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

G

G - Static variable in class util.FeatureExtractionExtension
 
gamma - Variable in class classifier.SVMOptions
for polynomial, rbf and sigmoid kernel function
GcContentClassificationFeature - Class in util.classificationFeatures.implementations.test
 
GcContentClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
GeneData - Class in util.parsers
 
GeneData() - Constructor for class util.parsers.GeneData
 
generateArffHeader(boolean, boolean, int) - Method in class util.io.ArffFileSupport
 
generateCompositionalTypes(int) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Recursively computes all possible n-nucleotides (with n being the length)
generateFeatureString(List<Double>, Classifier.DATA_TYPE) - Method in interface classifier.Classifier
Creates a string of features for only one featurevector
generateFeatureString(List<Double>, Classifier.DATA_TYPE) - Method in class classifier.WekaSVM
Creates a string of features for only one featurevector
generateFullSecStructCompositionalTypes(int) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Recursively computes all possible combinations of stems and loops of length n 3 possible characters : ( ) .
generateGeneralCompositionalTypes(int, char[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Generates all possible combinations, according to the provided alphabet and the required length of the combinations.
generateGeneralCompositionalTypes(int, String[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Generates all possible combinations, according to the provided alphabet and the required length of the combinations.
generateGreedyScripts(List<RangeOption>, boolean, String, boolean, boolean) - Static method in class var.experimenter.ScriptGenerator
 
generateNonGreedyScripts(List<RangeOption>, boolean, String, boolean, boolean) - Static method in class var.experimenter.ScriptGenerator
 
generateReducedCompositionalTypes(int) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Recusrively computes all possible n-nucleotides that are reduced to the set of purines and pyrimidines.
generateReducedSecStructCompositionalTypes(int) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Recursively computes all possible combinations of stems and loops of length n 2 possible characters : | .
GeneTestResult - Class in util.parsers
 
GeneTestResult() - Constructor for class util.parsers.GeneTestResult
 
GeneTrainingData - Class in util.parsers
 
GeneTrainingData() - Constructor for class util.parsers.GeneTrainingData
 
getAcceptorMap() - Method in class util.results.PotentialResultsMap
 
getAcceptorSites() - Method in class util.parsers.GeneData
 
getAccuracy() - Method in class util.results.CrossValidationResult
Returns the accuracy of the crossvalidation
getAccuracy2() - Method in class util.results.CrossValidationResult
Returns another accuracy measurement
getAllActions() - Method in class var.experimenter.RangePanel
 
getAppropiateChar(int[], char[]) - Method in class util.conversions.implementations.TEST_Conversion
 
getApproximate_correlation() - Method in class util.results.CrossValidationResult
Returns the approximate correlation
getAuc() - Method in class util.results.CrossValidationResult
Returns the area under the roc-curve (a measurement for the performance of a classifier).
getBasePairScore(String, int, char[], int) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Computes basepairscores for possible branchpoints
getBoundaries() - Method in class util.parsers.embl.Embl_CDS_Data
 
getBoundaries() - Method in class util.parsers.GeneData
 
getBPScore(char, char) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
getBPVal(char) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Returns the place wihtin the basepairbinding matrix for a nucleotide
getBPVal(char) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
Returns the place wihtin the basepairbinding matrix for a nucleotide
getBuildLogisticModels() - Method in class classifier.wekaSVM.SMO
Get the value of buildLogisticModels.
getC() - Method in class classifier.wekaSVM.SMO
Get the value of C.
getCapabilities() - Method in class classifier.wekaSVM.SMO
Returns default capabilities of the classifier.
getCaString() - Method in class startup.gui.SprClassificationActionPanel
 
getCds_data_list() - Method in class util.parsers.embl.EmblFileData
 
getCds_length() - Method in class util.parsers.embl.Embl_CDS_Data
 
getCdsLength() - Method in class util.parsers.GeneData
 
getCfList() - Method in class var.featureSelection.FeatureFileContent
 
getChecksTurnedOff() - Method in class classifier.wekaSVM.SMO
Returns whether the checks are turned off or not.
getClassification() - Method in class util.results.ClassificationResult
 
getClassification_name() - Method in class startup.ClassificationAction
 
getClassification_name() - Method in class var.featureSelection.FeatureFileContent
 
getClassificationAction() - Method in class startup.gui.SprClassificationActionPanel
 
