@Override
protected void init(AlignMatrix<Double> matrix) {
matrix.set(0.0);
for (int row = 1; row < matrix.getRows(); row++) {
matrix.set(-1.0 * gapOpen * row, row, Position.FIRST);
}
for (int column = 1; column < matrix.getColumns(); column++) {
matrix.set(-1.0 * gapOpen * column, Position.FIRST, column);
}
}
@Override
protected double score(
AlignMatrix<Double> matrix,
int row,
int column,
CharSequence a,
CharSequence b,
int direction) {
double score = matrix.get(row, column);
if (direction == DIRECTION_DIAGONAL) {
score += this.match(a.charAt(row), b.charAt(column));
} else {
score -= gapOpen;
}
return score;
}