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P

pairwiseCoupling(double[][], double[][]) - Method in class classifier.wekaSVM.SMO
Implements pairwise coupling.
ParameterFileParser - Class in startup
This class is used for loading an parsing the parameterfile for the FunSiP project.
ParameterFileParser(Logger) - Constructor for class startup.ParameterFileParser
Constructor for the Parameter file parser.
parseConversionFromString(String[]) - Static method in class util.conversions.ConversionUtils
This method constructs the actual conversion and translation objects.
parseConversionFromString2(String) - Static method in class util.conversions.ConversionUtils
This method constructs the actual conversion and translation objects.
parseConversionFromStringJar(String[]) - Static method in class util.conversions.ConversionUtils
 
parseConversionFromStringNonJar(String[]) - Static method in class util.conversions.ConversionUtils
This method constructs the actual conversion and translation objects.
parseDirectory(String) - Static method in class util.parsers.embl.EmblUtils
 
parseFeatureFromString(String[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
 
parseFeatureFromString(String) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
This method creates a ClassificationFeature from a string, by using the java-reflection to locate the correct ClassificationFeature implementation.
parseFeatureFromStringJar(String[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
 
parseFeatureFromStringNonJar(String[]) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
 
parseFile(String) - Method in class startup.ParameterFileParser
This method parses a configuration file and sets all the appropiate values to the parameters defined in the configuration file.
parseFile(File) - Static method in class util.parsers.embl.EmblUtils
 
parseFirstLine(ExtractTrainingData.AnnotationData, String) - Method in class util.parsers.fasta.ExtractTrainingData
 
parseHeader1(String) - Method in class util.parsers.ExtractTrainingData
 
parseHeader2(String) - Method in class util.parsers.ExtractTrainingData
 
parseHeader3(List<String>) - Method in class util.parsers.ExtractTrainingData
 
parseHeaderFasta(String) - Method in class util.parsers.fasta.PrintData
 
parseModelFile(String) - Method in class util.io.ModelDataParser
 
parseModelInformationFile(String) - Method in class util.io.ModelInformationParser
 
parseOptions(List<String[]>) - Static method in class var.experimenter.ConfigurationFileReader
 
parseSQ(String) - Method in class util.parsers.ExtractTrainingData
 
parseType(String) - Method in class util.parsers.ExtractTrainingData
 
PentaClassificationFeature - Class in util.classificationFeatures.implementations.test
 
PentaClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.PentaClassificationFeature
 
perform_crossvalidation(Classifier, File, List<RocCurveData>, CrossValidationOutput) - Method in class startup.ClassificationAction
This method performs the actual crossvalidation.
performAttributeEvaluation(boolean, AttributeEvaluator) - Method in interface classifier.Classifier
Performs feature selection by evaluating different attributes.
performAttributeEvaluation(boolean, AttributeEvaluator) - Method in class classifier.WekaSVM
Performs feature selection by evaluating different attributes.
performOptimalComplexityCrossvalidation(Classifier, File) - Method in class startup.ClassificationAction
This method performs the complexity crossvalidation operation.
PhysicalPropertiesClassificationFeature - Class in util.classificationFeatures.implementations.test
 
PhysicalPropertiesClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
 
PositionalClassificationFeature - Class in util.classificationFeatures.implementations
 
PositionalClassificationFeature() - Constructor for class util.classificationFeatures.implementations.PositionalClassificationFeature
 
PositionalClassificationFeatureDrawing - Class in util.classificationFeatures.implementations
This class is designed to draw the scores assigned to features generated by the positional classificationfeature type.
PositionalClassificationFeatureDrawing(PositionalClassificationFeature) - Constructor for class util.classificationFeatures.implementations.PositionalClassificationFeatureDrawing
 
PositionalGeneralClassificationFeature - Class in util.classificationFeatures.implementations
 
PositionalGeneralClassificationFeature() - Constructor for class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
 
PositionalSecondaryStructureClassificationFeature - Class in util.classificationFeatures.implementations.test
 
PositionalSecondaryStructureClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
 
PositionalSecondaryStructureClassificationFeatureDrawing - Class in util.classificationFeatures.implementations.test
 
PositionalSecondaryStructureClassificationFeatureDrawing(PositionalSecondaryStructureClassificationFeature) - Constructor for class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeatureDrawing
 
positiveFileAcceptor - Variable in class util.Options
 
positiveFileDonor - Variable in class util.Options
 
POSSIBLE_SOLUTIONS - Static variable in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
PotentialResultsMap - Class in util.results
 
PotentialResultsMap() - Constructor for class util.results.PotentialResultsMap
 
PotentialResultsMap(Map<Integer, Instances>, Map<Integer, Instances>, String) - Constructor for class util.results.PotentialResultsMap
 
prepareCrossvalidationCommand(int, String, String) - Method in interface classifier.Classifier
Creates an array with string values, to be parsed by the implementation of the classifier.
prepareCrossvalidationCommand(int, String, String) - Method in class classifier.WekaSVM
Creates an array with string values, to be parsed by the implementation of the classifier.
prepareTrainingCommand(String, String) - Method in interface classifier.Classifier
Creates an array with string values, to be parsed by the classifier.
prepareTrainingCommand(String, String) - Method in class classifier.WekaSVM
Creates an array with string values, to be parsed by the classifier.
previous(WizardFramework.WIZARD_STATE) - Static method in enum startup.gui.WizardFramework.WIZARD_STATE
 
PrintData - Class in util.parsers.fasta
 
PrintData(String) - Constructor for class util.parsers.fasta.PrintData
 
printFeatures(List<Double>) - Method in class startup.features.FeatureRecognition
 
printScores(List<Double>) - Method in class startup.features.FeatureRecognition
 
printTestResult() - Method in class util.parsers.GeneTestResult
 
produceSecStruc(String, int) - Method in class util.secondaryStructure.CreateSS
 
PURE_DNA - Static variable in class util.parsers.fasta.ExtractTrainingData
 

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