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- 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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