Package org.biojava.nbio.alignment

Class StandardRescoreRefiner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

org.biojava.nbio.alignment.StandardRescoreRefiner<S,C>

All Implemented Interfaces:

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

public class StandardRescoreRefiner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends AbstractScorer
implements RescoreRefiner<S,C>

Constructor Summary

Constructors

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

Method Summary

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.
org.biojava.nbio.core.alignment.template.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.

Methods inherited from class org.biojava.nbio.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.biojava.nbio.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the computation time in nanoseconds

getProfile

public org.biojava.nbio.core.alignment.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the alignment profile

getMaxScore

public double getMaxScore()

Description copied from interface: Scorer

Returns maximum possible score.

Specified by:

getMaxScore in interface Scorer

Returns:

maximum possible score

getMinScore

public double getMinScore()

Description copied from interface: Scorer

Returns minimum possible score.

Specified by:

getMinScore in interface Scorer

Returns:

minimum possible score

getScore

public double 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