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

S

saveModel(SMO, String) - Method in class classifier.WekaSVM
This method saves the SMO java-object to a file in the filesystem.
ScriptGenerator - Class in var.experimenter
 
ScriptGenerator() - Constructor for class var.experimenter.ScriptGenerator
 
ScriptOptionAbstractClass - Class in var.experimenter
 
ScriptOptionAbstractClass() - Constructor for class var.experimenter.ScriptOptionAbstractClass
 
ScriptOptionInterface - Interface in var.experimenter
 
SecondaryStructureData - Class in util.io
 
SecondaryStructureData() - Constructor for class util.io.SecondaryStructureData
 
SecondaryStructureData - Class in util.secondaryStructure
 
SecondaryStructureData() - Constructor for class util.secondaryStructure.SecondaryStructureData
 
SecondaryStructureExtraction - Class in util.secondaryStructure
This method is primarily used for buiding the secondary structure of non-training files (although it can also be used for this purpose, there are better ways of doing this).
SecondaryStructureExtraction(Logger) - Constructor for class util.secondaryStructure.SecondaryStructureExtraction
Constructor of the secondary structure builder class
SeconderyStructureClassificationFeature - Interface in util.classificationFeatures
 
SecStructEvalClassificationFeature - Class in util.classificationFeatures.implementations.test
 
SecStructEvalClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
 
SecStructEvalClassificationFeatureDrawing - Class in util.classificationFeatures.implementations.test
 
SecStructEvalClassificationFeatureDrawing(SecStructEvalClassificationFeature) - Constructor for class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeatureDrawing
 
SecStructSimpleClassificationFeature - Class in util.classificationFeatures.implementations.test
 
SecStructSimpleClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
 
SecStructSimpleClassificationFeatureDrawing - Class in util.classificationFeatures.implementations.test
 
SecStructSimpleClassificationFeatureDrawing(SecStructSimpleClassificationFeature) - Constructor for class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeatureDrawing
 
seperateData(SortedSet<Integer>, SortedSet<Integer>, File, File, File, File) - Static method in class util.io.FileUtils
 
serialVersionUID - Static variable in class startup.gui.OptionsPanel
 
serialVersionUID - Static variable in class startup.gui.SprClassificationActionPanel
 
serialVersionUID - Static variable in class startup.gui.SprClassificationFeaturePanel
 
serialVersionUID - Static variable in class startup.gui.SprOutputEditorWriter
 
serialVersionUID - Static variable in class startup.gui.SprOutputPanel
 
serialVersionUID - Static variable in class startup.gui.SprSplashScreen
 
serialVersionUID - Static variable in class startup.gui.SprWorkflowPanel
 
serialVersionUID - Static variable in class startup.gui.WizardFramework
 
serialVersionUID - Static variable in exception util.classificationFeatures.FeatureExtractionException
 
serialVersionUID - Static variable in exception util.classificationFeatures.IncorrectClassificationFeatureException
 
serialVersionUID - Static variable in exception util.FeatureException
 
serialVersionUID - Static variable in class util.featureSelection.implementations.TestAttribEval
 
serialVersionUID - Static variable in class var.experimenter.ActionPanel
 
serialVersionUID - Static variable in class var.experimenter.ActionsPanel
 
serialVersionUID - Static variable in class var.experimenter.ChoosePanel
 
serialVersionUID - Static variable in class var.experimenter.FixedOption
 
serialVersionUID - Static variable in class var.experimenter.FixedRangeOption
 
serialVersionUID - Static variable in class var.experimenter.OverridePanel
 
serialVersionUID - Static variable in class var.experimenter.RangeOption
 
serialVersionUID - Static variable in class var.experimenter.RangePanel
 
serialVersionUID - Static variable in class var.experimenter.ScriptOptionAbstractClass
 
serialVersionUID - Static variable in class var.Experimenter
 
serialVersionUID - Static variable in class var.experimenter.VariableRangeExpOption
 
serialVersionUID - Static variable in class var.experimenter.VariableRangeLinearOption
 
setAcceptorMap(Map<Integer, Instances>) - Method in class util.results.PotentialResultsMap
 
