Uses of Class
util.secondaryStructure.SecondaryStructureData

Packages that use SecondaryStructureData
startup   
util.io   
util.secondaryStructure   
 

Uses of SecondaryStructureData in startup
 

Methods in startup with parameters of type SecondaryStructureData
 java.io.File ClassificationAction.getFeaturesTrainingData(java.lang.String fileName, java.util.List<java.lang.String> sequences, SecondaryStructureData ssData, Classifier classifier, Classifier.DATA_TYPE data_type)
          This method extracts the features from a trainingfile (positive/negative), and stores the extracted features into the feature_output_file.
 

Uses of SecondaryStructureData in util.io
 

Methods in util.io that return SecondaryStructureData
 SecondaryStructureData FileParser.extractRandomSecondaryStructuresFromFile(java.lang.String fileName, int number)
          Extracts a given amount of secondary structure data from a given file.
 SecondaryStructureData FileParser.extractSecondaryStructuresFromFile(java.lang.String fileName)
          Extracts the secondarystructure data from a file, according to the way it was written in the file by RNAfold.
 

Uses of SecondaryStructureData in util.secondaryStructure
 

Methods in util.secondaryStructure that return SecondaryStructureData
 SecondaryStructureData SecondaryStructureExtraction.extractStructures(java.lang.String sequence, java.util.List<java.lang.Integer> locations, java.lang.String outputDirectory, int maxUp, int maxDown)
          This method extracts the actual secondary structures from the sequence, given by the list of possible splicesites.