Package org.biojava.nbio.alignment

Class FractionalSimilarityInProfileScorer<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.FractionalSimilarityScorer<S,C>

org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer<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:

PairInProfileScorer<S,C>, PairwiseSequenceScorer<S,C>, Scorer

public class FractionalSimilarityInProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends FractionalSimilarityScorer<S,C>
implements PairInProfileScorer<S,C>

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

Author:

Mark Chapman

Constructor Summary

Constructors

Constructor	Description
FractionalSimilarityInProfileScorer(org.biojava.nbio.core.alignment.template.Profile<S,C> profile, int query, int target)	Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.

Method Summary

Modifier and Type	Method	Description
org.biojava.nbio.core.alignment.template.Profile<S,C>	getProfile()	Returns the Profile from which the aligned pair originated.

Methods inherited from class org.biojava.nbio.alignment.FractionalSimilarityScorer

getMaxScore, getMinScore, getQuery, getScore, getTarget

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.PairwiseSequenceScorer

getQuery, getTarget

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Constructor Detail

FractionalSimilarityInProfileScorer

public FractionalSimilarityInProfileScorer(org.biojava.nbio.core.alignment.template.Profile<S,C> profile,
                                           int query,
                                           int target)

Creates a fractional similarity scorer for an aligned pair of sequences in the given alignment profile.

Parameters:

profile - alignment profile containing pair of sequences

query - index in the profile of the first sequence of the pair

target - index in the profile of the second sequence of the pair

Method Detail

getProfile

public org.biojava.nbio.core.alignment.template.Profile<S,C> getProfile()

Description copied from interface: PairInProfileScorer

Returns the Profile from which the aligned pair originated.

Specified by:

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

Returns:

the original profile