/**
 * A hit counter reports the number of matching words between two sequences.
 */
public interface HitCounter {

    /**
     * @param seq1 sequence 1
     * @param seq2 sequence 2
     * @param matrix the score matrix to be used to compare the sequences
     * @param T the similarity threshold
     * @param W the word size
     * @return the number of matching words of size W with similarity score at least T
     */
    public int countHits(String seq1, String seq2, ScoreMatrix matrix, int W, double T);
}