getClassificationActions() - Method in class startup.FunSiPWorkflow
 
getClassificationFeatureDrawing() - Method in interface util.classificationFeatures.ClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
getClassificationFeatureDrawing() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
Because all classificationfeatures need different algorithms to draw them, according to the specifications, these utilities are also moved to the implementations of the ClassificationFeatures.
getClassificationFeatures() - Method in class startup.ClassificationAction
 
getClassifier_options() - Method in class startup.ClassificationAction
 
getClassifier_type() - Method in class startup.ClassificationAction
 
getCommand() - Method in class startup.ClassificationAction
 
getCommandName() - Method in class var.experimenter.RangeOption
 
getComment() - Method in class util.SpliceSite
 
getConfigString(String, String) - Static method in class startup.ParameterFileParser
This method creates a string that contains both a parameter and its value.
getConfigString(String, String[]) - Static method in class startup.ParameterFileParser
This method creates a string that contains both a parameter and its values.
getConfigurationFileString(FunSiPWorkflow) - Static method in class startup.ParameterFileParser
This method creates a single string that contains the entire configuration file.
getConfigurationFileString(ClassificationAction) - Static method in class startup.ParameterFileParser
This method creates the string that is associated with the given classification action.
getConversion() - Method in interface util.classificationFeatures.ClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversion() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
getConversion() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
This method asks the classificationfeature for its conversion-type.
getConversionList() - Method in class startup.ClassificationAction
 
getConversionStrings(String) - Method in class startup.ClassificationAction
This method takes one string as input and produces all the conversions of this string
getCoords(String) - Method in class test.ExtractData
 
getCorrelation_coefficient() - Method in class util.results.CrossValidationResult
Returns the correlation coefficient of the crossvalidation
getCount(String, char) - Method in class util.conversions.implementations.TEST_Conversion
 
getCrossvalidation_fold() - Method in class startup.ClassificationAction
 
getCrossValidationTabFile() - Method in class startup.ClassificationAction
 
getCurrentActionPanelIndex() - Method in class var.experimenter.RangePanel
 
getData(String) - Method in class test.Test
 
getDefinedBasePairs() - Method in class util.parsers.embl.EmblFileData
 
getDefinedBP() - Method in class util.parsers.GeneTrainingData
 
getDifferentCharacters() - Method in interface util.conversions.Conversion
This method returns all possible different characters that occur after the conversion of a sequence.
getDifferentCharacters() - Method in class util.conversions.implementations.DNA_AA_Conversion
This method returns all possible different characters that occur after the conversion of a sequence.
getDifferentCharacters() - Method in class util.conversions.implementations.DNA_MK_Conversion
 
getDifferentCharacters() - Method in class util.conversions.implementations.DNA_RY_Conversion
 
getDifferentCharacters() - Method in class util.conversions.implementations.DNA_SW_Conversion
 
getDifferentCharacters() - Method in class util.conversions.implementations.FibonacciSwitchConversion
This method returns all possible different characters that occur after the conversion of a sequence.
getDifferentCharacters() - Method in class util.conversions.implementations.Test_2_Conversion
This method returns all possible different characters that occur after the conversion of a sequence.
getDifferentCharacters() - Method in class util.conversions.implementations.TEST_Conversion
 
getDipoleMoment(char) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
getDistance() - Method in class util.results.ClassificationResult
 
getDistances() - Method in class classifier.wekaSVM.SMO
 
getDistances() - Method in class util.results.CrossValidationResult
 
getDonorMap() - Method in class util.results.PotentialResultsMap
 
getDonorSites() - Method in class util.parsers.GeneData
 
getDouble_arg_1() - Method in class var.experimenter.RangeOption
 
getDoubleValues() - Method in class var.experimenter.ChoosePanel
 
getDoubleValues() - Method in class var.experimenter.FixedOption
 
getDoubleValues() - Method in class var.experimenter.FixedRangeOption
 
getDoubleValues() - Method in class var.experimenter.ScriptOptionAbstractClass
 
getDoubleValues() - Method in interface var.experimenter.ScriptOptionInterface
 
getDoubleValues() - Method in class var.experimenter.VariableRangeExpOption
 
getDoubleValues() - Method in class var.experimenter.VariableRangeLinearOption
 
getDownScore(String, int, char, int) - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
getDownstream_range() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
getEnergies() - Method in class util.io.SecondaryStructureData
 
