org.metaqtl.algo.MetaMapAlgorithm
 
MetaMapSummaryFactory - Class in org.metaqtl.factory
A factory to write out the information on a MetaMap.
MetaMapSummaryFactory() - 
Constructor for class org.metaqtl.factory.MetaMapSummaryFactory
 
metaQtlAnalysis - 
Variable in class org.metaqtl.Chromosome
The results of a meta-analysis of QTL.
MetaQtlAnalysis - Class in org.metaqtl
A QTL meta analysis consists in a clustering of QTL positions over
 chromosomes for different group of traits.
MetaQtlAnalysis(int) - 
Constructor for class org.metaqtl.MetaQtlAnalysis
Creates a new instance of a MetaQtlAnalysis
MetaQtlAnalysisAdapter - Class in org.metaqtl.adapter
 
MetaQtlAnalysisAdapter() - 
Constructor for class org.metaqtl.adapter.MetaQtlAnalysisAdapter
 
MetaQtlAnalysisFactory - Class in org.metaqtl.factory
A factory to deal with the result of a QTL meta-analysis.
MetaQtlAnalysisFactory() - 
Constructor for class org.metaqtl.factory.MetaQtlAnalysisFactory
 
MetaQtlAnalysisModelFactory - Class in org.metaqtl.factory
 
MetaQtlAnalysisModelFactory() - 
Constructor for class org.metaqtl.factory.MetaQtlAnalysisModelFactory
 
MetaQtlAnalysisSummaryFactory - Class in org.metaqtl.factory
A factory to deal with QTL meta-analysis result.
MetaQtlAnalysisSummaryFactory() - 
Constructor for class org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
 
MetaQtlData - Class in org.metaqtl
QTL meta analysis first requires to gather the QTL according
 to the group trait they belong and then to format the QTL data
 into data points to perfom clustering.
MetaQtlData(Qtl[]) - 
Constructor for class org.metaqtl.MetaQtlData
Create a new instance of MetaQtlData which
 will represent the given array of Qtl.
MetaQtlModel - Class in org.metaqtl
 
MetaQtlModel() - 
Constructor for class org.metaqtl.MetaQtlModel
 
MetaQtlModel(int) - 
Constructor for class org.metaqtl.MetaQtlModel
 
MetaQtlModelFactory - Class in org.metaqtl.factory
 
MetaQtlModelFactory() - 
Constructor for class org.metaqtl.factory.MetaQtlModelFactory
 
MetaQtlResult - Class in org.metaqtl
A MetaQtlResult is used to store the 
 results of a QTL meta analysis which has been performed
 for a given trait group on a given chromosome.
MetaQtlResult() - 
Constructor for class org.metaqtl.MetaQtlResult
 
MetaQtlResult(String, int) - 
Constructor for class org.metaqtl.MetaQtlResult
 
METHOD - 
Static variable in class org.metaqtl.algo.HClustAlgorithm
A global variable to control the custering
 method.
mfc - 
Variable in class org.metaqtl.Chromosome
The mapping function for this chromosome
mir - 
Variable in class org.metaqtl.EMCriteria
 
missing_sd_mode - 
Variable in class org.metaqtl.algo.ClustAlgorithm
This global variable defines the mode of imputation
 for the QTL for which the standard deviation of the position
 is not available.
MMapView - Class in org.metaqtl.main
 
MMapView() - 
Constructor for class org.metaqtl.main.MMapView
 
mode - 
Variable in class org.metaqtl.QtlPartition
The mode of representation
models - 
Variable in class org.metaqtl.MetaQtlModel
The number of Qtl per chromosome
 and per trait.
mqtls - 
Variable in class org.metaqtl.Chromosome
The meta Qtls on this chromosome.
MQTLView - Class in org.metaqtl.main
 
MQTLView() - 
Constructor for class org.metaqtl.main.MQTLView
 
mr - 
Variable in class org.metaqtl.Chromosome
The adjacent recombination rate between 
 ordered markers
mrkNames - 
Variable in class org.metaqtl.Chromosome
The ordered marker names
mrkNames - 
Variable in class org.metaqtl.MetaChrom
The ordered marker names.
mrkOc - 
Variable in class org.metaqtl.MetaChrom
The number of occurence per marker oved chromosomes.
mStep(double[], double[], EMResult, double) - 
Static method in class org.metaqtl.algo.EMAlgorithm
The Maximization step : here this step is straighforward and 
 simple analytical formula are applied to obtain the new parameter
 estimates.
mu - 
Variable in class org.metaqtl.EMResult
The means of the clusters.
MultiFitResult - Class in org.metaqtl
This class represents a result of a multilinear regression
 analysis.
MultiFitResult(int, int) - 
Constructor for class org.metaqtl.MultiFitResult
Creates a new instance of MultiFitResult
 with the given number of observations N
 and parameters M.
mut - 
Variable in class org.metaqtl.Chromosome
The mapping unit for this chromosome



N

n - 
Variable in class org.metaqtl.EMResult
The number of data points.
n - 
Variable in class org.metaqtl.MultiFitResult
The number of observations without missing data.
name - 
Variable in class org.metaqtl.bio.entity.bean.BioEntityBean
 
name - 
Variable in class org.metaqtl.bio.entity.bean.PropertyBean
 
name - 
Variable in class org.metaqtl.bio.entity.BioEntity
 
name - 
Variable in class org.metaqtl.bio.entity.BioEntityCollection
 
name - 
Variable in class org.metaqtl.ChromCluster
The name of the chromosome cluster.
name - 
Variable in class org.metaqtl.Chromosome
The name of the chromosome.
name - 
Variable in class org.metaqtl.graph.QtlUnit
 
name - 
Variable in class org.metaqtl.MetaChrom
The name of the meta chrom.
name - 
Variable in class org.metaqtl.Qtl
The name of the QTL.
name - 
Variable in class org.metaqtl.Qtl.QTLCross
The name of the cross design.
name - 
Variable in class org.metaqtl.Qtl.QTLTrait
The name of the trait.
nc - 
Variable in class org.metaqtl.MetaChrom
The number of chromosomes implied.
nchr - 
Variable in class org.metaqtl.MetaMap
The number of meta chromosmes.
nchr - 
Variable in class org.metaqtl.MetaQtlAnalysis
The number of chromosomes on which the meta-analysis
 has been performed.
ncs - 
Variable in class org.metaqtl.CMarkerSequence
The number of common sequences.
needToBeRescaled(IBioGenome) - 
Static method in class org.metaqtl.util.GeneticMapProperties
Returns true if the given map need to be rescaled - due
 to the mapping extansion for some pedigree designs.
NEG_COMMON - 
Static variable in class org.metaqtl.graph.ChromLayer
 
