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

A

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.

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