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D

DATADIRECTORY - Static variable in class util.parsers.fasta.ExtractTrainingData
 
degree - Variable in class classifier.SVMOptions
Degree, only applicable for polynomial kernel functions
deleteTrainingFile() - Method in class startup.ClassificationAction
This method attempts to delete the file that contains all the features used for training the classifier.
Determinant(double[][]) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
DeterminantClassificationFeature - Class in util.classificationFeatures.implementations.test
 
DeterminantClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
DIRECTORY - Static variable in class util.parsers.ExtractTrainingData
 
distributionForInstance(Instance) - Method in class classifier.wekaSVM.SMO
Estimates class probabilities for given instance.
distributionForInstance2(Instance) - Method in class classifier.wekaSVM.SMO
Estimates class probabilities for given instance.
divide(List<ClassificationFeature>, List<ValPosCombination>) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
 
DNA_AA_Conversion - Class in util.conversions.implementations
 
DNA_AA_Conversion() - Constructor for class util.conversions.implementations.DNA_AA_Conversion
 
DNA_MK_Conversion - Class in util.conversions.implementations
 
DNA_MK_Conversion() - Constructor for class util.conversions.implementations.DNA_MK_Conversion
 
DNA_RY_Conversion - Class in util.conversions.implementations
 
DNA_RY_Conversion() - Constructor for class util.conversions.implementations.DNA_RY_Conversion
 
DNA_SW_Conversion - Class in util.conversions.implementations
 
DNA_SW_Conversion() - Constructor for class util.conversions.implementations.DNA_SW_Conversion
 
dnaToAmino(String) - Static method in class util.FeatureExtractionExtension
 
dnaToAmino(char[]) - Static method in class util.FeatureExtractionExtension
 
DNAUtil - Class in util.gene
 
DNAUtil() - Constructor for class util.gene.DNAUtil
 
doFeatureSelection() - Method in class util.featureSelection.FeatureSelectionStub
 
doubleSort(double[], double[]) - Static method in class util.Util
Bubblesort algorithm which sorts one list, and sorts (changing of indices) another list in exactly the same way.
draw(Graphics2D, List<Integer>) - Method in interface util.classificationFeatures.ClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(SVGGraphics2D, List<Double>, int, int) - Method in interface util.classificationFeatures.ClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeatureDrawing
 
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.RFClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.RFClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
draw(Graphics2D, List<Integer>) - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeatureDrawing
This method draws the
draw(SVGGraphics2D, List<Double>, int, int) - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeatureDrawing
This method draws the scores assigned to each feature, that is generated by this corresponding ClassificationFeature.
DUAL_INTEGER_OPTION - Static variable in class var.experimenter.ConfigurationFileReader
 
DUAL_SELECT_OPTION - Static variable in class var.experimenter.ConfigurationFileReader
 
DualLocationList - Class in util
 
DualLocationList() - Constructor for class util.DualLocationList
 

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