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- Static variable in class contextFold.rna.
RNA
calcAlphabetSize(byte[])
- Static method in class contextFold.features.
SinglePosContext
calcValue(int[])
- Method in interface contextFold.features.
ElementValueCalculator
calcValue(int[])
- Method in class contextFold.features.
HpLengthCalculator
calcValue(int[])
- Method in class contextFold.features.
IlLengthCalculator
calcValue(int[])
- Method in class contextFold.features.
IntervalLengthCalculator
cardinality
- Variable in class contextFold.features.
Context
cardinality
- Variable in class contextFold.features.
FeatureExtractor
charToByte(char[])
- Static method in class contextFold.rna.
RNA
clear()
- Method in class contextFold.features.
AbstractFeatureVector
Sets all weights to 0.
clear()
- Method in class contextFold.features.
DenseFeatureVector
clear()
- Method in class contextFold.features.
SparseFeatureVector
CLOSE
- Static variable in class contextFold.rna.
RNA
close()
- Method in class contextFold.rna.
RNAWriter
close2open
- Static variable in class contextFold.rna.
RNA
CmdArgumentsHandler
- Class in
contextFold.common
CmdArgumentsHandler(String, String, boolean)
- Constructor for class contextFold.common.
CmdArgumentsHandler
CmdArgumentsHandler(String, String)
- Constructor for class contextFold.common.
CmdArgumentsHandler
CmdArgumentsHandler()
- Constructor for class contextFold.common.
CmdArgumentsHandler
compare(Object, Object)
- Method in class contextFold.common.
NumberComparator
compareTo(PredictionQuality)
- Method in class contextFold.scoring.
PredictionQuality
compress()
- Method in class contextFold.features.
DenseFeatureVector
compress(int)
- Method in class contextFold.features.
DenseFeatureVector
Maps all float weights to the given range of integers.
compress()
- Method in class contextFold.features.
FeatureManager
computeDPTables(StructreElementsScorer, List<int[]>, int)
- Method in class contextFold.rnaFolding.
Folder
Fills the dynamic programming scoring tables.
concatanations
- Variable in class contextFold.rnaFolding.
Folder
concreteModify(String)
- Method in class contextFold.common.
StringModifier
concreteModify(String)
- Method in class contextFold.common.
SuffixAdder
contained(ContextFeatureExtractor)
- Method in class contextFold.features.
ContextFeatureExtractor
contains(int[], int[])
- Static method in class contextFold.features.
SinglePosContext
Context
- Class in
contextFold.features
Context(int[], byte[])
- Constructor for class contextFold.features.
Context
ContextFeatureExtractor
- Class in
contextFold.features
ContextFeatureExtractor(int, int)
- Constructor for class contextFold.features.
ContextFeatureExtractor
contextFold
- package contextFold
The
contextFold
package supplies java source code for RNA secondary structure prediction utilities.
contextFold.app
- package contextFold.app
Contains java-executable programs that perform the main functionalities of the
contextFold
package.
contextFold.common
- package contextFold.common
Bundles general auxiliary functionalities.
contextFold.features
- package contextFold.features
Contains scoring model's parameterization related functionalities.
contextFold.learn
- package contextFold.learn
Contains weight learning related functionalities.
contextFold.models
- package contextFold.models
Contains a set of pre-defined (untrained) parameterizations.
contextFold.rna
- package contextFold.rna
Contains RNA representation related utilities.
contextFold.rnaFolding
- package contextFold.rnaFolding
Contains RNA secondary structure prediction related utilities.
contextFold.scoring
- package contextFold.scoring
Contains RNA secondary structure scoring and similarity computation related utilities.
costSensitivePAUpdate(RNA, int[], int[], float)
- Method in class contextFold.learn.
Learn
countNonZeroEntries()
- Method in class contextFold.features.
AbstractFeatureVector
countNonZeroEntries()
- Method in class contextFold.features.
DenseFeatureVector
countNonZeroEntries()
- Method in class contextFold.features.
SparseFeatureVector
csr
- Variable in class contextFold.models.
FeatureSetter
currProcessedSeq
- Variable in class contextFold.features.
FeatureExtractor
currWord
- Variable in class contextFold.features.
SinglePosContext
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