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

D

DEBUG_MODE - Static variable in class contextFold.common.Env
 
defaultModel - Static variable in class contextFold.common.Env
 
DenseFeatureVector - Class in contextFold.features
A dense implementation of a feature vector
DenseFeatureVector(int) - Constructor for class contextFold.features.DenseFeatureVector
A constructor.
DenseFeatureVector(int, float) - Constructor for class contextFold.features.DenseFeatureVector
A constructor.
DenseFeatureVector(DenseFeatureVector) - Constructor for class contextFold.features.DenseFeatureVector
A copy constructor.
differenceFeatureVector(int[], int[], AbstractFeatureVector, RNA) - Method in interface contextFold.scoring.FoldEvaluator
Computes the feature difference between two foldings.
differenceFeatureVector(int[], int[], RNA) - Method in interface contextFold.scoring.FoldEvaluator
 
differenceFeatureVector(int[], int[], AbstractFeatureVector, RNA) - Method in class contextFold.scoring.FoldEvaluatorImpl
 
differenceFeatureVector(int[], int[], RNA) - Method in class contextFold.scoring.FoldEvaluatorImpl
 
dim() - Method in class contextFold.features.DenseFeatureVector
 
dimension - Variable in class contextFold.features.DenseFeatureVector
 
doIter(int, List<RNA>, int, int) - Method in class contextFold.learn.Learn
 
dot(T) - Method in interface contextFold.common.Dotable
Computes the dot-product of two vectors.
dot(AbstractFeatureVector) - Method in class contextFold.features.AbstractFeatureVector
 
dot(AbstractFeatureVector) - Method in class contextFold.features.DenseFeatureVector
 
Dotable<T> - Interface in contextFold.common
 
DoublePosContext - Class in contextFold.features
 
DoublePosContext(ContextFeatureExtractor, ContextFeatureExtractor) - Constructor for class contextFold.features.DoublePosContext
 

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