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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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