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A
- Static variable in class contextFold.rna.
RNA
AbstractFeatureVector
- Class in
contextFold.features
A weight vector object.
AbstractFeatureVector()
- Constructor for class contextFold.features.
AbstractFeatureVector
absWeightComparator
- Static variable in class contextFold.features.
FeatureManager
acc
- Variable in class contextFold.features.
DenseFeatureVector
add(AbstractFeatureVector, float)
- Method in class contextFold.features.
AbstractFeatureVector
Adds to this object another weight vector.
add(AbstractFeatureVector)
- Method in class contextFold.features.
AbstractFeatureVector
The same as
add(AbstractFeatureVector, float)
, where
amount
= 1.
add(AbstractFeatureVector)
- Method in class contextFold.features.
DenseFeatureVector
addAllBasepairContextUpToLength(int)
- Method in class contextFold.features.
FeatureManager
addAndBindLengthTemplates(int...)
- Method in class contextFold.models.
FeatureSetter
addArg(String, String, String)
- Method in class contextFold.common.
CmdArgumentsHandler
addArg(String, String)
- Method in class contextFold.common.
CmdArgumentsHandler
addBaseContext(ContextFeatureExtractor, Boolean)
- Method in class contextFold.features.
FeatureManager
Context adding
addBaseContexts(SinglePosContext[])
- Method in class contextFold.features.
FeatureManager
addBasepairContext(ContextFeatureExtractor, Boolean)
- Method in class contextFold.features.
FeatureManager
addBasepairContext(FeatureExtractor, FeatureExtractor)
- Method in class contextFold.features.
FeatureManager
addBasepairTemplates(String)
- Method in class contextFold.features.
FeatureManager
addBaseTemplates(String)
- Method in class contextFold.features.
FeatureManager
addBinedArg(String, String, StringModifier, String)
- Method in class contextFold.common.
CmdArgumentsHandler
addEnumArg(String, String, int, String...)
- Method in class contextFold.common.
CmdArgumentsHandler
addFold(int[])
- Method in class contextFold.rna.
RNA
addFold(String)
- Method in class contextFold.rna.
RNA
addFold(String, int)
- Method in class contextFold.rna.
RNA
addRequiredArg(String, String)
- Method in class contextFold.common.
CmdArgumentsHandler
addTemplate(String, FeatureExtractor)
- Method in class contextFold.features.
FeatureManager
addTemplate(String, ValueCalculator)
- Method in class contextFold.features.
FeatureManager
addTemplates(String, FeatureExtractor...)
- Method in class contextFold.features.
FeatureManager
addTemplates(String, ContextFeatureExtractor[], int...)
- Method in class contextFold.models.
FeatureSetter
ALL_RNA_CHARS
- Static variable in class contextFold.rna.
RNA
allFeatureValues(Comparator<FeatureManager.Feature>, boolean)
- Method in class contextFold.features.
FeatureManager
ALPHABET_SIZE
- Static variable in class contextFold.features.
WordFeatureCalculator
alphabetIx
- Variable in class contextFold.features.
SinglePosContext
alphabetMap(int, int)
- Static method in class contextFold.features.
WordFeatureCalculator
alphabetMaps
- Static variable in class contextFold.features.
WordFeatureCalculator
ALPHABETS
- Static variable in class contextFold.features.
WordFeatureCalculator
ANNOTATION_GROUP
- Static variable in class contextFold.rna.
OneLineReader
AnnotationFilter
- Class in
contextFold.rna
AnnotationFilter(String, String)
- Constructor for class contextFold.rna.
AnnotationFilter
annotationLineStart
- Static variable in class contextFold.rna.
RNA
annotationPattern
- Static variable in class contextFold.rna.
RNA
annotationRegexp
- Static variable in class contextFold.rna.
RNA
annotations
- Variable in class contextFold.rna.
RNA
annotationsMap
- Variable in class contextFold.rna.
RNA
annotationSplit
- Static variable in class contextFold.rna.
RNA
average()
- Method in class contextFold.features.
DenseFeatureVector
Setting weights to the average values over all updates.
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