contextFold.scoring
Interface FoldEvaluator

All Known Implementing Classes:
FoldEvaluatorImpl

public interface FoldEvaluator


Method Summary
 void differenceFeatureVector(int[] guessFold, int[] goldFold, AbstractFeatureVector result, RNA rna)
          Computes the feature difference between two foldings.
 AbstractFeatureVector differenceFeatureVector(int[] guessFold, int[] goldFold, RNA rna)
           
 float scoreFold(RNA rna, int[] fold)
          Computes the score of a given sequence-folding pair.
 

Method Detail

scoreFold

float scoreFold(RNA rna,
                int[] fold)
Computes the score of a given sequence-folding pair.

Parameters:
rna - an RNA sequence.
fold - a folding of the sequence.
Returns:
the score of a given sequence-folding pair.

differenceFeatureVector

void differenceFeatureVector(int[] guessFold,
                             int[] goldFold,
                             AbstractFeatureVector result,
                             RNA rna)
Computes the feature difference between two foldings.

Parameters:
guessFold - a predicted folding of the RNA sequence.
goldFold - a known folding of the RNA sequence.
result - a feature vector, which feature weights correspond to feature differences between the two foldings. Negatively weighted features are those that appeared more in the predicted folding, positively weighted features are those that appeared more in the known folding, and zero weighted feature appeared the same in both foldings.
rna - an RNA sequence

differenceFeatureVector

AbstractFeatureVector differenceFeatureVector(int[] guessFold,
                                              int[] goldFold,
                                              RNA rna)