A B C D E F G H I K L M N O P Q R S T U V W X Y Z

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.thalia.bio.entity.IGeneticMapProperties

cartoFunctionHaldane - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties

cartoFunctionKey - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties

cartoFunctionKosambi - Static variable in interface org.thalia.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.TreeNode

Left and right children, or null

children - Variable in class org.thalia.bio.entity.bean.OntologyTermBean

The children of the term.

CHISQUARE - Static variable in interface org.metaqtl.IBioLGroupProperties

The key for the chisquare value.

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.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.

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.Option - Class in org.metaqtl.main

Representation of a command-line 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.UnknownOptionException - Exception in org.metaqtl.main

Thrown when the parsed command-line contains an option that is not recognised.

CmdLineParser.UnknownSuboptionException - Exception in org.metaqtl.main

Thrown when the parsed commandline contains multiple concatenated short options, such as -abcd, where one is unknown.

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.thalia.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.thalia.bio.util.BioEntityNameComparator

compare(Object, Object) - Method in class org.thalia.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

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.thalia.bio.entity

Class Description Here

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

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

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

crossToString(int, int) - Static method in class org.thalia.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.