NEG_COMMON_COLOR - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
newBioEntity(int) - 
Static method in class org.metaqtl.bio.entity.BioEntity
 
newCrossPopulation(int, String, IBioEntity) - 
Static method in class org.metaqtl.bio.entity.Population
 
newEstimatedLocusPosition(double, double) - 
Static method in class org.metaqtl.bio.util.LGroupPosition
 
newLocus(int) - 
Static method in class org.metaqtl.bio.entity.Locus
Returns a new Locus
 from the given locus type.
newLocus(String) - 
Static method in class org.metaqtl.bio.entity.Locus
Returns a new Locus
 from the given locus type.
newStaticLocusPosition(double) - 
Static method in class org.metaqtl.bio.util.LGroupPosition
 
nextValues(Hashtable) - 
Method in class org.metaqtl.bio.util.TabulatedWriter
Prints one line of tabulated values given the hashtable which links
 values and keys.
nextValues(String[]) - 
Method in class org.metaqtl.bio.util.TabulatedWriter
Print one line of tabulated values by assuming that they are in the same
 order than the keys.
ni - 
Variable in class org.metaqtl.ChromCluster
The total number of marker intervals.
ni - 
Variable in class org.metaqtl.MetaChrom
The number of marker intervals implied in this consensus.
nidx - 
Variable in class org.metaqtl.TreeNode
The indices of the sub-nodes
nm - 
Variable in class org.metaqtl.Chromosome
The number of markers.
nm - 
Variable in class org.metaqtl.MetaChrom
The number of markers.
nmc - 
Variable in class org.metaqtl.ChromCluster
Total number of common marker between clusters
nmc - 
Variable in class org.metaqtl.CMarkerSequence
The number of common marker between chromosomes
nmc - 
Variable in class org.metaqtl.MetaChrom
The number of marker per implied chromosome
nmqc - 
Variable in class org.metaqtl.MetaQtlResult
The number of meta qtl clusterings.
nodes - 
Variable in class org.metaqtl.Tree
The nodes of the tree.
np - 
Variable in class org.metaqtl.QtlPartition
The number of partition.
nqtl - 
Variable in class org.metaqtl.MetaQtlResult
The number of QTL
nqtl - 
Variable in class org.metaqtl.QtlPartition
The number of Qtl.
ntg - 
Variable in class org.metaqtl.MetaQtlData
The number of trait group.
ntgQtls - 
Variable in class org.metaqtl.MetaQtlData
The number of QTL in each
 trait group.
NumberFormat - Class in org.metaqtl.bio.util
 
NumberFormat() - 
Constructor for class org.metaqtl.bio.util.NumberFormat
 
NumericalUtilities - Class in org.metaqtl.numrec
Class Description Here
NumericalUtilities() - 
Constructor for class org.metaqtl.numrec.NumericalUtilities
 
NumericalUtilities.Function - Interface in org.metaqtl.numrec
 
NumericalUtilities.NRFunction - Interface in org.metaqtl.numrec
 


O

o_mrkIdxL - 
Variable in class org.metaqtl.Qtl.QTLProj
The original indice of the left
 flanking marker.
o_mrkIdxR - 
Variable in class org.metaqtl.Qtl.QTLProj
The original indice of the right 
 flanking marker.
OCCURENCE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the occurence of markers in a consensus map
ocov - 
Variable in class org.metaqtl.EMResult
The observed information (just for means).
OffspringManager - Class in org.metaqtl.util
Class Description Here
OffspringManager() - 
Constructor for class org.metaqtl.util.OffspringManager
 
OffspringManager.HaldaneWaddingtonProportion - Class in org.metaqtl.util
 
OffspringManager.HaldaneWaddingtonProportion() - 
Constructor for class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
 
olog - 
Variable in class org.metaqtl.EMResult
The observed loglikelihood.
ontology - 
Variable in class org.metaqtl.algo.ClustAlgorithm
The optional trait ontology to use to group Qtl.
Ontology - Class in org.metaqtl.bio.entity
 
Ontology() - 
Constructor for class org.metaqtl.bio.entity.Ontology
 
ONTOLOGY - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
 
ONTOLOGY_TERM - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
 
OntologyBean - Class in org.metaqtl.bio.entity.bean
 
OntologyBean() - 
Constructor for class org.metaqtl.bio.entity.bean.OntologyBean
 
OntologyBeanAdapter - Class in org.metaqtl.bio.entity.adapter
 
OntologyBeanAdapter() - 
Constructor for class org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
 
OntologyTabFactory - Class in org.metaqtl.bio.entity.factory
A factory to deal with Ontology.
OntologyTabFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.OntologyTabFactory
 
OntologyTerm - Class in org.metaqtl.bio.entity
 
OntologyTerm() - 
Constructor for class org.metaqtl.bio.entity.OntologyTerm
 
OntologyTermBean - Class in org.metaqtl.bio.entity.bean
 
OntologyTermBean() - 
Constructor for class org.metaqtl.bio.entity.bean.OntologyTermBean
 
OntologyTermBeanAdapter - Class in org.metaqtl.bio.entity.adapter
 
OntologyTermBeanAdapter() - 
Constructor for class org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
 
org.metaqtl - package org.metaqtl
 
org.metaqtl.adapter - package org.metaqtl.adapter
 
org.metaqtl.algo - package org.metaqtl.algo
 
org.metaqtl.bio - package org.metaqtl.bio
 
org.metaqtl.bio.entity - package org.metaqtl.bio.entity
 
org.metaqtl.bio.entity.adapter - package org.metaqtl.bio.entity.adapter
 
org.metaqtl.bio.entity.bean - package org.metaqtl.bio.entity.bean
 
org.metaqtl.bio.entity.factory - package org.metaqtl.bio.entity.factory
 
org.metaqtl.bio.util - package org.metaqtl.bio.util
 
org.metaqtl.factory - package org.metaqtl.factory
 
org.metaqtl.graph - package org.metaqtl.graph
 
org.metaqtl.main - package org.metaqtl.main
 
org.metaqtl.numrec - package org.metaqtl.numrec
 
org.metaqtl.util - package org.metaqtl.util
 


P

p1 - 
Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPoint
 
p2 - 
Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPoint
 
PaletteColor - Class in org.metaqtl.graph
 
PaletteColor() - 
Constructor for class org.metaqtl.graph.PaletteColor
 
parent - 
Variable in class org.metaqtl.bio.entity.BioEntity
 
parent - 
Variable in class org.metaqtl.bio.entity.BioEntityCollection
 
parent - 
Variable in class org.metaqtl.TreeNode
The parent of the node
parents - 
Variable in class org.metaqtl.bio.entity.Population
 
