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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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