getEnergies() - Method in class util.secondaryStructure.SecondaryStructureData
 
getEpsilon() - Method in class classifier.wekaSVM.SMO
Get the value of epsilon.
getError_rate() - Method in class util.results.CrossValidationResult
Returns the error rate of the crossvalidation
getExtension(String) - Static method in class util.io.FileUtils
Returns the extension of a filename
getExtra_energies() - Method in class util.secondaryStructure.SecondaryStructureData
 
getExtra_structures() - Method in class util.secondaryStructure.SecondaryStructureData
 
getExtraInfo() - Method in class util.io.CrossValidationOutput
 
getExtraInfoLabel() - Method in class util.io.CrossValidationOutput
 
getF1_measure() - Method in class util.results.CrossValidationResult
Returns the F1-measure of the crossvalidation (f1-measure is the harmonic means of sensitivity and specificity)
getFalseNegatives() - Method in class util.results.CrossValidationResult
Returns the amount of false negatives of the crossvalidation
getFalsePositives() - Method in class util.results.CrossValidationResult
Returns the amount of false positives of the crossvalidation
getFeature_selection_input_file() - Method in class util.featureSelection.FeatureSelectionStub
 
getFeature_selection_output_file() - Method in class util.featureSelection.FeatureSelectionStub
 
getFeature_selection_purpose() - Method in class util.featureSelection.FeatureSelectionStub
 
getFeature_selection_type() - Method in class util.featureSelection.FeatureSelectionStub
 
getFeatures_output_file() - Method in class startup.ClassificationAction
 
getFeatureSelection() - Method in class startup.ClassificationAction
 
getFeaturesTrainingData(String, List<String>, SecondaryStructureData, Classifier, Classifier.DATA_TYPE) - Method in class startup.ClassificationAction
This method extracts the features from a trainingfile (positive/negative), and stores the extracted features into the feature_output_file.
getFileExtension() - Method in interface classifier.Classifier
 
getFileExtension() - Method in class classifier.WekaSVM
 
getFileName() - Method in class startup.FunSiPWorkflow
 
getFileName() - Method in class util.parsers.embl.EmblFileData
 
getFileName() - Method in class util.parsers.GeneTrainingData
 
getFileName() - Method in class util.RocCurveData
 
getFileName() - Method in class util.SVMUtil
 
getFileName() - Method in class var.featureSelection.FeatureFileContent
 
getFilterType() - Method in class classifier.wekaSVM.SMO
Gets how the training data will be transformed.
getFp5_measure() - Method in class util.results.CrossValidationResult
Returns the FP5% measure from the crossvalidation
getFp_rate() - Method in class util.results.CrossValidationResult
Returns the false positive rate of the crossvalidation
getFullTypes() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
getFullTypes() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
getFullTypes() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
getFullTypes() - Method in interface util.classificationFeatures.SeconderyStructureClassificationFeature
 
getGeneData() - Method in class util.parsers.GeneTrainingData
 
getHeatFormation(char) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
getIdentifier() - Method in class util.RocCurveData
 
getIdentifier() - Method in class var.experimenter.RangeOption
 
getIndex(WizardFramework.WIZARD_STATE[], WizardFramework.WIZARD_STATE) - Static method in enum startup.gui.WizardFramework.WIZARD_STATE
 
getIndex(char) - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
 
getInputMergeFiles() - Method in class startup.FunSiPWorkflow
 
getInstances() - Method in class util.SVMUtil
 
getInteger_arg_1() - Method in class var.experimenter.RangeOption
 
getInteger_arg_2() - Method in class var.experimenter.RangeOption
 
getIntegerValues() - Method in class var.experimenter.ChoosePanel
 
getIntValues() - Method in class var.experimenter.FixedOption
 
getIntValues() - Method in class var.experimenter.FixedRangeOption
 
getIntValues() - Method in class var.experimenter.ScriptOptionAbstractClass
 
getIntValues() - Method in interface var.experimenter.ScriptOptionInterface
 
getIntValues() - Method in class var.experimenter.VariableRangeExpOption
 
getIntValues() - Method in class var.experimenter.VariableRangeLinearOption
 
getKernel() - Method in class classifier.wekaSVM.SMO.BinarySMO
Returns the kernel to use
getKernel() - Method in class classifier.wekaSVM.SMO
Returns the kernel to use
getKeyName() - Method in class var.experimenter.RangeOption
 
