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

C

C - Static variable in class util.FeatureExtractionExtension
 
canBind(char, char) - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
 
cfList - Variable in class util.Options
 
changedUpdate(DocumentEvent) - Method in class startup.gui.WizardFramework
 
checkATG(String, int) - Method in class util.parsers.fasta.PrintData
 
checkCAT(String, int) - Method in class util.parsers.fasta.PrintData
 
checkMul3(List<Integer>) - Method in class util.parsers.fasta.PrintData
 
checkStop(String, int) - Method in class util.parsers.fasta.PrintData
 
checkStopReverse(String, int) - Method in class util.parsers.fasta.PrintData
 
checksTurnedOffTipText() - Method in class classifier.wekaSVM.SMO
Returns the tip text for this property
chooseClassifier(ClassificationAction.CLASSIFIERS) - Method in class startup.ClassificationAction
This method creates the right classifier implementation that implements the Classifier interface, according to the chosen enumeration.
ChoosePanel - Class in var.experimenter
 
ChoosePanel(String, ScriptOptionAbstractClass, ScriptOptionAbstractClass, ScriptOptionAbstractClass, ScriptOptionAbstractClass) - Constructor for class var.experimenter.ChoosePanel
 
ChoosePanel(String, ScriptOptionAbstractClass, ScriptOptionAbstractClass, ScriptOptionAbstractClass, ScriptOptionAbstractClass, int) - Constructor for class var.experimenter.ChoosePanel
 
classAttributeNames() - Method in class classifier.wekaSVM.SMO
 
ClassificationAction - Class in startup
This class represents the dataflow that is necessary to either build a classification model for a certain functional site, or evaluate a sequence for said functional site.
ClassificationAction(Logger, FunSiPWorkflow) - Constructor for class startup.ClassificationAction
Constructor for this classification action.
ClassificationAction.CLASSIFIERS - Enum in startup
Choice of different available classifiers.
ClassificationAction.COMMAND - Enum in startup
The different dataflow/workflow commands.
ClassificationAction.FILE_TYPE - Enum in startup
Possible filetypes which can be used when evaluating sequence files.
ClassificationAction.STRAND - Enum in startup
Possible strands which should be evaluated by the classification models.
ClassificationFeature - Interface in util.classificationFeatures
This interface contains all methods that a classification feature should implement to be fully functional.
ClassificationFeatureDrawing - Interface in util.classificationFeatures
 
ClassificationFeatureUtils - Class in util.classificationFeatures
This class contains some different utility methods for feature extraction.
ClassificationFeatureUtils.CLASSIFICATIONFEATURE_TYPES - Enum in util.classificationFeatures
 
ClassificationResult - Class in util.results
 
ClassificationResult() - Constructor for class util.results.ClassificationResult
 
classifier - package classifier
 
Classifier - Interface in classifier
This interface defines all the necessary methods that a classifier should conform to, in order to be compatible with FunSiP.
classifier - Variable in class classifier.SVMOptions
The type of classifier.
Classifier.DATA_TYPE - Enum in classifier
The possible types of data: POSITIVE_DATA indicates that the source is positive training data.
classifier.wekaSVM - package classifier.wekaSVM
 
ClassifierOptions - Interface in classifier
Super interface which defines the use of implementation specific classifier options.
classify(String, String) - Method in interface classifier.Classifier
Use the trained (or untrained, the modelfile must be set before though) SVM to classify data, and write the output to an outputfile
classify(String, String) - Method in class classifier.WekaSVM
Use the trained (or untrained, the modelfile must be set before though) SVM to classify data, and write the output to an outputfile
classify_single_instance(String) - Method in interface classifier.Classifier
Use the trained classifier to classify a single instance of data, defined by the instance parameter.
classify_single_instance(String) - Method in class classifier.WekaSVM
Use the trained classifier to classify a single instance of data, defined by the instance parameter.
classify_single_instance_fast(double[]) - Method in interface classifier.Classifier
Use the trained classifier to classify a single instance of data in a very fast way, without having to resort to string parsing procedures (recommanded method for doing these classifications).
classify_single_instance_fast(double[]) - Method in class classifier.WekaSVM
Use the trained classifier to classify a single instance of data in a very fast way, without having to resort to string parsing procedures (recommanded method for doing these classifications).
clear() - Method in class util.io.CrossValidationOutput
 
clearAllActions() - Method in class var.experimenter.RangePanel
 
ClusterClassificationAction - Class in startup.cluster
This class is a special wrapup around a normal classificationaction.
ClusterClassificationAction(ClassificationAction, FunSiPWorkflow, String, Logger) - Constructor for class startup.cluster.ClusterClassificationAction
Constructor.
coeff - Variable in class classifier.SVMOptions
for polynomial and sigmoid kernel
compareFeatureFiles(FeatureFileContent, FeatureFileContent) - Method in class var.FSCompare
This method compares the different contents of the featurefiles.
CompareFS - Class in util.featureSelection
 
CompareFS(String, String) - Constructor for class util.featureSelection.CompareFS
 
complexity - Variable in class classifier.SVMOptions
Complexity of the SVM
CompositionalClassificationFeature - Class in util.classificationFeatures.implementations
 
