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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.

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