parse(String[]) - 
Method in class org.metaqtl.main.CmdLineParser
Extract the options and non-option arguments from the given
 list of command-line arguments.
parse(String[], Locale) - 
Method in class org.metaqtl.main.CmdLineParser
Extract the options and non-option arguments from the given
 list of command-line arguments.
parseChromList(String) - 
Static method in class org.metaqtl.main.MetaMain
 
parseCmdLine(String[]) - 
Method in class org.metaqtl.main.MetaMain
 
parseCross(String) - 
Static method in class org.metaqtl.bio.util.BioCrossTypes
Parse the given string and return if valid the type of
 cross and the number of generations.
parseDouble(String) - 
Static method in class org.metaqtl.bio.util.NumberFormat
This method parse the given string to a double value.
parser - 
Variable in class org.metaqtl.main.MetaMain
 
parseType(String) - 
Static method in class org.metaqtl.bio.util.BioLocusTypes
 
parseValue(String, Locale) - 
Method in class org.metaqtl.main.CmdLineParser.Option.DoubleOption
 
parseValue(String, Locale) - 
Method in class org.metaqtl.main.CmdLineParser.Option.IntegerOption
 
parseValue(String, Locale) - 
Method in class org.metaqtl.main.CmdLineParser.Option.LongOption
 
parseValue(String, Locale) - 
Method in class org.metaqtl.main.CmdLineParser.Option
Override to extract and convert an option value passed on the
 command-line
parseValue(String, Locale) - 
Method in class org.metaqtl.main.CmdLineParser.Option.StringOption
 
partition - 
Variable in class org.metaqtl.graph.QtlUnit
 
path - 
Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPath
 
pi - 
Variable in class org.metaqtl.EMResult
The mixing proportions.
pnames - 
Variable in class org.metaqtl.QtlPartition
The partition names.
population - 
Variable in class org.metaqtl.bio.entity.Individual
 
Population - Class in org.metaqtl.bio.entity
Class Description Here
Population() - 
Constructor for class org.metaqtl.bio.entity.Population
 
Population(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.Population
 
POPULATION - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
The integer code for Population entity
pos - 
Variable in class org.metaqtl.graph.QtlUnit
 
POS_COMMON - 
Static variable in class org.metaqtl.graph.ChromLayer
 
POS_COMMON_COLOR - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
position - 
Variable in class org.metaqtl.bio.entity.bean.LocusBean
 
position - 
Variable in class org.metaqtl.bio.entity.Locus
 
position - 
Variable in class org.metaqtl.Qtl
The QTL most probable location on the chromosome.
printHelp() - 
Method in class org.metaqtl.main.A2Xml
 
printHelp() - 
Method in class org.metaqtl.main.ConsMap
 
printHelp() - 
Method in class org.metaqtl.main.InfoMap
 
printHelp() - 
Method in class org.metaqtl.main.MapView
 
printHelp() - 
Method in class org.metaqtl.main.MetaDB
 
printHelp() - 
Method in class org.metaqtl.main.MetaMain
 
printHelp() - 
Method in class org.metaqtl.main.MMapView
 
printHelp() - 
Method in class org.metaqtl.main.MQTLView
 
printHelp() - 
Method in class org.metaqtl.main.QTLClust
 
printHelp() - 
Method in class org.metaqtl.main.QTLClustInfo
 
printHelp() - 
Method in class org.metaqtl.main.QTLModel
 
printHelp() - 
Method in class org.metaqtl.main.QTLProj
 
printHelp() - 
Method in class org.metaqtl.main.QTLTree
 
printHelp() - 
Method in class org.metaqtl.main.Xml2A
 
printImgFormat(int) - 
Static method in class org.metaqtl.main.MetaMain
 
printLicense(String, String) - 
Static method in class org.metaqtl.main.MetaMain
 
printUsage() - 
Method in class org.metaqtl.main.A2Xml
 
printUsage() - 
Method in class org.metaqtl.main.ConsMap
 
printUsage() - 
Method in class org.metaqtl.main.InfoMap
 
printUsage() - 
Method in class org.metaqtl.main.MapView
 
printUsage() - 
Method in class org.metaqtl.main.MetaDB
 
printUsage() - 
Method in class org.metaqtl.main.MetaMain
 
printUsage() - 
Method in class org.metaqtl.main.MMapView
 
printUsage() - 
Method in class org.metaqtl.main.MQTLView
 
printUsage() - 
Method in class org.metaqtl.main.QTLClust
 
printUsage() - 
Method in class org.metaqtl.main.QTLClustInfo
 
printUsage() - 
Method in class org.metaqtl.main.QTLModel
 
printUsage() - 
Method in class org.metaqtl.main.QTLProj
 
printUsage() - 
Method in class org.metaqtl.main.QTLTree
 
printUsage() - 
Method in class org.metaqtl.main.Xml2A
 
proba - 
Variable in class org.metaqtl.Chromosome
Probabilities defined along the chromosome.
proba - 
Variable in class org.metaqtl.QtlPartition
The probabilities of each Qtl to
 belong to each partition.
PROBA_BIN - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
PROBA_FROM_COLOR - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
PROBA_PALETTE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
PROBA_TO_COLOR - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
proj - 
Variable in class org.metaqtl.Qtl
The QTL projection properties.
properties - 
Variable in class org.metaqtl.bio.entity.bean.BioEntityBean
 
properties - 
Variable in class org.metaqtl.bio.entity.BioEntity
 
properties - 
Variable in class org.metaqtl.bio.entity.BioEntityCollection
 
PropertyBean - Class in org.metaqtl.bio.entity.bean
Class Description Here
PropertyBean() - 
Constructor for class org.metaqtl.bio.entity.bean.PropertyBean
 
PropertyBean(String, String) - 
Constructor for class org.metaqtl.bio.entity.bean.PropertyBean
 
PVALUE - 
Static variable in interface org.metaqtl.IBioLGroupProperties
The key for the p-value.
pvalue - 
Variable in class org.metaqtl.MetaChrom
The p-value of this chromosome.
pvalue - 
Variable in class org.metaqtl.MultiFitResult
The p-value of the model.
PYTHAG(double, double) - 
Static method in class org.metaqtl.numrec.NumericalUtilities
Computes sqrt(a^2+b^2)



Q

QTL - Class in org.metaqtl.bio.entity
Class Description Here
QTL() - 
Constructor for class org.metaqtl.bio.entity.QTL
 
QTL(String, IBioEntity) - 
Constructor for class org.metaqtl.bio.entity.QTL
 
QTL - 
Static variable in interface org.metaqtl.bio.IBioLocus
 
Qtl - Class in org.metaqtl
A QTL (Quantitative Trait Loci)
Qtl() - 
Constructor for class org.metaqtl.Qtl
 
