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C

C - Static variable in class contextFold.rna.RNA
 
calcAlphabetSize(byte[]) - Static method in class contextFold.features.SinglePosContext
 
calcValue(int[]) - Method in interface contextFold.features.ElementValueCalculator
 
calcValue(int[]) - Method in class contextFold.features.HpLengthCalculator
 
calcValue(int[]) - Method in class contextFold.features.IlLengthCalculator
 
calcValue(int[]) - Method in class contextFold.features.IntervalLengthCalculator
 
cardinality - Variable in class contextFold.features.Context
 
cardinality - Variable in class contextFold.features.FeatureExtractor
 
charToByte(char[]) - Static method in class contextFold.rna.RNA
 
clear() - Method in class contextFold.features.AbstractFeatureVector
Sets all weights to 0.
clear() - Method in class contextFold.features.DenseFeatureVector
 
clear() - Method in class contextFold.features.SparseFeatureVector
 
CLOSE - Static variable in class contextFold.rna.RNA
 
close() - Method in class contextFold.rna.RNAWriter
 
close2open - Static variable in class contextFold.rna.RNA
 
CmdArgumentsHandler - Class in contextFold.common
 
CmdArgumentsHandler(String, String, boolean) - Constructor for class contextFold.common.CmdArgumentsHandler
 
CmdArgumentsHandler(String, String) - Constructor for class contextFold.common.CmdArgumentsHandler
 
CmdArgumentsHandler() - Constructor for class contextFold.common.CmdArgumentsHandler
 
compare(Object, Object) - Method in class contextFold.common.NumberComparator
 
compareTo(PredictionQuality) - Method in class contextFold.scoring.PredictionQuality
 
compress() - Method in class contextFold.features.DenseFeatureVector
 
compress(int) - Method in class contextFold.features.DenseFeatureVector
Maps all float weights to the given range of integers.
compress() - Method in class contextFold.features.FeatureManager
 
computeDPTables(StructreElementsScorer, List<int[]>, int) - Method in class contextFold.rnaFolding.Folder
Fills the dynamic programming scoring tables.
concatanations - Variable in class contextFold.rnaFolding.Folder
 
concreteModify(String) - Method in class contextFold.common.StringModifier
 
concreteModify(String) - Method in class contextFold.common.SuffixAdder
 
contained(ContextFeatureExtractor) - Method in class contextFold.features.ContextFeatureExtractor
 
contains(int[], int[]) - Static method in class contextFold.features.SinglePosContext
 
Context - Class in contextFold.features
 
Context(int[], byte[]) - Constructor for class contextFold.features.Context
 
ContextFeatureExtractor - Class in contextFold.features
 
ContextFeatureExtractor(int, int) - Constructor for class contextFold.features.ContextFeatureExtractor
 
contextFold - package contextFold
The contextFold package supplies java source code for RNA secondary structure prediction utilities.
contextFold.app - package contextFold.app
Contains java-executable programs that perform the main functionalities of the contextFold package.
contextFold.common - package contextFold.common
Bundles general auxiliary functionalities.
contextFold.features - package contextFold.features
Contains scoring model's parameterization related functionalities.
contextFold.learn - package contextFold.learn
Contains weight learning related functionalities.
contextFold.models - package contextFold.models
Contains a set of pre-defined (untrained) parameterizations.
contextFold.rna - package contextFold.rna
Contains RNA representation related utilities.
contextFold.rnaFolding - package contextFold.rnaFolding
Contains RNA secondary structure prediction related utilities.
contextFold.scoring - package contextFold.scoring
Contains RNA secondary structure scoring and similarity computation related utilities.
costSensitivePAUpdate(RNA, int[], int[], float) - Method in class contextFold.learn.Learn
 
countNonZeroEntries() - Method in class contextFold.features.AbstractFeatureVector
 
countNonZeroEntries() - Method in class contextFold.features.DenseFeatureVector
 
countNonZeroEntries() - Method in class contextFold.features.SparseFeatureVector
 
csr - Variable in class contextFold.models.FeatureSetter
 
currProcessedSeq - Variable in class contextFold.features.FeatureExtractor
 
currWord - Variable in class contextFold.features.SinglePosContext
 

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