setAcceptorSites(List<Integer>) - Method in class util.parsers.GeneData
 
setAccordingToCheck(boolean, JCheckBox, JPanel) - Method in class startup.gui.SprClassificationActionPanel
 
setAccordingToCheck(boolean, JCheckBox, JPanel) - Method in class startup.gui.SprWorkflowPanel
 
setAccuracy(double) - Method in class util.results.CrossValidationResult
 
setAccuracy2(double) - Method in class util.results.CrossValidationResult
 
setActions(List<ActionPanel>) - Method in class var.experimenter.RangePanel
 
setApproximate_correlation(double) - Method in class util.results.CrossValidationResult
 
setAuc(double) - Method in class util.results.CrossValidationResult
 
setBeUsed(boolean) - Method in class var.experimenter.RangeOption
 
setBoundaries(List<String>) - Method in class util.parsers.embl.Embl_CDS_Data
 
setBoundaries(List<String>) - Method in class util.parsers.GeneData
 
setBuildLogisticModels(boolean) - Method in class classifier.wekaSVM.SMO
Set the value of buildLogisticModels.
setButtons() - Method in class startup.gui.WizardFramework
 
setC(double) - Method in class classifier.wekaSVM.SMO
Set the value of C.
setCds_data_list(List<Embl_CDS_Data>) - Method in class util.parsers.embl.EmblFileData
 
setCds_length(int) - Method in class util.parsers.embl.Embl_CDS_Data
 
setCdsLength(int) - Method in class util.parsers.GeneData
 
setCfList(List<ClassificationFeature>) - Method in class var.featureSelection.FeatureFileContent
 
setChecksTurnedOff(boolean) - Method in class classifier.wekaSVM.SMO
Disables or enables the checks (which could be time-consuming).
setClassification(String) - Method in class util.results.ClassificationResult
 
setClassification_name(String) - Method in class startup.ClassificationAction
 
setClassification_name(String) - Method in class var.featureSelection.FeatureFileContent
 
setClassificationActions(List<ClassificationAction>) - Method in class startup.FunSiPWorkflow
 
setClassificationFeatures(List<ClassificationFeature>) - Method in class startup.ClassificationAction
 
setClassifier_options(String[]) - Method in class startup.ClassificationAction
 
setClassifier_type(ClassificationAction.CLASSIFIERS) - Method in class startup.ClassificationAction
 
setClassifier_type(String) - Method in class startup.ClassificationAction
 
setCommand(ClassificationAction.COMMAND) - Method in class startup.ClassificationAction
 
setCommand(String) - Method in class startup.ClassificationAction
 
setCommandLinePath(String) - Method in class util.secondaryStructure.CreateSS
 
setCommandName(String) - Method in class var.experimenter.RangeOption
 
setComment(String) - Method in class util.SpliceSite
 
setComplexityCrossvalidation(boolean) - Method in class startup.ClassificationAction
 
setConversionList(List<Conversion>) - Method in class startup.ClassificationAction
 
setCorrectCDSLength(boolean) - Method in class util.parsers.embl.Embl_CDS_Data
 
setCorrectFilePath(String) - Static method in class main.FunSiPJar
Changes the pathname when running from a jar-file (some indicators change for some weird reason).
setCorrectStartCodon(boolean) - Method in class util.parsers.embl.Embl_CDS_Data
 
setCorrectStopCodon(boolean) - Method in class util.parsers.embl.Embl_CDS_Data
 
setCorrectTest(boolean) - Method in class util.parsers.GeneTestResult
 
setCorrelation_coefficient(double) - Method in class util.results.CrossValidationResult
 
setCrossvalidation_fold(int) - Method in class startup.ClassificationAction
 
setCrossValidationTabFile(File) - Method in class startup.ClassificationAction
 
setDefinedBasePairs(int) - Method in class util.parsers.embl.EmblFileData
 
setDefinedBP(int) - Method in class util.parsers.GeneTrainingData
 
setDimensions(Dimension, Component) - Method in class startup.gui.WizardFramework
 