CompositionalClassificationFeature() - Constructor for class util.classificationFeatures.implementations.CompositionalClassificationFeature
 
CompositionalClassificationFeatureDrawing - Class in util.classificationFeatures.implementations
 
CompositionalClassificationFeatureDrawing(CompositionalClassificationFeature) - Constructor for class util.classificationFeatures.implementations.CompositionalClassificationFeatureDrawing
 
CompositionalGeneralClassificationFeature - Class in util.classificationFeatures.implementations
 
CompositionalGeneralClassificationFeature() - Constructor for class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
 
CompositionalSecondaryStructureClassificationFeature - Class in util.classificationFeatures.implementations
 
CompositionalSecondaryStructureClassificationFeature() - Constructor for class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
 
CompositionalSecondaryStructureClassificationFeatureDrawing - Class in util.classificationFeatures.implementations
 
CompositionalSecondaryStructureClassificationFeatureDrawing(CompositionalSecondaryStructureClassificationFeature) - Constructor for class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeatureDrawing
 
compute_roc() - Method in class util.results.CrossValidationResult
computes the roc-curve data from the distances and labels that are provided.
computeDeductedData() - Method in class util.results.CrossValidationResult
This method computes all the other results, following the given basic data of the false positives/true positives/...
computeOptimalisationStrings() - Method in class startup.ClassificationAction
This method is a more or less necessary evil.
ConfigurationFileReader - Class in var.experimenter
 
ConfigurationFileReader() - Constructor for class var.experimenter.ConfigurationFileReader
 
Conversion - Interface in util.conversions
This interface describes the functionality that is offered by conversions/translations from one sequence to another.
Conversions - Class in util.wekaUtilities
 
Conversions(Logger) - Constructor for class util.wekaUtilities.Conversions
 
ConversionUtils - Class in util.conversions
 
convertArffFileToNtrFile(boolean) - Method in class util.io.ArffFileSupport
 
convertArffToNtr(String) - Method in class util.io.ArffFileSupport
 
convertArffToNtrOld(String) - Method in class util.io.ArffFileSupport
 
convertFullSecToReducedSec(String) - Static method in class util.classificationFeatures.ClassificationFeatureUtils
Replace all ( and ) by | in the secondary structure string
convertToGenomeViewOutput(File) - Method in class startup.FunSiPWorkflow
 
convertToIntArray(char[]) - Static method in class util.FeatureExtractionExtension
 
copyMerge(String, String, String) - Method in class util.SpliceFileInfo
 
copyNormal(String, String) - Method in class util.SpliceFileInfo
 
countInterAg(String, int, int) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Finds the number of other possible acceptorsites ("AG") between two locations (mostly used between a branchpoint and an acceptorsite)
countOccurences(String, String) - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
countPyrimidines(String, int, int) - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Counts the number of pyrimidines between the possible splicesite and the possible acceptorsite
createColor(double) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeatureDrawing
 
createColor(int) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeatureDrawing
 
createColor(double) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeatureDrawing
 
createColor(int) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeatureDrawing
 
createColorValue(double, double) - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeatureDrawing
 
createColorValue(double, double) - Method in class util.classificationFeatures.implementations.PositionalClassificationFeatureDrawing
 
createConfigurationFile(String) - Method in class main.FunSiPGui
Creates the configuration file, with the currently loaded SPRWorkflow object as content.
createConfigurationFile(ClassificationAction, String) - Static method in class startup.ParameterFileParser
This method creates the configuration file for a single classification-action, so the classification can be started remotely.
createContent(ClassificationAction) - Method in class startup.gui.SprClassificationFeaturePanel
 
createFilter(List<ValPosCombination>) - Method in class util.featureSelection.FeatureSelectionStub
 
createFinalBuildConfig() - Method in class startup.gui.WizardFramework
 
createFinalUseConfig() - Method in class startup.gui.WizardFramework
 
createOption(String[]) - Static method in class var.experimenter.ConfigurationFileReader
 
createPanel(Component, Dimension) - Method in class var.experimenter.RangeOption
 
CreateSS - Class in util.secondaryStructure
 
CreateSS() - Constructor for class util.secondaryStructure.CreateSS
 
crossValidate(int, int, int) - Method in interface classifier.Classifier
Performs a crossvalidation of trainingfile.
crossValidate(int, int, int) - Method in class classifier.WekaSVM
Performs a crossvalidation of trainingfile.
CrossValidationData - Class in util.io
 
CrossValidationData() - Constructor for class util.io.CrossValidationData
 
CrossValidationData(File, File) - Constructor for class util.io.CrossValidationData
 
CrossValidationOutput - Class in util.io
 
CrossValidationOutput(ClassificationAction, Logger) - Constructor for class util.io.CrossValidationOutput
 
CrossValidationResult - Class in util.results
This class contains the normal results of a crossvalidation (number of false positives/false negatives/true positives/true negatives and the distances and labels of the results).
CrossValidationResult() - Constructor for class util.results.CrossValidationResult
Creates a CrossValidationResult object.
cTipText() - Method in class classifier.wekaSVM.SMO
Returns the tip text for this property
cutoffConfidence - Variable in class util.Options
 

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