Aligner<S,C>, RescoreRefiner<S,C>, Scorerpublic class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound> extends AbstractScorer implements RescoreRefiner<S,C>
| Constructor | Description |
|---|---|
StandardRescoreRefiner(Alignments.PairInProfileScorerType pips,
Alignments.ProfileProfileAlignerType ppa) |
| Modifier and Type | Method | Description |
|---|---|---|
long |
getComputationTime() |
Returns the computation time needed for an alignment computed in nanoseconds.
|
double |
getMaxScore() |
Returns maximum possible score.
|
double |
getMinScore() |
Returns minimum possible score.
|
Alignments.PairInProfileScorerType |
getPairInProfileScorer() |
Returns class type of pairwise scoring subroutine.
|
Profile<S,C> |
getProfile() |
Returns the alignment
Profile produced by this alignment algorithm. |
Alignments.ProfileProfileAlignerType |
getProfileProfileAligner() |
Returns class type of profile-profile alignment subroutine.
|
double |
getScore() |
Returns score resulting from algorithm.
|
getDistance, getDistance, getSimilarity, getSimilarityclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetDistance, getDistance, getSimilarity, getSimilaritypublic StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)
public Alignments.PairInProfileScorerType getPairInProfileScorer()
RescoreRefinergetPairInProfileScorer in interface RescoreRefiner<S extends Sequence<C>,C extends Compound>public Alignments.ProfileProfileAlignerType getProfileProfileAligner()
RescoreRefinergetProfileProfileAligner in interface RescoreRefiner<S extends Sequence<C>,C extends Compound>public long getComputationTime()
Alignerpublic Profile<S,C> getProfile()
AlignerProfile produced by this alignment algorithm.public double getMaxScore()
ScorergetMaxScore in interface Scorerpublic double getMinScore()
ScorergetMinScore in interface Scorerpublic double getScore()
ScorerScorer.getScore() - Scorer.getMinScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).