setDistance(double) - Method in class util.results.ClassificationResult
 
setDistances(double[]) - Method in class util.results.CrossValidationResult
Sets the distancesto the hyperplane for all training examples
setDonor(boolean) - Method in class util.results.ClassificationResult
 
setDonorMap(Map<Integer, Instances>) - Method in class util.results.PotentialResultsMap
 
setDonorSites(List<Integer>) - Method in class util.parsers.GeneData
 
setDouble_arg_1(double) - Method in class var.experimenter.RangeOption
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
setDownstream_range(int) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
setEnergies(List<Double>) - Method in class util.io.SecondaryStructureData
 
setEnergies(List<Double>) - Method in class util.secondaryStructure.SecondaryStructureData
 
setEpsilon(double) - Method in class classifier.wekaSVM.SMO
Set the value of epsilon.
setError_rate(double) - Method in class util.results.CrossValidationResult
 
setExplicitFiles(File[]) - Method in class startup.FunSiPWorkflow
This method is used when additional fastafiles that need to be evaluated are provided on the commandline by the user.
setExtended_structure(boolean) - Method in class util.secondaryStructure.SecondaryStructureData
 
setExtra_energies(List<Double>) - Method in class util.secondaryStructure.SecondaryStructureData
 
setExtra_structures(List<String>) - Method in class util.secondaryStructure.SecondaryStructureData
 
setExtraInfo(List<String>) - Method in class util.io.CrossValidationOutput
 
setExtraInfoLabel(String) - Method in class util.io.CrossValidationOutput
 
setF1_measure(double) - Method in class util.results.CrossValidationResult
 
setFalseNegatives(int) - Method in class util.results.CrossValidationResult
Sets the amount of false negatives of the crossvalidation
setFalsePositives(int) - Method in class util.results.CrossValidationResult
Sets the amount of false positives
setFeature_selection_input_file(String) - Method in class util.featureSelection.FeatureSelectionStub
 
setFeature_selection_output_file(String) - Method in class util.featureSelection.FeatureSelectionStub
 
setFeature_selection_purpose(FeatureSelectionStub.FEATURE_SELECTION_PURPOSE) - Method in class util.featureSelection.FeatureSelectionStub
 
setFeature_selection_purpose(String) - Method in class util.featureSelection.FeatureSelectionStub
 
setFeature_selection_type(FeatureSelectionStub.FEATURE_SELECTION_TYPE) - Method in class util.featureSelection.FeatureSelectionStub
 
setFeature_selection_type(String) - Method in class util.featureSelection.FeatureSelectionStub
 
setFeatures_output_file(String) - Method in class startup.ClassificationAction
 
setFeatureSelection(FeatureSelectionStub) - Method in class startup.ClassificationAction
 
setFileEnabled(boolean) - Method in class startup.gui.SprOutputPanel
 
setFileName(String) - Method in class startup.FunSiPWorkflow
 
setFileName(String) - Method in class util.parsers.embl.EmblFileData
 
setFileName(String) - Method in class util.parsers.GeneTrainingData
 
setFileName(String) - Method in class util.RocCurveData
 
setFileName(String) - Method in class util.SVMUtil
 
setFileName(String) - Method in class var.featureSelection.FeatureFileContent
 
setFilter(List<Integer>) - Method in class util.featureSelection.FeatureSelectionStub
 
setFilterType(SelectedTag) - Method in class classifier.wekaSVM.SMO
Sets how the training data will be transformed.
setForwardStrand(boolean) - Method in class util.parsers.GeneData
 
setFp5_measure(double) - Method in class util.results.CrossValidationResult
 
setFp_rate(double) - Method in class util.results.CrossValidationResult
 
setFullTypes(String[]) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
setFullTypes(String[]) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
setFullTypes(String[]) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
setFullTypes(String[]) - Method in interface util.classificationFeatures.SeconderyStructureClassificationFeature
 
