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F

FEATURE_1_EXTRACTOR - Static variable in class contextFold.features.FeatureExtractor
 
FeatureExtractor - Class in contextFold.features
 
FeatureExtractor(int) - Constructor for class contextFold.features.FeatureExtractor
 
featureExtractor - Variable in class contextFold.features.FeatureTemplate
 
FeatureManager - Class in contextFold.features
A parameterization object.
FeatureManager(StructureRecognizer) - Constructor for class contextFold.features.FeatureManager
 
featureManager - Variable in class contextFold.models.FeatureSetter
 
FeatureManager.Feature - Class in contextFold.features
 
FeatureManager.Feature(String, float) - Constructor for class contextFold.features.FeatureManager.Feature
 
featureNames - Variable in class contextFold.features.AbstractFeatureVector
 
FeatureSetter - Class in contextFold.models
 
FeatureSetter() - Constructor for class contextFold.models.FeatureSetter
 
FeatureSetter(int, int[], int[]) - Constructor for class contextFold.models.FeatureSetter
 
FeatureSetterFactory - Class in contextFold.models
 
FeatureSetterFactory() - Constructor for class contextFold.models.FeatureSetterFactory
 
FeatureTemplate - Class in contextFold.features
 
FeatureTemplate(String, FeatureExtractor) - Constructor for class contextFold.features.FeatureTemplate
 
FeatureTemplate(String, ValueCalculator) - Constructor for class contextFold.features.FeatureTemplate
 
FeatureTemplate(String, FeatureExtractor, ValueCalculator) - Constructor for class contextFold.features.FeatureTemplate
 
filter(float) - Method in class contextFold.features.AbstractFeatureVector
 
filter(RNA) - Method in class contextFold.rna.AnnotationFilter
 
filter(List<RNA>, String) - Static method in class contextFold.rna.RNA
 
filter(List<RNA>, int) - Static method in class contextFold.rna.RNA
 
filter(RNA) - Method in class contextFold.rna.RNA_Filter
 
filter(Collection<RNA>) - Method in class contextFold.rna.RNA_Filter
 
filter(Collection<RNA>, int, boolean) - Method in class contextFold.rna.RNA_Filter
 
filterWeights(float) - Method in class contextFold.features.FeatureManager
 
finalize() - Method in class contextFold.features.FeatureManager
 
first - Variable in class contextFold.common.Pair
 
FIRST_BASE_TYPE - Variable in class contextFold.rnaFolding.StructureRecognizerImpl
 
FIRST_LENGTH_TYPE - Variable in class contextFold.rnaFolding.StructureRecognizerImpl
 
FIRST_LOOP_TERMINATION_TYPE - Variable in class contextFold.rnaFolding.StructureRecognizerImpl
 
firstPosContext - Variable in class contextFold.features.DoublePosContext
 
firstVectorIx - Variable in class contextFold.features.FeatureTemplate
 
floatEquals(float, float) - Static method in class contextFold.common.Utils
 
floatSmaller(float, float) - Static method in class contextFold.common.Utils
 
floatValue(String) - Method in class contextFold.common.CmdArgumentsHandler
 
fm - Variable in class contextFold.rnaFolding.Folder
 
fMeasure() - Method in class contextFold.scoring.PredictionQuality
 
FMeasureLossCalculator - Class in contextFold.scoring
 
FMeasureLossCalculator(float) - Constructor for class contextFold.scoring.FMeasureLossCalculator
 
FMeasureLossCalculator() - Constructor for class contextFold.scoring.FMeasureLossCalculator
 
Fold - Interface in contextFold.rnaFolding
 
Folder - Class in contextFold.rnaFolding
An object that implements the (dynamic programming Zuker-like) RNA folding prediction algorithm.
Folder() - Constructor for class contextFold.rnaFolding.Folder
Constructs a Folder object.
Folder(FeatureManager) - Constructor for class contextFold.rnaFolding.Folder
Construct a folder which uses the scoring model of the given feature manager.
Folder(String) - Constructor for class contextFold.rnaFolding.Folder
Construct a folder which uses the scoring model of the given feature manager.
FoldEvaluator - Interface in contextFold.scoring
 
FoldEvaluatorImpl - Class in contextFold.scoring
 
FoldEvaluatorImpl(FeatureManager) - Constructor for class contextFold.scoring.FoldEvaluatorImpl
 
FoldingLineRegexp - Static variable in class contextFold.rna.OneLineReader
 
FoldingRegexp - Static variable in class contextFold.rna.OneLineReader
 
foldings - Variable in class contextFold.rna.RNA
 
foldToBracets(int[]) - Static method in class contextFold.rna.RNA
 
foldToBracets(int[], int) - Static method in class contextFold.rna.RNA
 
FULL - Static variable in class contextFold.features.WordFeatureCalculator
 
FULL_ALPHABET - Static variable in class contextFold.features.WordFeatureCalculator
 

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