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E

em(JTextField) - Method in class startup.gui.SprWorkflowPanel
 
Embl_CDS_Data - Class in util.parsers.embl
 
Embl_CDS_Data() - Constructor for class util.parsers.embl.Embl_CDS_Data
 
EmblFileData - Class in util.parsers.embl
 
EmblFileData() - Constructor for class util.parsers.embl.EmblFileData
 
EmblUtils - Class in util.parsers.embl
 
EmblUtils() - Constructor for class util.parsers.embl.EmblUtils
 
epsilonTipText() - Method in class classifier.wekaSVM.SMO
Returns the tip text for this property
ERROR_STRING - Static variable in interface util.classificationFeatures.ClassificationFeature
 
evals - Variable in class util.featureSelection.implementations.TestAttribEval
 
evaluate_model(Classifier) - Method in class startup.ClassificationAction
Evaluate the content of sequence files with the supplied classifier (and accompagnied classification model).
evaluateAttribute(int) - Method in class util.featureSelection.implementations.TestAttribEval
 
exclude(JCheckBox, JPanel) - Method in class startup.gui.SprClassificationActionPanel
 
Experimenter - Class in var
 
Experimenter(String[]) - Constructor for class var.Experimenter
 
explanation - Variable in class util.classificationFeatures.AttributeDescription
 
explanation(int, List<List<ValPosCombination>>, List<ClassificationFeature>) - Method in class var.FSCompare
Generates an explanation for the located feature.
extractAndClassify(String, Classifier, List<Integer>, List<Integer>, String, String, int, int) - Method in class startup.ClassificationAction
This method extracts features around functional sites in a sequence, and then uses the provided classifier to classify that particular functional site.
extractAndEvaluateData(File, Classifier, int) - Method in class startup.ClassificationAction
Evaluate the content of a specific file with the supplied classification model.
extractAndWriteNonRandom(File, File, int, boolean) - Method in class util.SMOSizeDataExtractor
 
extractAndWriteRandom(File, File, int, boolean) - Method in class util.SMOSizeDataExtractor
 
extractContent(File) - Method in class var.FSCompare
This method extracts the content of a featurefile, parses it and then goes on to store it all in one object.
ExtractData - Class in test
 
ExtractData(String[]) - Constructor for class test.ExtractData
 
extractData(String, List<Integer>) - Method in class test.ExtractData
 
extractDataEnsembl(File, BufferedWriter) - Method in class util.parsers.fasta.PrintData
 
extractDataFasta(File, BufferedWriter) - Method in class util.parsers.fasta.PrintData
 
extractDataFromFastaEmblFile(File) - Method in class util.io.FileParser
 
extractDataFromFastaFile(File) - Method in class util.io.FileParser
Reads all the fasta data from a fastafile.
extractDoubleValue(String, double) - Method in class var.experimenter.ScriptOptionAbstractClass
 
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in interface util.classificationFeatures.ClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.RFClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeatures2(String[], int, String[], List<Conversion>, String[]) - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
extractFeaturesFromSequence(String, String, Double, String[], int) - Method in class startup.ClassificationAction
This method is part of the main-loop that extracts the different features.
extractFeaturesFromTrainingData(Classifier) - Method in class startup.ClassificationAction
This method extracts the necessary features in order to train a classifier with these features.
extractFromData(GeneTrainingData, BufferedWriter, BufferedWriter, BufferedWriter, BufferedWriter) - Method in class util.parsers.ExtractTrainingData
 
extractFromFile(File, ExtractTrainingData.DATATYPES) - Method in class util.parsers.ExtractTrainingData
 
extractFromFileEctocarpus(File) - Method in class util.parsers.ExtractTrainingData
 
extractFromFileMicromonas(File) - Method in class util.parsers.ExtractTrainingData
 
extractFromFileOstreococcus(File) - Method in class util.parsers.ExtractTrainingData
 
extractFromMap(Map<String, ?>) - Static method in class util.Util
Extracts a list of strings from the values of a map, but it keeps the normal alphabetical order between the keys of the map.
extractFromSequence(int, String) - Method in class util.parsers.fasta.ExtractTrainingData
 
extractIntValue(String, int) - Method in class var.experimenter.ScriptOptionAbstractClass
 
ExtractionResult - Class in util.results
This class is to be used as an instance as the result of a featureExtraction from a rf or a compositional feature.
ExtractionResult(Map<String, Integer>, int) - Constructor for class util.results.ExtractionResult
 
ExtractionResult() - Constructor for class util.results.ExtractionResult
 
extractModels(List<ModelDataParser.ModelData>) - Method in class startup.gui.WizardFramework
 
extractNegativeAcceptors(List<Integer>, String, BufferedWriter) - Method in class util.parsers.ExtractTrainingData
 
extractNegativeDonors(List<Integer>, String, BufferedWriter) - Method in class util.parsers.ExtractTrainingData
 
extractPositiveAcceptors(List<Integer>, String, BufferedWriter, boolean) - Method in class util.parsers.ExtractTrainingData
 
extractPositiveDonors(List<Integer>, String, BufferedWriter, boolean) - Method in class util.parsers.ExtractTrainingData
 
extractRandomSecondaryStructuresFromFile(String, int) - Method in class util.io.FileParser
Extracts a given amount of secondary structure data from a given file.
extractRandomSequencesFromFile(String, int) - Method in class util.io.FileParser
This method extracts at random a certain number of unique lines from a file.
extractSecondaryStructuresFromFile(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.
extractSequencesFromFile(String) - Method in class util.io.FileParser
Static method for extracting all DNA sequences (simple format, one sequence on each line, those sequences should all have their (pseudo-) splicesites aligned at the same position (defined in main.Jaspr.SPLICESITE).
extractSequenceString(String, int, int, int) - Method in class util.secondaryStructure.SecondaryStructureExtraction
This method extracts a string of the same length for all possible maximum upstream and downstream lengths, relative to the splicesite location.
extractStructures(String, List<Integer>, String, int, int) - Method in class util.secondaryStructure.SecondaryStructureExtraction
This method extracts the actual secondary structures from the sequence, given by the list of possible splicesites.
ExtractTrainingData - Class in util.parsers
 
ExtractTrainingData(boolean) - Constructor for class util.parsers.ExtractTrainingData
 
ExtractTrainingData() - Constructor for class util.parsers.ExtractTrainingData
 
ExtractTrainingData(String[]) - Constructor for class util.parsers.ExtractTrainingData
 
ExtractTrainingData - Class in util.parsers.fasta
 
ExtractTrainingData(String) - Constructor for class util.parsers.fasta.ExtractTrainingData
 
ExtractTrainingData(String[]) - Constructor for class util.parsers.fasta.ExtractTrainingData
 
ExtractTrainingData.DATATYPES - Enum in util.parsers
 
extractUpDown(int, String, boolean) - Method in class util.parsers.ExtractTrainingData
 

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