Qtl.QTLCross - Class in org.metaqtl
This class stores the informations on the cross
 design used to detect the QTL.
Qtl.QTLCross() - 
Constructor for class org.metaqtl.Qtl.QTLCross
 
Qtl.QTLProj - Class in org.metaqtl
This class stores the QTL projection
 properties.
Qtl.QTLProj() - 
Constructor for class org.metaqtl.Qtl.QTLProj
 
Qtl.QTLStats - Class in org.metaqtl
This class stores the usual statistics for the QTL.
Qtl.QTLStats() - 
Constructor for class org.metaqtl.Qtl.QTLStats
 
Qtl.QTLSupport - Class in org.metaqtl
This class stores information
 on the QTL Confidence Interval
Qtl.QTLSupport() - 
Constructor for class org.metaqtl.Qtl.QTLSupport
 
Qtl.QTLTrait - Class in org.metaqtl
This class stores the trait description of a QTL
Qtl.QTLTrait() - 
Constructor for class org.metaqtl.Qtl.QTLTrait
 
QTL_CI_FROM - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL confidence interval lower boundary.
QTL_CI_LOD_DECREASE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL confidence interval LOD decrease.
QTL_CI_TO - 
Static variable in interface org.metaqtl.IBioLocusProperties
THe key for the QTL confidence interval upper boundary.
QTL_CI_WIDTH - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_CI_WIDTH_CEX - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_CROSS_NAME - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL cross name.
QTL_CROSS_SIZE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL cross size.
QTL_CROSS_TYPE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL cross type.
QTL_HSPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The horizontal space between Qtl shapes.
QTL_NAME_COLOR - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The color of the QTL names.
QTL_NAME_FONT - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The font used for the Qtl names.
QTL_NAME_SPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_NAME_VSPACE_CEX - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The space magnification between the Qtl name and the Qtl confidence
 interval.
QTL_PALETTE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The color palete for the QTL partition.
QTL_PCH_SIZE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_POS_HEIGHT_CEX - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_POS_WIDTH_CEX - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_PROB_WIDTH - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_PROJ_INTSCALE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL flanking marker interval projection
 rate.
QTL_PROJ_MAPSCALE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL confidence interval projection rate.
QTL_PROJ_ORIGIN - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the map of origin of the QTL.
QTL_PROJ_SHAREFLANKING - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL flanking marker interval order preservation.
QTL_PROJ_SWAPFLANKING - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL flanking marker interval reverse order.
QTL_STATS_ADDITIVE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL additive effect.
QTL_STATS_DOMINANCE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL dominance effect.
QTL_STATS_RSQUARE - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL rsquare.
QTL_TICK_WIDTH_CEX - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The magnification for the tick of the QTL.
QTL_TRAIT_GROUP - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL trait group.
QTL_TRAIT_NAME - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL trait name.
QTL_TRAIT_UNIT - 
Static variable in interface org.metaqtl.IBioLocusProperties
The key for the QTL trait unit.
QTL_TREE_SCALE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_TREE_SPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
QTL_VSPACE - 
Static variable in class org.metaqtl.graph.MetaGraphPar
The vertical space between Qtl shapes.
QtlAdapter - Class in org.metaqtl.adapter
This class defines some usefull methods to adapt Qtl
 object into other kinds of objects or the inverse.
QtlAdapter() - 
Constructor for class org.metaqtl.adapter.QtlAdapter
 
qtlByChrom - 
Variable in class org.metaqtl.MetaQtlAnalysis
The matrix of qtl by chromosome
qtlCI - 
Variable in class org.metaqtl.QtlPartition
The Qtl confidence intervals.
QTLClust - Class in org.metaqtl.main
 
QTLClust() - 
Constructor for class org.metaqtl.main.QTLClust
 
QtlClustAlgorithm - Class in org.metaqtl.algo
This class defines methods to perform a QTL meta-analysis
 on a genetic map by applying a clustering of QTL
 based on a gaussian mixture model and the EM-algorihtm.
QtlClustAlgorithm(IBioGenome, IBioOntology) - 
Constructor for class org.metaqtl.algo.QtlClustAlgorithm
 
QtlClustAlgorithm(IBioGenome, String, IBioOntology) - 
Constructor for class org.metaqtl.algo.QtlClustAlgorithm
 
QTLClustInfo - Class in org.metaqtl.main
 
QTLClustInfo() - 
Constructor for class org.metaqtl.main.QTLClustInfo
 
qtlIdx - 
Variable in class org.metaqtl.MetaQtlResult
The indices of QTL which are implied
 in the analysis.
QtlLayer - Class in org.metaqtl.graph
 
QtlLayer(double, double) - 
Constructor for class org.metaqtl.graph.QtlLayer
 
QtlLayerBuffer - Class in org.metaqtl.graph
 
QtlLayerBuffer() - 
Constructor for class org.metaqtl.graph.QtlLayerBuffer
 
QTLLOCUS - 
Static variable in interface org.metaqtl.bio.IBioEntityTypes
 
QTLModel - Class in org.metaqtl.main
 
QTLModel() - 
Constructor for class org.metaqtl.main.QTLModel
 
qtlNames - 
Variable in class org.metaqtl.QtlPartition
The qtl names
qtlPart - 
Variable in class org.metaqtl.graph.ChromGraph
The Qtl partition
QtlPartition - Class in org.metaqtl
 
QtlPartition() - 
Constructor for class org.metaqtl.QtlPartition
 
QtlPartitionAdapter - Class in org.metaqtl.adapter
This class defines some methods to adapt complient
 objects into a QtlPartition object.
QtlPartitionAdapter() - 
Constructor for class org.metaqtl.adapter.QtlPartitionAdapter
 
QtlPartitionLayer - Class in org.metaqtl.graph
 
QtlPartitionLayer(double, double) - 
Constructor for class org.metaqtl.graph.QtlPartitionLayer
 
qtlPos - 
Variable in class org.metaqtl.QtlPartition
The Qtl positions
QTLProj - Class in org.metaqtl.main
 
QTLProj() - 
Constructor for class org.metaqtl.main.QTLProj
 
QtlProjAlgorithm - Class in org.metaqtl.algo
This class defines some methods to project QTL positions from 
 a genetic map to another.
QtlProjAlgorithm(IBioGenome[], IBioGenome, IBioLocus[]) - 
Constructor for class org.metaqtl.algo.QtlProjAlgorithm
Creates a new instance of QtlProjAlgorithm for
 the given configuration of projection.
qtls - 
Variable in class org.metaqtl.Chromosome
The QTLs located on this chromosome.
qtls - 
Variable in class org.metaqtl.MetaQtlData
The QTL.
QtlShape - Class in org.metaqtl.graph
 
