public SubstitutionMatrixScorer(SequencePair<S, C> pair, SubstitutionMatrix<C> matrix) {
super();
this.query = pair.getQuery().getOriginalSequence();
this.target = pair.getTarget().getOriginalSequence();
this.matrix = matrix;
for (int i = 1; i <= pair.getLength(); i++) {
C query = pair.getCompoundAt(1, i);
C target = pair.getCompoundAt(2, i);
score += matrix.getValue(query, target);
}
}
/**
* @return The minimum score the query could be assigned when aligned against any target sequence.
*/
@Override
public double getMinScore() {
// assume nothing about the matrix
double score = 0;
for (C queryC : query.getAsList()) {
short min = Short.MAX_VALUE;
for (Short value : matrix.getRow(queryC).values()) {
if (value < min) min = value;
}
score += min;
}
return score;
}
/**
* @return The maximum score the query could be assigned when aligned against any target sequence.
*/
@Override
public double getMaxScore() {
// assume nothing about the matrix
double score = 0;
for (C queryC : query.getAsList()) {
short max = Short.MIN_VALUE;
for (Short value : matrix.getRow(queryC).values()) {
if (value > max) max = value;
}
score += max;
}
return score;
}