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W

waitForSync() - Method in class startup.FunSiPWorkflow
This method is used for synchronization purposes between the different spawned threads.
WaveContentClassificationFeature - Class in util.classificationFeatures.implementations.test
 
WaveContentClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
 
WekaSVM - Class in classifier
This class represents the implementation of the classifier interface, suited to be used with the SMO (SVM) implementation of the WEKA(TM) machine learning library.
WekaSVM(Logger, ClassificationAction) - Constructor for class classifier.WekaSVM
Constructor, just initiates the necessary variables.
windowActivated(WindowEvent) - Method in class main.FunSiPGui
 
windowActivated(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowClosed(WindowEvent) - Method in class main.FunSiPGui
 
windowClosed(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowClosing(WindowEvent) - Method in class main.FunSiPGui
 
windowClosing(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowDeactivated(WindowEvent) - Method in class main.FunSiPGui
 
windowDeactivated(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowDeiconified(WindowEvent) - Method in class main.FunSiPGui
 
windowDeiconified(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowGainedFocus(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowIconified(WindowEvent) - Method in class main.FunSiPGui
 
windowIconified(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowLostFocus(WindowEvent) - Method in class startup.gui.WizardFramework
 
windowOpened(WindowEvent) - Method in class main.FunSiPGui
 
windowOpened(WindowEvent) - Method in class startup.gui.WizardFramework
 
WizardFramework - Class in startup.gui
 
WizardFramework(FunSiPGui, JFrame) - Constructor for class startup.gui.WizardFramework
 
WizardFramework.WIZARD_STATE - Enum in startup.gui
 
writeAcceptors(BufferedWriter, BufferedWriter, ExtractTrainingData.AnnotationData) - Method in class util.parsers.fasta.ExtractTrainingData
 
writeClassification(List<ClassificationResult>) - Method in class util.io.OutputClassification
This method writes the classification (of the possible splicesites in a testfile) to an outputfile whose name is taken from the testfileheader.
writeConclomOne(String) - Method in class var.SimpleExperimenter
 
writeConclomZero(String) - Method in class var.SimpleExperimenter
 
writeCrossValidation(CrossValidationResult, Options, Logger, boolean, File, int, int, int, int) - Static method in class util.io.FileUtils
This methods writes the results of a crossvalidation to a file.
writeCrossValidation(CrossValidationResult, File, int, int, int, int) - Method in class util.io.IOUtils
This methods writes the results of a crossvalidation to a file.
writeDonors(BufferedWriter, BufferedWriter, ExtractTrainingData.AnnotationData) - Method in class util.parsers.fasta.ExtractTrainingData
 
writeFeatureSelectionFile(String, List<Integer>) - Method in class util.featureSelection.FeatureSelectionStub
 
writeFeatureSelectionFileFull(String, List<ValPosCombination>) - Method in class util.featureSelection.FeatureSelectionStub
 
writeFull(boolean, String, String) - Method in class var.SimpleExperimenter
 
writeNtrData(File, List<List<Double>>, Classifier.DATA_TYPE) - Method in class util.io.NtrFileSupport
 
writeResults(File, List<RocCurveData>) - Method in class util.io.CrossValidationOutput
 
writeRocCurveData(double[], double[], String) - Method in class util.io.CrossValidationOutput
 
writeRocGnuPlotCommand(List<RocCurveData>, String, boolean) - Static method in class util.io.FileUtils
This method generates the Gnuplot-commands to display the roc-curves (only possible with cross-validation).
writeRocGnuPlotCommand(List<RocCurveData>, String) - Method in class util.io.IOUtils
This method generates the Gnuplot-commands to display the roc-curves (only possible with cross-validation).
writeTemporaryFeatureData(String, boolean, List<List<Double>>, Classifier.DATA_TYPE) - Method in interface classifier.Classifier
This method writes the temporary featuredata (being all the features extracted from 1 sequence, each feature in a different list) to a file.
writeTemporaryFeatureData(String, List<List<Double>>, Classifier.DATA_TYPE) - Method in interface classifier.Classifier
This method writes the temporary featuredata (being all the features extracted from 1 sequence, each feature in a different list) to a file.
writeTemporaryFeatureData(String, boolean, List<List<Double>>, Classifier.DATA_TYPE) - Method in class classifier.WekaSVM
This method writes the temporary featuredata (being all the features extracted from 1 sequence, each feature in a different list) to a file.
writeTemporaryFeatureData(String, List<List<Double>>, Classifier.DATA_TYPE) - Method in class classifier.WekaSVM
This method writes the temporary featuredata (being all the features extracted from 1 sequence, each feature in a different list) to a file.
writeTrainingData(List<String>, String) - Method in class test.ExtractData
 

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