QtlShape() - 
Constructor for class org.metaqtl.graph.QtlShape
 
qtlShapes - 
Variable in class org.metaqtl.graph.QtlLayer
The Qtl shapes.
QTLTree - Class in org.metaqtl.main
 
QTLTree() - 
Constructor for class org.metaqtl.main.QTLTree
 
QtlTreeAlgorithm - Class in org.metaqtl.algo
This class defines methods to perform agglomerative
 hierarchical QTL clustering.
QtlTreeAlgorithm(IBioGenome, IBioOntology) - 
Constructor for class org.metaqtl.algo.QtlTreeAlgorithm
 
QtlTreeLayer - Class in org.metaqtl.graph
 
QtlTreeLayer(double, double) - 
Constructor for class org.metaqtl.graph.QtlTreeLayer
 
QtlUnit - Class in org.metaqtl.graph
 
QtlUnit() - 
Constructor for class org.metaqtl.graph.QtlUnit
 



R

r2R() - 
Method in class org.metaqtl.Chromosome
 
r2R(int, int) - 
Method in class org.metaqtl.Chromosome
Re-scale the chromosome assuming that the distances
 and recombination fractions are based on the frequency of
 recombinant genotypes R instead of the real recombination
 fraction r.
R2r() - 
Method in class org.metaqtl.Chromosome
 
R2r(int, int) - 
Method in class org.metaqtl.Chromosome
Re-scale the chromosome assuming that the distances
 and recombination fractions are based on the frequency of
 recombinant genotypes R instead of the real recombination
 fraction r.
R2r(double, int, int) - 
Static method in class org.metaqtl.util.OffspringManager
This routine returns the recombination rate r for a given 
 value of the propertion of recombibant genotypes R according
 to the cross design.
r2R(double, int, int) - 
Static method in class org.metaqtl.util.OffspringManager
This routine returns the recombination rate r for a given 
 value of the propertion of recombibant genotypes R according
 to the cross design.
rate - 
Variable in class org.metaqtl.EMResult
The quadratric rate of convergence
 of the algorithm.
read(Reader) - 
Static method in class org.metaqtl.factory.DubiousLocusFactory
This routine reads the list of dubious markers from
 the given file location and returns if succeed an
 array of IBioLocus objects.
read(BufferedReader) - 
Static method in class org.metaqtl.factory.EMResultFactory
 
read(Reader) - 
Static method in class org.metaqtl.factory.MapDBFactory
This method reads a file formated as follows :
 
 map    property1  property2  property3 ...
read(Reader) - 
Static method in class org.metaqtl.factory.MetaDicoFactory
 
read(InputStream) - 
Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
 
read(Reader) - 
Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
 
read(Reader) - 
Static method in class org.metaqtl.factory.MetaQtlModelFactory
This method reads a file formated as follows :
 
 Chromosome \t Trait \t Model
read(Reader) - 
Static method in class org.metaqtl.factory.TreeFactory
 
read(String) - 
Static method in class org.metaqtl.factory.TreeFactory
 
read_newick(Reader) - 
Static method in class org.metaqtl.factory.TreeFactory
 
read_newick(String) - 
Static method in class org.metaqtl.factory.TreeFactory
 
rebuildPartition(String[]) - 
Method in class org.metaqtl.QtlPartition
 
recombination(double, int, int) - 
Static method in class org.metaqtl.util.MappingFunction
Returns the recombination rate from the distance.
removeAllele(String) - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
removeAllele(String) - 
Method in interface org.metaqtl.bio.IBioLocus
 
removeEntity(String) - 
Method in class org.metaqtl.bio.entity.BioEntityContainer
 
removeGroup(String) - 
Method in class org.metaqtl.bio.entity.GroupContainer
 
removeGroup(String) - 
Method in interface org.metaqtl.bio.IBioGenome
 
removeIndividual(String) - 
Method in class org.metaqtl.bio.entity.IndividualContainer
 
removeIndividual(String) - 
Method in interface org.metaqtl.bio.IBioPopulation
 
removeLocus(String) - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
removeLocus(String) - 
Method in interface org.metaqtl.bio.IBioLGroup
 
removeLocus(IBioGenome[], String) - 
Static method in class org.metaqtl.main.MetaMain
 
result - 
Variable in class org.metaqtl.algo.ClustAlgorithm
The result of the clustering.
resultByChrom - 
Variable in class org.metaqtl.MetaQtlAnalysis
The matrix of results where the rows are the chromosomes.
RF - 
Static variable in interface org.metaqtl.bio.IBioCrossTypes
 
RIGHT_LABEL - 
Static variable in class org.metaqtl.graph.ChromLayer
 
RIGHT_LABEL - 
Static variable in class org.metaqtl.graph.ChromShape
 
RILSe - 
Static variable in interface org.metaqtl.bio.IBioCrossTypes
 
RILSi - 
Static variable in interface org.metaqtl.bio.IBioCrossTypes
 
root - 
Variable in class org.metaqtl.bio.entity.bean.OntologyBean
The root of the ontology.
root - 
Variable in class org.metaqtl.Tree
The root of the tree.
rsd - 
Variable in class org.metaqtl.MetaChrom
The standardized residual between original marker intervals
 and those of the meta chromosome.
rsd - 
Variable in class org.metaqtl.MultiFitResult
The residual standard deviations.
rsquare - 
Variable in class org.metaqtl.Qtl.QTLStats
The r-square, i.e the proportion of variance 
 explained by the QTL.
rtsafe(NumericalUtilities.NRFunction, double, double, double) - 
Static method in class org.metaqtl.numrec.NumericalUtilities
 
run(Chromosome, Chromosome) - 
Static method in class org.metaqtl.algo.CMSAlgorithm
This methods find the common marker sequences between the 
 two given chromosomes.
run(double[], double[]) - 
Static method in class org.metaqtl.algo.HClustAlgorithm
This method performs a agglomerative clustering
 of the given data points where x is the 
 vector of observed values and sd the
 vector of their standard deviations.
run() - 
Method in class org.metaqtl.algo.MetaMapAlgorithm
This method builds a consensus genetic map from the given
 array of maps.
run() - 
Method in class org.metaqtl.algo.QtlClustAlgorithm
This method performs a QTL meta-analysis on each chromosome 
 of the given map.
run() - 
Method in class org.metaqtl.algo.QtlProjAlgorithm
This routine performs the projection of the QTL from the maps onto the 
 skeleton and returns the chromosomes on which the projection has been
 done.
run() - 
Method in class org.metaqtl.algo.QtlTreeAlgorithm
This method performs an agglomerative hierarchical QTL clustering 
 on each chromosome and returns the result as a MetaQtlAnalysis
 object.
run() - 
Method in interface org.metaqtl.IMetaAlgorithm
Run the algorithm.