setGeneData(List<GeneData>) - Method in class util.parsers.GeneTrainingData
 
setIdentifier(int) - Method in class util.RocCurveData
 
setIdentifier(int) - Method in class var.experimenter.RangeOption
 
setInputMergeFiles(List<List<String>>) - Method in class startup.FunSiPWorkflow
 
setInstances(Instances) - Method in class util.SVMUtil
 
setInteger_arg_1(int) - Method in class var.experimenter.RangeOption
 
setInteger_arg_2(int) - Method in class var.experimenter.RangeOption
 
setKernel(Kernel) - Method in class classifier.wekaSVM.SMO.BinarySMO
sets the kernel to use
setKernel(Kernel) - Method in class classifier.wekaSVM.SMO
sets the kernel to use
setKeyName(String) - Method in class var.experimenter.RangeOption
 
setLabels(double[]) - Method in class util.results.CrossValidationResult
Sets the labels (1/-1 for positive/negative) for all the training examples.
setLength(int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
setLength(int) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
setLocation_in_forward(List<Integer>) - Method in class util.DualLocationList
 
setLocation_in_local(List<Integer>) - Method in class util.DualLocationList
 
setLocations(String) - Method in class util.io.ModelDataParser.ModelData
 
setMainPanel() - Method in class startup.gui.WizardFramework
 
setMax(int) - Method in class util.results.ExtractionResult
 
setMaximum_crossvalidation(int) - Method in class startup.ClassificationAction
 
setMaxNumFeatures(int) - Method in class util.featureSelection.FeatureSelectionStub
 
setMeanSquaredError(double) - Method in class util.results.CrossValidationResult
 
setMergeResults(boolean) - Method in class startup.FunSiPWorkflow
 
setModel_file(String) - Method in class startup.ClassificationAction
 
setModelFile(String) - Method in interface classifier.Classifier
Changes the model for the classifier by changing the name of the modelfile.
setModelFile(String) - Method in class classifier.WekaSVM
Changes the model for the classifier by changing the name of the modelfile.
setName(String) - Method in class startup.ClassificationAction
 
setName(String) - Method in class util.FastaFileData
 
setName(String) - Method in class util.FileInfo
 
setName(String) - Method in class util.parsers.embl.Embl_CDS_Data
 
setName(String) - Method in class util.results.PotentialResultsMap
 
setName(String) - Method in class var.experimenter.ActionPanel
 
setName(String) - Method in class var.experimenter.RangeOption
 
setNegative_training_amount(int) - Method in class startup.ClassificationAction
 
setNegative_training_file(String) - Method in class startup.ClassificationAction
 
setNegative_training_file_secstruct(String) - Method in class startup.ClassificationAction
 
setNewConfiguration(String) - Method in class main.FunSiPGui
Sets a new configuration file as standard loaded configuration file.
setNumExons(int) - Method in class util.parsers.embl.Embl_CDS_Data
 
setNumExons(int) - Method in class util.parsers.GeneData
 
setNumFolds(int) - Method in class classifier.wekaSVM.SMO
Set the value of numFolds.
setOf(SprOutputPanel.OUTPUT_FILTER) - Method in class startup.gui.SprOutputPanel
 
setOptimizer(boolean) - Method in class startup.FunSiPWorkflow
 
setOptimizer_steps(int, int, int) - Method in class startup.FunSiPWorkflow
 
setOptions(ClassifierOptions) - Method in interface classifier.Classifier
Changes the various options of this classifier.
setOptions(ClassifierOptions) - Method in class classifier.WekaSVM
Changes the various options of this classifier.
setOptions(String[]) - Method in class classifier.wekaSVM.SMO
Parses a given list of options.
setOptions() - Method in class startup.gui.OptionsPanel
 
setOptions(String[]) - Method in interface util.conversions.Conversion
This method sets the possible options for this conversion.
setOptions(String[]) - Method in class util.conversions.implementations.DNA_AA_Conversion
This method sets the possible options for this conversion.
setOptions(String[]) - Method in class util.conversions.implementations.DNA_MK_Conversion
 
setOptions(String[]) - Method in class util.conversions.implementations.DNA_RY_Conversion
 
setOptions(String[]) - Method in class util.conversions.implementations.DNA_SW_Conversion
 
