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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
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