org.biojava3.alignment
Class FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound>
java.lang.Object
org.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.FractionalIdentityScorer<S,C>
org.biojava3.alignment.FractionalIdentityInProfileScorer<S,C>
- Type Parameters:
S
- each Sequence
of the alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type C
- All Implemented Interfaces:
- PairInProfileScorer<S,C>, PairwiseSequenceScorer<S,C>, Scorer
public class FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound>
- extends FractionalIdentityScorer<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 identical Compound
s.
- Author:
- Mark Chapman
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FractionalIdentityInProfileScorer
public FractionalIdentityInProfileScorer(Profile<S,C> profile,
int query,
int target)
- Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
- Parameters:
profile
- alignment profile containing pair of sequencesquery
- index in the profile of the first sequence of the pairtarget
- index in the profile of the second sequence of the pair
getProfile
public 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 Sequence<C>,C extends Compound>
- Returns:
- the original profile