org.biojava.nbio.alignment

Class SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

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

Type Parameters:

S -

C -

All Implemented Interfaces:

PairwiseSequenceScorer<S,C>, Scorer

public class SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound>
extends AbstractScorer
implements PairwiseSequenceScorer<S,C>

Scores using a substitution matrix. Specifically, the score is the sum of the substitution matrix entries corresponding to the alignment. Gaps are scored according to the substitution matrix, just as matches and mismatches.

Author:

dmyersturnbull

Constructor Summary

Constructors

Constructor and Description
SubstitutionMatrixScorer(SequencePair<S,C> pair, SubstitutionMatrix<C> matrix)

Method Summary

Methods

Modifier and Type	Method and 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

SubstitutionMatrixScorer

public SubstitutionMatrixScorer(SequencePair<S,C> pair,
                        SubstitutionMatrix<C> matrix)

Method Detail

getMaxScore

public double getMaxScore()

Description copied from interface: Scorer

Returns maximum possible score.

Specified by:

getMaxScore in interface Scorer

Returns:

The maximum score the query could be assigned when aligned against any target sequence.

getMinScore

public double getMinScore()

Description copied from interface: Scorer

Returns minimum possible score.

Specified by:

getMinScore in interface Scorer

Returns:

The minimum score the query could be assigned when aligned against any target sequence.

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

getQuery

public S getQuery()

Description copied from interface: PairwiseSequenceScorer

Returns the first sequence of the pair.

Specified by:

getQuery in interface PairwiseSequenceScorer<S extends Sequence<C>,C extends 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 Sequence<C>,C extends Compound>

Returns:

the second sequence of the pair