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P

Pair<T1,T2> - Class in contextFold.common
 
Pair(T1, T2) - Constructor for class contextFold.common.Pair
 
PAIRED - Static variable in class contextFold.rnaFolding.Traceback
 
possibleReplacements - Static variable in class contextFold.rna.RNA
 
PPV() - Method in class contextFold.scoring.PredictionQuality
 
Predict - Class in contextFold.app
Produces secondary structure predictions for RNA sequences.
Predict() - Constructor for class contextFold.app.Predict
 
predictAll(FeatureManager, String, List<RNA>) - Static method in class contextFold.app.Predict
 
predictAll(FeatureManager, String, List<RNA>, String) - Static method in class contextFold.app.Predict
 
predicted - Variable in class contextFold.rna.RNA
 
predictFolding(String) - Method in class contextFold.rnaFolding.Folder
 
PredictionQuality - Class in contextFold.scoring
 
PredictionQuality(int[], int[]) - Constructor for class contextFold.scoring.PredictionQuality
 
PredictionQuality(int[], int[], float) - Constructor for class contextFold.scoring.PredictionQuality
 
predictionStatistics(String) - Static method in class contextFold.scoring.PredictionQuality
 
predictionStatistics(String, int) - Static method in class contextFold.scoring.PredictionQuality
 
predictionStatistics(String, int, boolean) - Static method in class contextFold.scoring.PredictionQuality
 
predictionStatistics(List<RNA>, int) - Static method in class contextFold.scoring.PredictionQuality
 
predictionStatistics(List<RNA>, int, boolean) - Static method in class contextFold.scoring.PredictionQuality
 
preprocess(byte[]) - Method in class contextFold.features.BinnedLengthFeatureExtractor
 
preprocess(byte[]) - Method in class contextFold.features.DoublePosContext
 
preprocess(byte[]) - Method in class contextFold.features.FeatureExtractor
 
preprocess(byte[]) - Method in class contextFold.features.SinglePosContext
 
PrintModelFeatures - Class in contextFold.app
Prints feature names and their weights for a given scoring model.
PrintModelFeatures() - Constructor for class contextFold.app.PrintModelFeatures
 
printStructure(int[], int[]) - Static method in class contextFold.rnaFolding.Folder
 
processArgs(String[]) - Method in class contextFold.common.CmdArgumentsHandler
 
PS_CLOSE - Static variable in class contextFold.rna.RNA
 
PS_OPEN - Static variable in class contextFold.rna.RNA
 
pseudoClose - Static variable in class contextFold.rna.RNA
 
pseudoClosePattern - Static variable in class contextFold.rna.RNA
 
pseudoFoldPattern - Static variable in class contextFold.rna.RNA
 
pseudoOpen - Static variable in class contextFold.rna.RNA
 
pseudoOpenPattern - Static variable in class contextFold.rna.RNA
 

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