org.biojava3.alignment
Class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>

java.lang.Object
  org.biojava3.alignment.template.AbstractScorer
      org.biojava3.alignment.StandardRescoreRefiner<S,C>

All Implemented Interfaces:

Aligner<S,C>, RescoreRefiner<S,C>, Scorer

public class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
extends AbstractScorer
implements RescoreRefiner<S,C>

Constructor Summary

StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)

Method Summary

long	getComputationTime() Returns the computation time needed for an alignment computed in nanoseconds.
int	getMaxScore() Returns maximum possible score.
int	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.
int	getScore() Returns score resulting from algorithm.

Methods inherited from class org.biojava3.alignment.template.AbstractScorer

getDistance, getDistance, getSimilarity, getSimilarity

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava3.alignment.template.Scorer

getDistance, getDistance, getSimilarity, getSimilarity

Constructor Detail

StandardRescoreRefiner

public StandardRescoreRefiner(Alignments.PairInProfileScorerType pips,
                              Alignments.ProfileProfileAlignerType ppa)

Method Detail

getPairInProfileScorer

public Alignments.PairInProfileScorerType getPairInProfileScorer()

Description copied from interface: RescoreRefiner

Returns class type of pairwise scoring subroutine.

Specified by:

getPairInProfileScorer in interface RescoreRefiner<S extends Sequence<C>,C extends Compound>

Returns:

class type of pairwise scoring subroutine

getProfileProfileAligner

public Alignments.ProfileProfileAlignerType getProfileProfileAligner()

Description copied from interface: RescoreRefiner

Returns class type of profile-profile alignment subroutine.

Specified by:

getProfileProfileAligner in interface RescoreRefiner<S extends Sequence<C>,C extends Compound>

Returns:

class type of profile-profile alignment subroutine

getComputationTime

public long getComputationTime()

Description copied from interface: Aligner

Returns the computation time needed for an alignment computed in nanoseconds.

Specified by:

getComputationTime in interface Aligner<S extends Sequence<C>,C extends Compound>

Returns:

the computation time in nanoseconds

getProfile

public Profile<S,C> getProfile()

Description copied from interface: Aligner

Returns the alignment Profile produced by this alignment algorithm.

Specified by:

getProfile in interface Aligner<S extends Sequence<C>,C extends Compound>

Returns:

the alignment profile

getMaxScore

public int getMaxScore()

Description copied from interface: Scorer

Returns maximum possible score.

Specified by:

getMaxScore in interface Scorer

Returns:

maximum possible score

getMinScore

public int getMinScore()

Description copied from interface: Scorer

Returns minimum possible score.

Specified by:

getMinScore in interface Scorer

Returns:

minimum possible score

getScore

public int getScore()

Description copied from interface: Scorer

Returns score resulting from algorithm. This should normalize between 0 and 1 by calculating (Scorer.getScore() - Scorer.getMinScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).

Specified by:

getScore in interface Scorer

Returns:

score resulting from algorithm