Aligner<S,C>
, MatrixAligner<S,C>
, PairInProfileScorer<S,C>
, PairwiseSequenceAligner<S,C>
, PairwiseSequenceScorer<S,C>
, PartitionRefiner<S,C>
, ProfileProfileAligner<S,C>
, ProfileProfileScorer<S,C>
, RescoreRefiner<S,C>
AbstractMatrixAligner
, AbstractPairwiseSequenceAligner
, AbstractProfileProfileAligner
, AbstractScorer
, AnchoredPairwiseSequenceAligner
, FractionalIdentityInProfileScorer
, FractionalIdentityScorer
, FractionalSimilarityInProfileScorer
, FractionalSimilarityScorer
, GuanUberbacher
, NeedlemanWunsch
, SimpleProfileProfileAligner
, SmithWaterman
, StandardRescoreRefiner
, SubstitutionMatrixScorer
public interface Scorer
Modifier and Type | Method | Description |
---|---|---|
double |
getDistance() |
Returns score as a distance between 0.0 and 1.0.
|
double |
getDistance(double scale) |
Returns score as a distance between 0.0 and scale.
|
double |
getMaxScore() |
Returns maximum possible score.
|
double |
getMinScore() |
Returns minimum possible score.
|
double |
getScore() |
Returns score resulting from algorithm.
|
double |
getSimilarity() |
Returns score as a similarity between 0.0 and 1.0.
|
double |
getSimilarity(double scale) |
Returns score as a similarity between 0.0 and scale.
|
double getDistance()
getMaxScore()
- getScore()
) /
(getMaxScore()
- getMinScore()
).double getDistance(double scale)
getMaxScore()
-
getScore()
) / (getMaxScore()
- getMinScore()
).scale
- maximum distancedouble getMaxScore()
double getMinScore()
double getScore()
getScore()
- getMinScore()
) / (getMaxScore()
- getMinScore()
).double getSimilarity()
getScore()
- getMinScore()
) /
(getMaxScore()
- getMinScore()
).double getSimilarity(double scale)
getScore()
-
getMinScore()
) / (getMaxScore()
- getMinScore()
).scale
- maximum similarity