Package org.biojava.nbio.alignment

Class FractionalIdentityScorer<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.FractionalIdentityScorer<S,C>

Type Parameters:

S - each Sequence of the alignment pair is of type S

C - each element of an AlignedSequence is a Compound of type C

All Implemented Interfaces:

PairwiseSequenceScorer<S,C>, Scorer

Direct Known Subclasses:

FractionalIdentityInProfileScorer

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

Implements an algorithm which computes a score for a sequence alignment pair. The reported score is the number of alignment columns which have identical Compounds.

Author:

Mark Chapman

Constructor Summary

Constructors

Constructor	Description
FractionalIdentityScorer(PairwiseSequenceAligner<S,C> aligner)	Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
FractionalIdentityScorer(org.biojava.nbio.core.alignment.template.SequencePair<S,C> pair)	Creates a fractional identity scorer for an aligned pair of sequences.

Method Summary

Modifier and Type	Method	Description
double	getMaxScore()	Returns maximum possible score.
double	getMinScore()	Returns minimum possible score.
S	getQuery()	Returns the first sequence of the pair.
double	getScore()	Returns score resulting from algorithm.
S	getTarget()	Returns the second sequence of the pair.

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

FractionalIdentityScorer

public FractionalIdentityScorer(PairwiseSequenceAligner<S,C> aligner)

Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.

Parameters:

aligner - a pairwise sequence aligner

FractionalIdentityScorer

public FractionalIdentityScorer(org.biojava.nbio.core.alignment.template.SequencePair<S,C> pair)

Creates a fractional identity scorer for an aligned pair of sequences.

Parameters:

pair - an aligned pair of sequences

Method Detail

getQuery

public S getQuery()

Description copied from interface: PairwiseSequenceScorer

Returns the first sequence of the pair.

Specified by:

getQuery in interface PairwiseSequenceScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the first sequence of the pair

getTarget

public S getTarget()

Description copied from interface: PairwiseSequenceScorer

Returns the second sequence of the pair.

Specified by:

getTarget in interface PairwiseSequenceScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the second sequence of the pair

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