A B C D E F G H I K L M N O P R S T U V W

M

main - package main
 
main(String[]) - Static method in class classifier.wekaSVM.SMO
Main method for testing this class.
main(String[]) - Static method in class main.FunSiP
Main method for FunSiP.
main(String[]) - Static method in class main.FunSiPFeatures
Main method for FunSiP.
main(String[]) - Static method in class main.FunSiPGui
Main method for FunSiPGui.
main(String[]) - Static method in class main.FunSiPJar
Main method (indicated by the manifest file).
main(String[]) - Static method in class main.FunSiPResultGui
Launches the program
main(String[]) - Static method in class test.ExtractData
 
main(String[]) - Static method in class test.Test
 
main(String[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
 
main(String[]) - Static method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
main(String[]) - Static method in class util.conversions.implementations.FibonacciSwitchConversion
 
main(String[]) - Static method in class util.conversions.implementations.Test_2_Conversion
 
main(String[]) - Static method in class util.conversions.implementations.TEST_Conversion
 
main(String[]) - Static method in class util.FeatureExtractionExtension
 
main(String[]) - Static method in class util.featureSelection.CompareFS
 
main(String[]) - Static method in class util.featureSelection.FeatureSelectionSupport
 
main(String[]) - Static method in class util.io.FileUtils
 
main(String[]) - Static method in class util.parsers.embl.EmblUtils
 
main(String[]) - Static method in class util.parsers.ExtractTrainingData
 
main(String[]) - Static method in class util.parsers.fasta.ExtractTrainingData
 
main(String[]) - Static method in class util.parsers.fasta.PrintData
 
main(String[]) - Static method in class util.results.SigmoidFunction
 
main(String[]) - Static method in class util.secondaryStructure.SecondaryStructureExtraction
 
main(String[]) - Static method in class util.SMOSizeDataExtractor
 
main(String[]) - Static method in class util.SortingAlgorithms
 
main(String[]) - Static method in class util.SpliceFileInfo
 
main(String[]) - Static method in class util.wekaUtilities.Conversions
 
main(String[]) - Static method in class var.Experimenter
 
main(String[]) - Static method in class var.FSCompare
 
main(String[]) - Static method in class var.SimpleExperimenter
 
make_copy() - Method in class startup.ClassificationAction
This method makes a copy of the current classification action.
make_copy() - Method in interface util.classificationFeatures.ClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
make_copy() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
 
make_copy() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
Makes a copy of this particular classificationfeature.
make_copy() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
make_copy() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
Makes a copy of this particular classificationfeature.
makeButtonPanel() - Method in class var.experimenter.ChoosePanel
 
makeContentPanel() - Method in class var.experimenter.ChoosePanel
 
makeConversion(String) - Method in interface util.conversions.Conversion
This method performs the actual conversion from one string to another.
makeConversion(String) - Method in class util.conversions.implementations.DNA_AA_Conversion
This method performs the actual conversion from one string to another.
makeConversion(String) - Method in class util.conversions.implementations.DNA_MK_Conversion
 
makeConversion(String) - Method in class util.conversions.implementations.DNA_RY_Conversion
 
makeConversion(String) - Method in class util.conversions.implementations.DNA_SW_Conversion
 
makeConversion(String) - Method in class util.conversions.implementations.FibonacciSwitchConversion
This method performs the actual conversion from one string to another.
makeConversion(String) - Method in class util.conversions.implementations.Test_2_Conversion
This method performs the actual conversion from one string to another.
makeConversion(String) - Method in class util.conversions.implementations.TEST_Conversion
This method performs the actual conversion from one string to another.
makeConversion1(String) - Method in class util.conversions.implementations.TEST_Conversion
 
makeConversion2(String) - Method in class util.conversions.implementations.TEST_Conversion
 
makeCopy_DestroyOriginal(File) - Static method in class util.io.FileUtils
This method makes an identical copy of a file (new filename is old filename with _copy attached at the end), and then deletes the original.
makeCopyAndDestroyOriginal(File) - Method in class util.io.IOUtils
Makes a copy of the file (with a new name), and then destroys the original.
makesMatch(String, String) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
MAX_EXTRACT - Static variable in class util.parsers.fasta.ExtractTrainingData
 
mergeAndDeleteResults(File, File, File, File, String) - Static method in class util.io.FileUtils
This method merges the results from 4 different files, by sorting them on the number which is in the first column (it is assumed that the files are thus well-formatted).
mergeFeatureFiles(File, File) - Method in interface classifier.Classifier
Merges the featurefiles (one with positive training features, one with negative training features), in order to make the actual training file.
mergeFeatureFiles(File, File) - Method in class classifier.WekaSVM
Merges the featurefiles (one with positive training features, one with negative training features), in order to make the actual training file.
mergeFeatureFiles(boolean, File, File) - Method in class util.io.ArffFileSupport
 
mergeFiles(File, File[]) - Static method in class util.io.IOUtils
Merges a number of files, by which it is assumed that the lines are space-formatted, and contain space seperated fields.
mergeListFeatureVector(List<Integer>, int[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Adds all items from the featurevector (represented by an array) to the list with items.
mergeNtrData(File, File, boolean) - Method in class util.io.NtrFileSupport
 
mergeNtrData(File, File, File) - Method in class util.io.NtrFileSupport
 
mergeSortDual(double[], int[]) - Static method in class util.SortingAlgorithms
 
mergeUpDownInt(List<Integer>, List<Integer>) - Static method in class util.Util
Merges 2 lists of integer data to one list of string data.
MIN_TABS - Static variable in class startup.ParameterFileParser
 
ModelDataParser - Class in util.io
 
ModelDataParser() - Constructor for class util.io.ModelDataParser
 
ModelDataParser.ModelData - Class in util.io
 
ModelDataParser.ModelData(String, String, String) - Constructor for class util.io.ModelDataParser.ModelData
 
ModelInformationParser - Class in util.io
 
ModelInformationParser() - Constructor for class util.io.ModelInformationParser
 
mustBeUsed() - Method in class var.experimenter.RangeOption
 
mustExtractSecondaryStructures() - Method in class startup.ClassificationAction
This method determines whether or not the class should extract the secondary structures, according to the types of classificationfeatures

A B C D E F G H I K L M N O P R S T U V W