setOptions(String[]) - Method in class util.conversions.implementations.FibonacciSwitchConversion
This method sets the possible options for this conversion.
setOptions(String[]) - Method in class util.conversions.implementations.Test_2_Conversion
This method sets the possible options for this conversion.
setOptions(String[]) - Method in class util.conversions.implementations.TEST_Conversion
 
setOutput(SprOutputPanel.OUTPUT) - Method in class startup.gui.SprOutputPanel
 
setOutput_fixed_alpha(Double) - Method in class startup.ClassificationAction
 
setOutput_fixed_beta(Double) - Method in class startup.ClassificationAction
 
setOutputdirectory(String) - Method in class startup.ClassificationAction
 
setOutputMergeFile(List<String>) - Method in class startup.FunSiPWorkflow
 
setParameters(String[]) - Method in interface classifier.ClassifierOptions
Sets classifier parameters by parsing them from an array of strings.
setParameters(String[]) - Method in class classifier.SVMOptions
Sets classifier parameters by parsing them from an array of strings.
setParameters(String[]) - Method in interface util.classificationFeatures.ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.RFClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
setParameters(String[]) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setPattern(String) - Method in class startup.ClassificationAction
 
setPattern_classification_location(int) - Method in class startup.ClassificationAction
 
setPattern_classification_output_f(int) - Method in class startup.ClassificationAction
 
setPattern_classification_output_r(int) - Method in class startup.ClassificationAction
 
setPattern_regexp(boolean) - Method in class startup.ClassificationAction
 
setPosition(int) - Method in class util.featureSelection.ValPosCombination
 
setPositive_training_amount(int) - Method in class startup.ClassificationAction
 
setPositive_training_file(String) - Method in class startup.ClassificationAction
 
setPositive_training_file_secstruct(String) - Method in class startup.ClassificationAction
 
setPredictionOutputFiles(String[]) - Method in class startup.ClassificationAction
 
setPurpose(String) - Method in class util.io.ModelDataParser.ModelData
 
setRandomSeed(int) - Method in class classifier.wekaSVM.SMO
Set the value of randomSeed.
setRangeOptions(List<RangeOption>) - Method in class var.experimenter.ActionPanel
 
setReducedTypes(String[]) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
setReducedTypes(String[]) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
setReducedTypes(String[]) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
setReducedTypes(String[]) - Method in interface util.classificationFeatures.SeconderyStructureClassificationFeature
 
setResult(Map<String, Integer>) - Method in class util.results.ExtractionResult
 
setReverse(boolean) - Method in class util.parsers.embl.Embl_CDS_Data
 
setRoc_fp_rate(double[]) - Method in class util.results.CrossValidationResult
 
setRoc_tp_rate(double[]) - Method in class util.results.CrossValidationResult
 
setRuntimeFunSiP(FunSiPGui) - Method in class startup.gui.SprOutputEditorWriter
 
setSelect_arg_1(List<String>) - Method in class var.experimenter.RangeOption
 
setSelect_arg_2(List<String>) - Method in class var.experimenter.RangeOption
 
setSensitivity(double) - Method in class util.results.CrossValidationResult
 
setSeqName(String) - Method in class util.results.ClassificationResult
 
setSequence(String) - Method in class util.FastaFileData
 
setSequence(String) - Method in class util.FileInfo
 
setSequence(String) - Method in class util.parsers.embl.EmblFileData
 
setSequence(String) - Method in class util.parsers.GeneTrainingData
 
setSequences(List<String>) - Method in class util.secondaryStructure.SecondaryStructureData
 
setSigmoid_A(double) - Method in interface classifier.Classifier
Changes the sigmoid variable A (see documentation about restructuring the output by use of sigmoid curves)
setSigmoid_A(double) - Method in class classifier.WekaSVM
Changes the sigmoid variable A (see documentation about restructuring the output by use of sigmoid curves)
setSigmoid_B(double) - Method in interface classifier.Classifier
Changes the sigmoid variable B (see documentation about restructuring the output by use of sigmoid curves)
setSigmoid_B(double) - Method in class classifier.WekaSVM
Changes the sigmoid variable B (see documentation about restructuring the output by use of sigmoid curves)
setSmo(SMO) - Method in class util.SVMUtil
 
