A B C D E F G H I J L M N O P R S T U V W X

S

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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