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save(Serializable, String)
- Static method in class contextFold.common.
Utils
scoreFold(RNA, int[])
- Method in interface contextFold.scoring.
FoldEvaluator
Computes the score of a given sequence-folding pair.
scoreFold(RNA, int[])
- Method in class contextFold.scoring.
FoldEvaluatorImpl
second
- Variable in class contextFold.common.
Pair
secondPosContext
- Variable in class contextFold.features.
DoublePosContext
sensitivity()
- Method in class contextFold.scoring.
PredictionQuality
seq
- Variable in class contextFold.rna.
RNA
seqFeatures
- Variable in class contextFold.features.
FeatureExtractor
seqPerLength
- Variable in class contextFold.rnaFolding.
Folder
seqString
- Variable in class contextFold.rna.
RNA
sequence()
- Method in class contextFold.rna.
RNA
SEQUENCE_GROUP
- Static variable in class contextFold.rna.
OneLineReader
sequenceLength()
- Method in interface contextFold.scoring.
StructreElementsScorer
sequenceLength()
- Method in class contextFold.scoring.
StructreElementsScorerImpl
setFeatureManager(FeatureManager)
- Method in class contextFold.rnaFolding.
Folder
A setter to the feature manager of the folder (the scoring model).
setFeatureManager(String)
- Method in class contextFold.rnaFolding.
Folder
A setter to the feature manager of the folder (the scoring model).
setFeatureNames(Map<Integer, String>)
- Method in class contextFold.features.
AbstractFeatureVector
setFeatures()
- Method in class contextFold.models.
FeatureSetter
setFeatureWeight(int, float)
- Method in class contextFold.features.
AbstractFeatureVector
Sets the weight of a given feature.
setFeatureWeight(int, float)
- Method in class contextFold.features.
DenseFeatureVector
setFeatureWeight(int, float)
- Method in class contextFold.features.
SparseFeatureVector
setFirstVectorIx(int)
- Method in class contextFold.features.
FeatureTemplate
setInitialWeight(float, String)
- Method in class contextFold.features.
FeatureTemplate
setManagerAndRNA(FeatureManager, RNA)
- Method in class contextFold.scoring.
StructreElementsScorerImpl
setRandomSeed(long)
- Static method in class contextFold.rna.
RNA
setRandomSeed()
- Static method in class contextFold.rna.
RNA
setSequence(byte[])
- Method in class contextFold.features.
FeatureExtractor
SHARP
- Static variable in class contextFold.rna.
RNA
SHORT
- Static variable in class contextFold.models.
FeatureSetter
SinglePosContext
- Class in
contextFold.features
SinglePosContext(int, int...)
- Constructor for class contextFold.features.
SinglePosContext
sortElements(List<int[]>)
- Method in interface contextFold.rnaFolding.
StructureRecognizer
sortElements(List<int[]>)
- Method in class contextFold.rnaFolding.
StructureRecognizerImpl
SPACE_RPLACE
- Static variable in class contextFold.rna.
AnnotationFilter
sparseByOcts
- Variable in class contextFold.rnaFolding.
Folder
sparseBySteps
- Variable in class contextFold.rnaFolding.
Folder
SparseFeatureVector
- Class in
contextFold.features
SparseFeatureVector()
- Constructor for class contextFold.features.
SparseFeatureVector
SparseFeatureVector(AbstractFeatureVector)
- Constructor for class contextFold.features.
SparseFeatureVector
splitsPerLength
- Variable in class contextFold.rnaFolding.
Folder
SQRT_VALUE_CALCULATOR
- Static variable in class contextFold.features.
ValueCalculator
sr
- Variable in class contextFold.features.
FeatureManager
STANDARD_RNA_CHARS
- Static variable in class contextFold.rna.
RNA
standardClose
- Static variable in class contextFold.rna.
RNA
standardClosePattern
- Static variable in class contextFold.rna.
RNA
standardComplementary
- Static variable in class contextFold.rna.
RNA
standardFoldPattern
- Static variable in class contextFold.rna.
RNA
standardized(String, String)
- Static method in class contextFold.rna.
RNA
Replacing ambiguous characters by RNA nucleotides, for the sake of efficient learning.
standardOpen
- Static variable in class contextFold.rna.
RNA
standardOpenPattern
- Static variable in class contextFold.rna.
RNA
StHighCoHigh
- Class in
contextFold.models
StHighCoHigh()
- Constructor for class contextFold.models.
StHighCoHigh
StHighCoMed
- Class in
contextFold.models
StHighCoMed()
- Constructor for class contextFold.models.
StHighCoMed
StMedCoHigh
- Class in
contextFold.models
StMedCoHigh()
- Constructor for class contextFold.models.
StMedCoHigh
StMedCoMed
- Class in
contextFold.models
StMedCoMed()
- Constructor for class contextFold.models.
StMedCoMed
StringModifier
- Class in
contextFold.common
StringModifier()
- Constructor for class contextFold.common.
StringModifier
StringModifier(StringModifier)
- Constructor for class contextFold.common.
StringModifier
stringToByte(String)
- Static method in class contextFold.rna.
RNA
stringValue(String)
- Method in class contextFold.common.
CmdArgumentsHandler
structFormat
- Static variable in class contextFold.rna.
RNA
StructreElementsScorer
- Interface in
contextFold.scoring
A sequence specific contextFold.scoring object.
StructreElementsScorerImpl
- Class in
contextFold.scoring
StructreElementsScorerImpl(int[][][], int[][][], int)
- Constructor for class contextFold.scoring.
StructreElementsScorerImpl
STRUCTURE_GROUP
- Static variable in class contextFold.rna.
OneLineReader
StructureRecognizer
- Interface in
contextFold.rnaFolding
StructureRecognizerImpl
- Class in
contextFold.rnaFolding
This class defines the structural elements which are considered by the Folder class.
StructureRecognizerImpl(int, int[], int[])
- Constructor for class contextFold.rnaFolding.
StructureRecognizerImpl
StructureRecognizerImpl()
- Constructor for class contextFold.rnaFolding.
StructureRecognizerImpl
sub(AbstractFeatureVector, float)
- Method in class contextFold.features.
AbstractFeatureVector
The same as
add(AbstractFeatureVector, float)
, where
other
is being subtracted rather than added.
sub(AbstractFeatureVector)
- Method in class contextFold.features.
AbstractFeatureVector
The same as
sub(AbstractFeatureVector, float)
, where
amount
= 1.
sub(AbstractFeatureVector, float)
- Method in class contextFold.features.
DenseFeatureVector
sub(AbstractFeatureVector)
- Method in class contextFold.features.
DenseFeatureVector
SuffixAdder
- Class in
contextFold.common
SuffixAdder(String)
- Constructor for class contextFold.common.
SuffixAdder
SuffixAdder(StringModifier, String)
- Constructor for class contextFold.common.
SuffixAdder
sum()
- Method in class contextFold.features.
AbstractFeatureVector
superAlphabet(int, int)
- Static method in class contextFold.features.
WordFeatureCalculator
superOffsets(int[], int[])
- Static method in class contextFold.features.
SinglePosContext
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