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.ClustAlgorithm
This global variable defines the mode of compuation of
 the standard deviation of the QTL positions.
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.metaqtl.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.metaqtl.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.metaqtl.bio.entity.Ontology
Set the function of the ontology.
setGeneration(int) - 
Method in class org.metaqtl.bio.entity.Population
 
setGenome(IBioGenome) - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
setGenome(IBioGenome) - 
Method in interface org.metaqtl.bio.IBioLGroup
 
setGroup(IBioLGroup) - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
setGroup(IBioLGroup) - 
Method in class org.metaqtl.bio.entity.Locus
 
setGroup(IBioLGroup) - 
Method in interface org.metaqtl.bio.IBioLocus
 
setGroups(ArrayList) - 
Method in class org.metaqtl.bio.entity.bean.GeneticMapBean
 
setID(long) - 
Method in class org.metaqtl.bio.entity.OntologyTerm
Sets the indentifient of the term.
setIgnore(boolean) - 
Method in class org.metaqtl.Qtl
Set the status of the QTL.
setKeys(String[]) - 
Method in class org.metaqtl.bio.util.TabulatedWriter
 
setLabelSide(int) - 
Method in class org.metaqtl.graph.ChromLayer
 
setLabelSide(int) - 
Method in class org.metaqtl.graph.ChromShape
 
setLoci(IBioLocus[]) - 
Method in class org.metaqtl.bio.entity.LocusContainer
 
setLoci(IBioLocus[]) - 
Method in interface org.metaqtl.bio.IBioLGroup
 
setLocus(ArrayList) - 
Method in class org.metaqtl.bio.entity.bean.LGroupBean
 
setLocus(IBioLocus) - 
Method in interface org.metaqtl.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.metaqtl.bio.entity.bean.BioEntityBean
 
setName(String) - 
Method in class org.metaqtl.bio.entity.bean.PropertyBean
 
setName(String) - 
Method in class org.metaqtl.bio.entity.BioEntity
 
setName(String) - 
Method in class org.metaqtl.bio.entity.BioEntityCollection
 
setName(String) - 
Method in interface org.metaqtl.bio.IBioEntity
 
setParameter(String) - 
Static method in class org.metaqtl.main.MetaMain
 
setParentTerm(IBioOntologyTerm) - 
Method in class org.metaqtl.bio.entity.OntologyTerm
Sets the parent of the term.
setPedigree(IBioIndividualTree) - 
Method in class org.metaqtl.bio.entity.Individual
 
setPopulation(IBioPopulation) - 
Method in class org.metaqtl.bio.entity.Individual
 
setPopulation(IBioPopulation) - 
Method in interface org.metaqtl.bio.IBioIndividual
 
setPosition(ILGroupPosition) - 
Method in class org.metaqtl.bio.entity.AlleleContainer
 
setPosition(ILGroupPosition) - 
Method in class org.metaqtl.bio.entity.Locus
 
setPosition(double) - 
Method in class org.metaqtl.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.metaqtl.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.metaqtl.bio.IBioLocus
 
setPosition(double) - 
Method in interface org.metaqtl.bio.IBioLocus
 
setPosition(double, double) - 
Method in interface org.metaqtl.bio.IBioLocus
 
setProba(double[][]) - 
Method in class org.metaqtl.Chromosome
 
setProperties(ArrayList) - 
Method in class org.metaqtl.bio.entity.bean.BioEntityBean
 
setProperties(Properties) - 
Method in class org.metaqtl.bio.entity.BioEntity
 
setProperties(Properties) - 
Method in class org.metaqtl.bio.entity.BioEntityCollection
 
setProperties(Properties) - 
Method in interface org.metaqtl.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.metaqtl.bio.entity.Ontology
 
setRoot(OntologyTerm) - 
Method in class org.metaqtl.bio.entity.Ontology
 
setRoot(IBioOntologyTerm) - 
Method in interface org.metaqtl.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.metaqtl.bio.entity.Population
Set the population size.
setTerm(String, List) - 
Method in class org.metaqtl.MetaDico
 
setToken(String) - 
Method in class org.metaqtl.bio.util.TabulatedReader
 
setToken(String) - 
Method in class org.metaqtl.bio.util.TabulatedWriter
 
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.metaqtl.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.metaqtl.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.bio.entity.Population
 
size() - 
Method in class org.metaqtl.bio.util.TabulatedReader
Returns the number of keys, i.e the number of columns in the file.
size() - 
Method in class org.metaqtl.bio.util.TabulatedWriter
 
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.metaqtl.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.metaqtl.bio.util.ILGroupPosition
 
standardError() - 
Method in class org.metaqtl.bio.util.LGroupPosition
 
STATIC - 
Static variable in interface org.metaqtl.bio.util.ILGroupPosition
 
StaticLocusPosition - Class in org.metaqtl.bio.util
Class Description Here
StaticLocusPosition(double) - 
Constructor for class org.metaqtl.bio.util.StaticLocusPosition
 
stats - 
Variable in class org.metaqtl.Qtl
The QTL statistics
status - 
Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPath
 
status - 
Variable in class org.metaqtl.graph.ChromLayer.CMrkTickPoint
 
stderr - 
Variable in class org.metaqtl.bio.entity.bean.LocusBean
 
stderr - 
Variable in class org.metaqtl.bio.util.LGroupPosition
 
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.metaqtl.bio.IOntologyTermProperties
The synonyms property for a term in a ontology.



