S
- C
- PairwiseSequenceScorer<S,C>
, Scorer
public class SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound> extends AbstractScorer implements PairwiseSequenceScorer<S,C>
Constructor | Description |
---|---|
SubstitutionMatrixScorer(SequencePair<S,C> pair,
SubstitutionMatrix<C> matrix) |
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.
|
getDistance, getDistance, getSimilarity, getSimilarity
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getDistance, getDistance, getSimilarity, getSimilarity
public SubstitutionMatrixScorer(SequencePair<S,C> pair, SubstitutionMatrix<C> matrix)
public double getMaxScore()
Scorer
getMaxScore
in interface Scorer
public double getMinScore()
Scorer
getMinScore
in interface Scorer
public double getScore()
Scorer
Scorer.getScore()
- Scorer.getMinScore()
) / (Scorer.getMaxScore()
- Scorer.getMinScore()
).public S getQuery()
PairwiseSequenceScorer
public S getTarget()
PairwiseSequenceScorer