getLabels() - Method in class util.results.CrossValidationResult
 
getLength() - Method in interface util.classificationFeatures.ClassificationFeature
This method returns the length of the feature.
getLength() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
This method returns the length of the feature.
getLength() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
This method returns the length of the feature.
getLength() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
getLength() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
getLinesInFile(File) - Static method in class util.io.FileUtils
Returns the number of lines (terminated by a carriage return) in the file
getLinesInFile(File) - Method in class util.io.IOUtils
Returns the number of lines (terminated by a carriage return) in the file
getLocation_in_forward() - Method in class util.DualLocationList
 
getLocation_in_local() - Method in class util.DualLocationList
 
getLocationDescription(int) - Method in interface util.classificationFeatures.ClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.RFClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
Returns a standardized description of the location that is indicated.
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
getLocationDescription(int) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
Returns a standardized description of the location that is indicated.
getLocations() - Method in class util.io.ModelDataParser.ModelData
 
getLogger() - Method in class main.FunSiP
 
getLoggingStyle() - Method in class startup.FunSiPWorkflow
 
getMax() - Method in class util.results.ExtractionResult
 
getMaximum(List<Integer>) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Selects and returns te maximum value of integers in a list.
getMaximum_crossvalidation() - Method in class startup.ClassificationAction
 
getMaximum_upstream() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
 
getMaximumSecondaryDownRange() - Method in class startup.ClassificationAction
This method returns the maximum downstreamrange of all ClassificationFeatures that implement secondary structure features.
getMaximumSecondaryUpRange() - Method in class startup.ClassificationAction
This method returns the maximum upstreamrange of all ClassificationFeatures that implement secondary structure features.
getMaxNumFeatures() - Method in class util.featureSelection.FeatureSelectionStub
 
getMeanSquaredError() - Method in class util.results.CrossValidationResult
Returns the mean squared error of the crossvalidation
getMinimum_upstream() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
 
getModel_file() - Method in class startup.ClassificationAction
 
getModelData(String) - Method in class util.io.ModelDataParser
 
getModelFile() - Method in interface classifier.Classifier
 
getModelFile() - Method in class classifier.WekaSVM
 
getModelLocation(String, String) - Method in class startup.gui.WizardFramework
 
getName() - Method in class startup.ClassificationAction
 
getName() - Method in interface util.conversions.Conversion
Returns the name of conversion.
getName() - Method in class util.conversions.implementations.DNA_AA_Conversion
Returns the name of conversion.
getName() - Method in class util.conversions.implementations.DNA_MK_Conversion
 
getName() - Method in class util.conversions.implementations.DNA_RY_Conversion
 
getName() - Method in class util.conversions.implementations.DNA_SW_Conversion
 
getName() - Method in class util.conversions.implementations.FibonacciSwitchConversion
Returns the name of conversion.
getName() - Method in class util.conversions.implementations.Test_2_Conversion
Returns the name of conversion.
getName() - Method in class util.conversions.implementations.TEST_Conversion
Returns the name of conversion.
getName() - Method in class util.FastaFileData
 
getName() - Method in class util.FileInfo
 
getName() - Method in class util.parsers.embl.Embl_CDS_Data
 
getName() - Method in class util.results.PotentialResultsMap
 
getName() - Method in class var.experimenter.ActionPanel
 
getName() - Method in class var.experimenter.RangeOption
 
getNegative_training_amount() - Method in class startup.ClassificationAction
 
getNegative_training_file() - Method in class startup.ClassificationAction
 
getNegative_training_file_secstruct() - Method in class startup.ClassificationAction
 
getNoRangeCLOptions() - Method in class var.experimenter.RangeOption
 
getNumberOfAttributes() - Method in interface util.classificationFeatures.ClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
getNumberOfAttributes() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
Returns the number of attributes that are created by this classificationfeature, according to the internal parameters (e.g. up- and downstreamranges).
getNumberOfDifferentCharacters() - Method in interface util.conversions.Conversion
This method returns the number of different characters present in the final representation after a conversion on a sequence has occured (excluding the 'N' character).
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.DNA_AA_Conversion
This method returns the number of different characters present in the final representation after a conversion on a sequence has occured (excluding the 'N' character).
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.DNA_MK_Conversion
 