T

TabulatedReader - Class in org.metaqtl.bio.util
This class can be used to parse tabulated file in which the first line
 contains the label of the tabulated fields.
TabulatedReader(Reader) - 
Constructor for class org.metaqtl.bio.util.TabulatedReader
 
TabulatedReader(InputStream) - 
Constructor for class org.metaqtl.bio.util.TabulatedReader
 
TabulatedWriter - Class in org.metaqtl.bio.util
General comments must be added here.
TabulatedWriter(OutputStream) - 
Constructor for class org.metaqtl.bio.util.TabulatedWriter
 
TabulatedWriter(Writer) - 
Constructor for class org.metaqtl.bio.util.TabulatedWriter
 
TEXT_WIDTH - 
Static variable in class org.metaqtl.graph.QtlLayer
The default width of the Text attribute of the
 Qtl
tgidx - 
Variable in class org.metaqtl.MetaQtlData
The indices of the QTL in the trait
 groups.
tgnames - 
Variable in class org.metaqtl.MetaQtlData
The trait group names.
theta - 
Variable in class org.metaqtl.MultiFitResult
The parameter estimates.
TICK_CEX_HEIGHT - 
Static variable in class org.metaqtl.graph.QtlLayer
The default cex parameter for the tick height
 of the Qtl
TICK_CEX_WIDTH - 
Static variable in class org.metaqtl.graph.QtlLayer
The default cex parameter for the tick width
 of the Qtl
TINY_MAPPING_DISTANCE - 
Static variable in interface org.metaqtl.IMetaQtlConstants
The minimal distance in morgan
TINY_MAPPING_VARIANCE - 
Static variable in interface org.metaqtl.IMetaQtlConstants
the minimal variance in morgan
TINY_Z_PROBA - 
Static variable in class org.metaqtl.algo.EMAlgorithm
The minimal value for Z proba in EM-clustering
to - 
Variable in class org.metaqtl.graph.QtlUnit
 
to - 
Variable in class org.metaqtl.Qtl.QTLSupport
The position from the first marker 
 to the right border of the IC.
toChromosome(IBioLGroup, IBioCross, int, int) - 
Static method in class org.metaqtl.adapter.ChromosomeAdapter
This method converts a linkage group into a chromosome of type
 Chromosome with the given cross design
 and the given mapping context.
toChromosomes(IBioGenome) - 
Static method in class org.metaqtl.adapter.ChromosomeAdapter
This methods converts the given map
 into an array of Chromosome which represents
 the chromosomes of the input mpe.
toEntity(BioEntityBean, IBioEntity) - 
Static method in class org.metaqtl.bio.entity.adapter.BioEntityAdapter
 
toEntity(Object) - 
Method in class org.metaqtl.bio.entity.adapter.BioEntityCollectionAdapter
 
toEntity(Object) - 
Method in class org.metaqtl.bio.entity.adapter.GeneticMapBeanAdapter
 
toEntity(Object) - 
Method in class org.metaqtl.bio.entity.adapter.LGroupBeanAdapter
 
toEntity(Object) - 
Method in class org.metaqtl.bio.entity.adapter.LocusBeanAdapter
 
toEntity(Object) - 
Method in class org.metaqtl.bio.entity.adapter.OntologyBeanAdapter
 
toEntity(Object) - 
Method in class org.metaqtl.bio.entity.adapter.OntologyTermBeanAdapter
 
toEntity(Object) - 
Method in interface org.metaqtl.bio.IBioAdapter
Convert the given bio entity object into
 another compliant object.
toIBioGenome(Chromosome[], int) - 
Static method in class org.metaqtl.adapter.ChromosomeAdapter
This routine converts an array of chromosomes into a genetic map
 with as many chromosomes as the length of the array.
toIBioGenome(MetaMap) - 
Static method in class org.metaqtl.adapter.MetaMapAdapter
This methos convert a MetaMap object into
 an object which is consistent with the IBioGenome
 interface.
toQTL(IBioLocus) - 
Static method in class org.metaqtl.adapter.QtlAdapter
This method converts an object which class
 implements the IBioLocus interface
 into a Qtl.
toString() - 
Method in class org.metaqtl.bio.entity.LGroup
 
toString() - 
Method in class org.metaqtl.Chromosome
 
toString() - 
Method in class org.metaqtl.MultiFitResult
 
totd - 
Variable in class org.metaqtl.Chromosome
The total distance of the chromosome.
trait - 
Variable in class org.metaqtl.MetaQtlResult
The name of the trait.
trait - 
Variable in class org.metaqtl.Qtl
The QTL trait data.
traitNames - 
Variable in class org.metaqtl.MetaQtlModel
The trait names per chromosome.
transformY(double) - 
Method in class org.metaqtl.graph.ChromAxe
Do a affine transformation of the given
 position d which is assumed
 to be in [0,dmax] in order to have its
 representation in the chromosome axe.
tree - 
Variable in class org.metaqtl.MetaQtlResult
The qtl tree
tree - 
Variable in class org.metaqtl.QtlPartition
The Qtl tree.
Tree - Class in org.metaqtl
This class defines a tree.
Tree() - 
Constructor for class org.metaqtl.Tree
 
Tree(TreeNode) - 
Constructor for class org.metaqtl.Tree
 
tree_method - 
Variable in class org.metaqtl.algo.QtlTreeAlgorithm
This global variable defines the method used by the aglomerative
 hierarchical clustering.
TREE_NODE_WIDTH - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
TreeFactory - Class in org.metaqtl.factory
A factory to deal with distance trees.
TreeFactory() - 
Constructor for class org.metaqtl.factory.TreeFactory
 
TreeNode - Class in org.metaqtl
This class represents a node in a binary Tree obtained
 when applying usual hirarchical clustering methods.
TreeNode(int) - 
Constructor for class org.metaqtl.TreeNode
Creates a new instance of TreeNode
 with the given indice idx.
TreeNode(int, TreeNode[]) - 
Constructor for class org.metaqtl.TreeNode
Creates a new instance of  TreeNode with the
 given indice idx and the children of the node.
TreeNode() - 
Constructor for class org.metaqtl.TreeNode
Creates a new instance of TreeNode with
 default attribute values.
type - 
Variable in class org.metaqtl.bio.entity.bean.LocusBean
 
type - 
Static variable in class org.metaqtl.bio.util.BioCrossTypes
 
type - 
Variable in class org.metaqtl.Qtl.QTLCross
The type of the cross.
TypesString - 
Static variable in interface org.metaqtl.bio.IBioLocus
 
typeToString(int) - 
Static method in class org.metaqtl.bio.util.BioLocusTypes
 



U

unit - 
Variable in class org.metaqtl.Qtl.QTLTrait
The unit of the trait.
UNKNOWN - 
Static variable in interface org.metaqtl.bio.IBioCrossTypes
 
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
 
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.BioEntityFactory
 
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.MapChartFactory
TODO (non-Javadoc)
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapChartFactory
TODO (non-Javadoc)
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
 
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapMakerFactory
 
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.MapRawFactory
 
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapRawFactory
 
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.MapTabFactory
 
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.MapTabFactory
 
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
 
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.OntologyTabFactory
 
unload(IBioEntity, OutputStream) - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
unload(IBioEntity, Writer) - 
Method in class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
update(Reader) - 
Static method in class org.metaqtl.factory.MetaGraphParFactory
 
updateLeafIdx(int[]) - 
Method in class org.metaqtl.Tree
 
updateLoglikelihood(double[], double[], EMResult) - 
Static method in class org.metaqtl.algo.EMAlgorithm
Updates the loglikelihood value.
updateMappingContext(int, int) - 
Method in class org.metaqtl.Chromosome
Updates the mapping context of the chromosome.
updateMuVector(double[], double[], EMResult) - 
Static method in class org.metaqtl.algo.EMAlgorithm
Updates the vector of mixture components and returns the new
 values.
updatePiVector(EMResult) - 
Static method in class org.metaqtl.algo.EMAlgorithm
Updates the vector of mixture mixings and returns the new
 values.
updateZMatrix(double[], double[], EMResult) - 
Static method in class org.metaqtl.algo.EMAlgorithm
Updates the Z matrix.



