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

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.thalia.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.thalia.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.thalia.bio.entity.IGeneticMapProperties

distanceUnitKey - Static variable in interface org.thalia.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