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T

T - Static variable in class contextFold.rna.RNA
 
tagMany(String) - Method in interface contextFold.rnaFolding.Fold
 
tagMany(String) - Method in class contextFold.rnaFolding.Folder
 
tagOne(String) - Method in interface contextFold.rnaFolding.Fold
 
tagOne(String) - Method in class contextFold.rnaFolding.Folder
Deprecated. 
tick() - Method in class contextFold.features.DenseFeatureVector
Increases time stamp by one.
toStrArr(List<String>) - Static method in class contextFold.common.CmdArgumentsHandler
 
toString() - Method in class contextFold.common.CmdArgumentsHandler
 
toString() - Method in class contextFold.features.BinnedLengthFeatureExtractor
 
toString() - Method in class contextFold.features.Context
 
toString() - Method in class contextFold.features.DoublePosContext
 
toString() - Method in class contextFold.features.FeatureTemplate
 
toString() - Method in class contextFold.features.SinglePosContext
 
toString() - Method in class contextFold.features.SparseFeatureVector
 
toString(AbstractFeatureVector) - Method in class contextFold.features.SparseFeatureVector
 
toString(AbstractFeatureVector, boolean) - Method in class contextFold.features.SparseFeatureVector
 
toString() - Method in class contextFold.rna.RNA
 
Traceback - Class in contextFold.rnaFolding
Contains methods for tracing-back score tables, in order to produce optimal foldings.
Traceback() - Constructor for class contextFold.rnaFolding.Traceback
 
traceback(int[][], int[], int[], int[], int[], int[][], StructreElementsScorer, int, int[], int[], int[], int[], int[][], int[], StructureRecognizerImpl) - Method in class contextFold.rnaFolding.Traceback
 
traceback3(int, int, int) - Method in class contextFold.rnaFolding.Traceback
Resolving the next external branch, from left (5') to right (3').
Train - Class in contextFold.app
Obtains feature weight parameters of scoring models via a machine-learning procedure.
Train() - Constructor for class contextFold.app.Train
 
TrainAnnotations - Class in contextFold.common
 
TrainAnnotations() - Constructor for class contextFold.common.TrainAnnotations
 
TRIVIAL - Static variable in class contextFold.features.WordFeatureCalculator
 
TRIVIAL_ALPHABET - Static variable in class contextFold.features.WordFeatureCalculator
 

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