V

value - 
Variable in class org.metaqtl.bio.entity.bean.PropertyBean
 
varianceDistance(double, double, int, int) - 
Static method in class org.metaqtl.util.MappingFunction
Returns the variance of the distance for a given recombination
 rate r, its variance and the mapping function.
verbose - 
Variable in class org.metaqtl.main.MetaMain
 
VERSION - 
Static variable in interface org.metaqtl.IMetaQtlConstants
The version of the package.
VERTICAL_MODE - 
Static variable in class org.metaqtl.QtlPartition
 
virtual - 
Variable in class org.metaqtl.bio.entity.bean.OntologyTermBean
The virual status of the term.



W

wantsValue() - 
Method in class org.metaqtl.main.CmdLineParser.Option
Tells whether or not this option wants a value
WARD_METHOD - 
Static variable in class org.metaqtl.algo.HClustAlgorithm
Ward method
WardMethod(double[], double[]) - 
Static method in class org.metaqtl.algo.HClustAlgorithm
This method performs a hierarchical clustering
 of the given data points using the Ward's method.
WIDTH - 
Static variable in class org.metaqtl.graph.GraphFactory
 
width - 
Variable in class org.metaqtl.graph.GraphShape
 
width - 
Variable in class org.metaqtl.graph.Layer
The width of the layer.
width - 
Variable in class org.metaqtl.graph.QtlUnit
 
WITH_CHROM_NAME - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
WITH_COMMON_MARKER - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
WITH_LEGEND - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
WITH_MAP_NAME - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
WITH_MARKER_NAME - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
WITH_MARKER_POSITION - 
Static variable in class org.metaqtl.graph.MetaGraphPar
 
WITH_QTL_NAME - 
Static variable in class org.metaqtl.graph.MetaGraphPar
Add the Qtl name.
workAmount - 
Variable in class org.metaqtl.algo.MetaAlgorithm
The amount of work to do.
workProgress - 
Variable in class org.metaqtl.algo.MetaAlgorithm
The amount of work done.
write(EMResult, OutputStream) - 
Static method in class org.metaqtl.factory.EMResultFactory
 
write(EMResult, PrintWriter) - 
Static method in class org.metaqtl.factory.EMResultFactory
 
write(OutputStream) - 
Static method in class org.metaqtl.factory.MetaGraphParFactory
 
write(Writer) - 
Static method in class org.metaqtl.factory.MetaGraphParFactory
 
write(MetaMap, OutputStream) - 
Static method in class org.metaqtl.factory.MetaMapSummaryFactory
This methods writes out the summary for a consensus genetic map into
 a given output stream stream.
write(MetaQtlAnalysis, OutputStream) - 
Static method in class org.metaqtl.factory.MetaQtlAnalysisFactory
This methods writes out in the given stream the results
 of a QTL meta-analysis.
write(MetaQtlAnalysis, OutputStream) - 
Static method in class org.metaqtl.factory.MetaQtlAnalysisModelFactory
 
write(MetaQtlAnalysis, Writer) - 
Static method in class org.metaqtl.factory.MetaQtlAnalysisModelFactory
 
write(MetaQtlAnalysis, OutputStream) - 
Static method in class org.metaqtl.factory.MetaQtlAnalysisSummaryFactory
This method writes out the summary for a givene QTL meta-analysis result
 analysis on the given output stream stream.
write(MetaQtlModel, OutputStream) - 
Static method in class org.metaqtl.factory.MetaQtlModelFactory
 
write(MetaQtlModel, Writer) - 
Static method in class org.metaqtl.factory.MetaQtlModelFactory
 
write(Tree, OutputStream) - 
Static method in class org.metaqtl.factory.TreeFactory
This method writes out the given tree nodes as an array of 
 TreeNode on the given output stream stream.
write(Tree, PrintWriter) - 
Static method in class org.metaqtl.factory.TreeFactory
This method writes out the given tree nodes as an array of 
 TreeNode using the given writer writer.
writeImg(ChromGraph[], File, String) - 
Static method in class org.metaqtl.main.MetaMain
 
writeMap(IBioGenome, String, String) - 
Static method in class org.metaqtl.main.MetaMain
 
writeMap(IBioGenome, String) - 
Static method in class org.metaqtl.main.MetaMain
 
writePar(File) - 
Static method in class org.metaqtl.main.MetaMain
 



X

x - 
Variable in class org.metaqtl.graph.AnchoredElement
 
x - 
Variable in class org.metaqtl.graph.GraphShape
 
x - 
Variable in class org.metaqtl.graph.QtlUnit
 
x - 
Variable in class org.metaqtl.MetaQtlResult
The QTL positions.
x - 
Variable in class org.metaqtl.TreeNode
 
xc - 
Variable in class org.metaqtl.TreeNode
 
Xml2A - Class in org.metaqtl.main
 
Xml2A() - 
Constructor for class org.metaqtl.main.Xml2A
 
XmlBioEntitiesFactory - Class in org.metaqtl.bio.entity.factory
Class Description Here
XmlBioEntitiesFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.XmlBioEntitiesFactory
 
XmlBioEntityFactory - Class in org.metaqtl.bio.entity.factory
Class Description Here
XmlBioEntityFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.XmlBioEntityFactory
 
XmlGeneticMapFactory - Class in org.metaqtl.bio.entity.factory
Class Description Here
XmlGeneticMapFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.XmlGeneticMapFactory
 
XmlOntologyFactory - Class in org.metaqtl.bio.entity.factory
 
XmlOntologyFactory() - 
Constructor for class org.metaqtl.bio.entity.factory.XmlOntologyFactory
 



Y

y - 
Variable in class org.metaqtl.graph.AnchoredElement
 
y - 
Variable in class org.metaqtl.graph.GraphShape
 
y - 
Variable in class org.metaqtl.TreeNode
 
y_from - 
Variable in class org.metaqtl.graph.QtlShape
 
y_pos - 
Variable in class org.metaqtl.graph.QtlShape
 



Z

z - 
Variable in class org.metaqtl.EMResult
The cluster membership probabilties.


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