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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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