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.DNA_RY_Conversion
 
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.DNA_SW_Conversion
 
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.FibonacciSwitchConversion
This method returns the number of different characters present in the final representation after a conversion on a sequence has occured (excluding the 'N' character).
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.Test_2_Conversion
This method returns the number of different characters present in the final representation after a conversion on a sequence has occured (excluding the 'N' character).
getNumberOfDifferentCharacters() - Method in class util.conversions.implementations.TEST_Conversion
 
getNumExons() - Method in class util.parsers.embl.Embl_CDS_Data
 
getNumExons() - Method in class util.parsers.GeneData
 
getNumFeaturesArffFile(String) - Method in class util.io.ArffFileSupport
 
getNumFolds() - Method in class classifier.wekaSVM.SMO
Get the value of numFolds.
getNumLines(File) - Method in class startup.cluster.ClusterClassificationAction
This method simply tries to return the number of lines in a file.
getOf() - Method in class startup.gui.SprOutputPanel
 
getOptimizer_step() - Method in class startup.FunSiPWorkflow
 
getOptimizerData() - Method in class startup.FunSiPWorkflow
 
getOptions() - Method in class classifier.wekaSVM.SMO
Gets the current settings of the classifier.
getOutput() - Method in class startup.gui.SprOutputPanel
 
getOutput_fixed_alpha() - Method in class startup.ClassificationAction
 
getOutput_fixed_beta() - Method in class startup.ClassificationAction
 
getOutputdirectory() - Method in class startup.ClassificationAction
 
getOutputFile() - Method in class startup.gui.SprOutputPanel
 
getOutputMergeFile() - Method in class startup.FunSiPWorkflow
 
getPanel() - Method in class var.experimenter.RangeOption
 
getParamName() - Method in interface util.conversions.Conversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.DNA_AA_Conversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.DNA_MK_Conversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.DNA_RY_Conversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.DNA_SW_Conversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.FibonacciSwitchConversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.Test_2_Conversion
Returns the parameter name of the conversion.
getParamName() - Method in class util.conversions.implementations.TEST_Conversion
Returns the parameter name of the conversion.
getPattern() - Method in class startup.ClassificationAction
 
getPattern_classification_location() - Method in class startup.ClassificationAction
 
getPattern_classification_output_f() - Method in class startup.ClassificationAction
 
getPattern_classification_output_r() - Method in class startup.ClassificationAction
 
getPosition() - Method in class util.featureSelection.ValPosCombination
 
getPositive_training_amount() - Method in class startup.ClassificationAction
 
getPositive_training_file() - Method in class startup.ClassificationAction
 
getPositive_training_file_secstruct() - Method in class startup.ClassificationAction
 
getPosNegExamplesInFile(File) - Method in interface classifier.Classifier
Returns the amount of positive and negative examples in a trainingfile.
getPosNegExamplesInFile(File) - Method in class classifier.WekaSVM
Returns the amount of positive and negative examples in a trainingfile.
getPosNegNumberInFile(File) - Method in class util.io.NtrFileSupport
 
getPossibleActions(String) - Method in class startup.gui.WizardFramework
 
getPossibleLocations(String, String, boolean) - Method in class util.gene.DNAUtil
 
getPossibleLocations2(String, String, boolean) - Method in class util.gene.DNAUtil
 
getPredictionOutputFiles() - Method in class startup.ClassificationAction
 
getPurpose() - Method in class util.io.ModelDataParser.ModelData
 
getRandomSeed() - Method in class classifier.wekaSVM.SMO
Get the value of randomSeed.
getRangeCLOptions() - Method in class var.experimenter.RangeOption
 
getRangeOptions() - Method in class var.experimenter.ActionPanel
 
getReader(String) - Method in class util.io.FileParser
Extracts the secondarystructure data from a file, according to the way it was written in the file by RNAfold.
getReducedTypes() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
getReducedTypes() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
getReducedTypes() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
getReducedTypes() - Method in interface util.classificationFeatures.SeconderyStructureClassificationFeature
 
getResult() - Method in class util.results.ExtractionResult
 
getResultingConfigurationFileName() - Method in class startup.gui.WizardFramework
 
getRoc_fp_rate() - Method in class util.results.CrossValidationResult
Returns the false positive rate for the roc curve
getRoc_tp_rate() - Method in class util.results.CrossValidationResult
Returns the true positive rate for the roc curve
getSelect_arg_1() - Method in class var.experimenter.RangeOption
 
getSelect_arg_2() - Method in class var.experimenter.RangeOption
 
getSensitivity() - Method in class util.results.CrossValidationResult
Returns the sensitivity of the crossvalidation
getSeqName() - Method in class util.results.ClassificationResult
 