setSpecies(String) - Method in class util.io.ModelDataParser.ModelData
 
setSpecificity(double) - Method in class util.results.CrossValidationResult
 
setSplicesite(int) - Method in class util.results.ClassificationResult
 
setSplicesites(List<SpliceSite>) - Method in class util.FileInfo
 
setSplicesites(List<Integer>) - Method in class util.parsers.embl.Embl_CDS_Data
 
setSplicesites(List<Integer>) - Method in class util.parsers.GeneData
 
setSpliceVariant(String) - Method in class util.FileInfo
 
setSprOutput(FunSiP, SprOutputPanel) - Method in class main.FunSiPGui
Changes the output of the supplied FunSiP program, according to the content of the output panel.
setSquaredCorrelationCoefficient(double) - Method in class util.results.CrossValidationResult
 
setStart(Integer) - Method in class util.SpliceSite
 
setStartCodon(String) - Method in class util.parsers.embl.Embl_CDS_Data
 
setStartCodon(String) - Method in class util.parsers.GeneData
 
setStop(Integer) - Method in class util.SpliceSite
 
setStopCodon(String) - Method in class util.parsers.embl.Embl_CDS_Data
 
setStopCodon(String) - Method in class util.parsers.GeneData
 
setStrand(ClassificationAction.STRAND) - Method in class startup.ClassificationAction
 
setStrand(String) - Method in class startup.ClassificationAction
 
setStrand(char) - Method in class util.FileInfo
 
setString_arg_1(String) - Method in class var.experimenter.RangeOption
 
setStructures(List<String>) - Method in class util.io.SecondaryStructureData
 
setStructures(List<String>) - Method in class util.secondaryStructure.SecondaryStructureData
 
setSvmType(ClassificationAction.CLASSIFIERS) - Method in class util.SVMUtil
 
setTarget(FeatureRecognition.TARGET) - Method in class startup.features.FeatureRecognition
 
setTestFile(File) - Method in class util.io.CrossValidationData
 
setTestfiles(String[]) - Method in class startup.ClassificationAction
 
setTestfiles_filetype(ClassificationAction.FILE_TYPE) - Method in class startup.ClassificationAction
 
setTestfiles_filetype(String) - Method in class startup.ClassificationAction
 
setThreading(String) - Method in class startup.FunSiPWorkflow
 
setToleranceParameter(double) - Method in class classifier.wekaSVM.SMO
Set the value of tolerance parameter.
setTotalNegatives(int) - Method in class util.results.CrossValidationResult
Sets the total amount of negatives
setTotalPositives(int) - Method in class util.results.CrossValidationResult
Sets the total amount of positives
setTraining_functional_site_position(int) - Method in class startup.ClassificationAction
 
setTrainingFile(File) - Method in class util.io.CrossValidationData
 
setTrueNegatives(int) - Method in class util.results.CrossValidationResult
Sets the amount of true negatives
setTruePositives(int) - Method in class util.results.CrossValidationResult
Sets the amount of true positives
setType(RangeOption.TYPE) - Method in class var.experimenter.RangeOption
 
setUpDownRanges(int, int) - Method in interface util.classificationFeatures.ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.RFClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
setUpDownRanges(int, int) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
This method sets the new upstream and downstream ranges
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
setUpstream_range(int) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
setValue(double) - Method in class util.featureSelection.ValPosCombination
 
setVisible(boolean) - Method in class var.experimenter.RangeOption
 
setVpcList(List<ValPosCombination>) - Method in class var.featureSelection.FeatureFileContent
 
SigmoidFunction - Class in util.results
Class that computes the alfa and beta values for a sigmoid function.
SigmoidFunction() - Constructor for class util.results.SigmoidFunction
 
SimpleExperimenter - Class in var
 
SimpleExperimenter(String[]) - Constructor for class var.SimpleExperimenter
 
SINGLE_DOUBLE_OPTION - Static variable in class var.experimenter.ConfigurationFileReader
 
SINGLE_INTEGER_OPTION - Static variable in class var.experimenter.ConfigurationFileReader
 
