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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
 

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