getSequence(String) - Method in class test.ExtractData
 
getSequence() - Method in class util.FastaFileData
 
getSequence() - Method in class util.FileInfo
 
getSequence() - Method in class util.parsers.embl.EmblFileData
 
getSequence() - Method in class util.parsers.GeneTrainingData
 
getSequences() - Method in class util.secondaryStructure.SecondaryStructureData
 
getSigmoid_A() - Method in interface classifier.Classifier
 
getSigmoid_A() - Method in class classifier.WekaSVM
 
getSigmoid_B() - Method in interface classifier.Classifier
 
getSigmoid_B() - Method in class classifier.WekaSVM
 
getSmo() - Method in class util.SVMUtil
 
getSpecies() - Method in class util.io.ModelDataParser.ModelData
 
getSpecificity() - Method in class util.results.CrossValidationResult
Returns the specificity of the crossvalidation
getSplicesite() - Method in class util.results.ClassificationResult
 
getSplicesites() - Method in class util.FileInfo
 
getSplicesites() - Method in class util.parsers.embl.Embl_CDS_Data
 
getSplicesites() - Method in class util.parsers.GeneData
 
getSpliceVariant() - Method in class util.FileInfo
 
getSPRWorkflow(String) - Method in class main.FunSiPGui
This method tries to create a FunSiPWorkflow object (one of the basic building blocks of FunSiP) from a given configuration file.
getSquaredCorrelationCoefficient() - Method in class util.results.CrossValidationResult
Returns the squared correlation coefficient of the crossvalidation
getStandardClassifierFilter() - Method in class util.featureSelection.FeatureSelectionStub
 
getStart() - Method in class util.SpliceSite
 
getStartCodon() - Method in class util.parsers.embl.Embl_CDS_Data
 
getStartCodon() - Method in class util.parsers.GeneData
 
getStop() - Method in class util.SpliceSite
 
getStopCodon() - Method in class util.parsers.embl.Embl_CDS_Data
 
getStopCodon() - Method in class util.parsers.GeneData
 
getStrand() - Method in class startup.ClassificationAction
 
getStrand() - Method in class util.FileInfo
 
getString_arg_1() - Method in class var.experimenter.RangeOption
 
getStructures() - Method in class util.io.SecondaryStructureData
 
getStructures() - Method in class util.secondaryStructure.SecondaryStructureData
 
getSubmitNumber(File, File) - Method in class startup.cluster.ClusterClassificationAction
This method parses the submit-number from the outputfile.
getSVMOOutput(Instance) - Method in class classifier.wekaSVM.SMO
 
getSvmType() - Method in class util.SVMUtil
 
getTarget() - Method in class startup.features.FeatureRecognition
 
getTechnicalInformation() - Method in class classifier.wekaSVM.SMO
Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
getTestFile() - Method in class util.io.CrossValidationData
 
getTestfiles() - Method in class startup.ClassificationAction
 
getTestfiles_filetype() - Method in class startup.ClassificationAction
 
getThreading() - Method in class startup.FunSiPWorkflow
 
getToleranceParameter() - Method in class classifier.wekaSVM.SMO
Get the value of tolerance parameter.
getTotalNegatives() - Method in class util.results.CrossValidationResult
Returns the amount of total negatives
getTotalPositives() - Method in class util.results.CrossValidationResult
Returns the total amount of positives
getTraining_functional_site_position() - Method in class startup.ClassificationAction
 
getTrainingFile() - Method in class util.io.CrossValidationData
 
getTrainingFileInstances() - Method in interface classifier.Classifier
 
getTrainingFileInstances() - Method in class classifier.WekaSVM
Returns the the instances used for training the SMO.
getTrainingInstances() - Method in class classifier.wekaSVM.SMO
 
getTrueNegatives() - Method in class util.results.CrossValidationResult
Returns the amount of true negatives
getTruePositives() - Method in class util.results.CrossValidationResult
Returns the amount of true positives
getType() - Method in class var.experimenter.RangeOption
 
getUpDownRanges() - Method in interface util.classificationFeatures.ClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
getUpDownRanges() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
This method asks for the up- and downstreamranges of the feature
getUpScore(String, int, char, int) - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
getUpstream_range() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
getValue() - Method in class util.featureSelection.ValPosCombination
 
getValues() - Method in class var.experimenter.OverridePanel
 
getVpcList() - Method in class var.featureSelection.FeatureFileContent
 
getWriter() - Method in class startup.gui.SprOutputEditorWriter
 
globalInfo() - Method in class classifier.wekaSVM.SMO
Returns a string describing classifier

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