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java.lang.Objectorg.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.FractionalSimilarityScorer<S,C>
S
- each Sequence
of the alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic class FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound>
Implements an algorithm which computes a score for a sequence alignment pair. The reported score is the number of
alignment columns which have similar Compound
s.
Constructor Summary | |
---|---|
FractionalSimilarityScorer(PairwiseSequenceAligner<S,C> aligner)
Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner. |
|
FractionalSimilarityScorer(SequencePair<S,C> pair)
Creates a fractional similarity scorer for an aligned pair of sequences. |
Method Summary | |
---|---|
int |
getMaxScore()
Returns maximum possible score. |
int |
getMinScore()
Returns minimum possible score. |
S |
getQuery()
Returns the first sequence of the pair. |
int |
getScore()
Returns score resulting from algorithm. |
S |
getTarget()
Returns the second sequence of the pair. |
Methods inherited from class org.biojava3.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.biojava3.alignment.template.Scorer |
---|
getDistance, getDistance, getSimilarity, getSimilarity |
Constructor Detail |
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public FractionalSimilarityScorer(PairwiseSequenceAligner<S,C> aligner)
aligner
- a pairwise sequence alignerpublic FractionalSimilarityScorer(SequencePair<S,C> pair)
pair
- an aligned pair of sequencesMethod Detail |
---|
public S getQuery()
PairwiseSequenceScorer
getQuery
in interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
public S getTarget()
PairwiseSequenceScorer
getTarget
in interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
public int getMaxScore()
Scorer
getMaxScore
in interface Scorer
public int getMinScore()
Scorer
getMinScore
in interface Scorer
public int getScore()
Scorer
Scorer.getScore()
- Scorer.getMinScore()
) / (Scorer.getMaxScore()
- Scorer.getMinScore()
).
getScore
in interface Scorer
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