SINGLE_SELECT_OPTION - Static variable in class var.experimenter.ConfigurationFileReader
 
SINGLE_STRING_OPTION - Static variable in class var.experimenter.ConfigurationFileReader
 
SLEEP_TIME - Static variable in class startup.cluster.ClusterClassificationAction
The time a node waits between anouncing its finish (milliseconds).
SMO - Class in classifier.wekaSVM
Implements John Platt's sequential minimal optimization algorithm for training a support vector classifier.
SMO() - Constructor for class classifier.wekaSVM.SMO
 
SMO.BinarySMO - Class in classifier.wekaSVM
Class for building a binary support vector machine.
SMO.BinarySMO() - Constructor for class classifier.wekaSVM.SMO.BinarySMO
 
SMOSizeDataExtractor - Class in util
 
SMOSizeDataExtractor(String, String, int, int, boolean) - Constructor for class util.SMOSizeDataExtractor
 
sort(int[], char[]) - Method in class util.conversions.implementations.TEST_Conversion
 
SortingAlgorithms - Class in util
 
SortingAlgorithms() - Constructor for class util.SortingAlgorithms
 
sortScores(List<FunSiPWorkflow.OptimizationScore>) - Method in class startup.FunSiPWorkflow
Dummy bubblesort algorithm (normally list only consists of 2-10 items) for the OptimizationScore type.
sparseIndices() - Method in class classifier.wekaSVM.SMO
Returns the indices in sparse format.
sparseWeights() - Method in class classifier.wekaSVM.SMO
Returns the weights in sparse format.
SPLASH_SCREEN_IMAGE - Static variable in class startup.gui.SprSplashScreen
 
SpliceFileInfo - Class in util
 
SpliceFileInfo(int) - Constructor for class util.SpliceFileInfo
 
SPLICESITE - Static variable in class util.parsers.ExtractTrainingData
 
SpliceSite - Class in util
 
SpliceSite() - Constructor for class util.SpliceSite
 
splitFiles() - Method in class util.SpliceFileInfo
 
splitFiles2() - Method in class util.SpliceFileInfo
 
SprClassificationActionPanel - Class in startup.gui
 
SprClassificationActionPanel(ClassificationAction) - Constructor for class startup.gui.SprClassificationActionPanel
 
SprClassificationFeaturePanel - Class in startup.gui
 
SprClassificationFeaturePanel(ClassificationAction, Dimension) - Constructor for class startup.gui.SprClassificationFeaturePanel
 
SprOutputEditorWriter - Class in startup.gui
 
SprOutputEditorWriter() - Constructor for class startup.gui.SprOutputEditorWriter
 
SprOutputPanel - Class in startup.gui
 
SprOutputPanel() - Constructor for class startup.gui.SprOutputPanel
 
SprOutputPanel.OUTPUT - Enum in startup.gui
 
SprOutputPanel.OUTPUT_FILTER - Enum in startup.gui
 
SprSplashScreen - Class in startup.gui
 
SprSplashScreen() - Constructor for class startup.gui.SprSplashScreen
 
SprWorkflowPanel - Class in startup.gui
 
SprWorkflowPanel(FunSiPWorkflow) - Constructor for class startup.gui.SprWorkflowPanel
 
start_classification() - Method in class startup.ClassificationAction
This method starts the actual dataflow within the classification action.
startup - package startup
 
startup.cluster - package startup.cluster
 
startup.features - package startup.features
 
startup.gui - package startup.gui
 
svm_complexity - Variable in class util.Options
 
SVMOptions - Class in classifier
Class defining various classifier options that are specific to Support vector machines.
SVMOptions() - Constructor for class classifier.SVMOptions
 
SVMOptions.KERNEL_TYPE - Enum in classifier
The different kernel functions.
SVMOutput(int, Instance) - Method in class classifier.wekaSVM.SMO.BinarySMO
Computes SVM output for given instance.
SVMUtil - Class in util
 
SVMUtil() - Constructor for class util.SVMUtil
 
SVMUtil(SMO, Instances) - Constructor for class util.SVMUtil
 

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