/**
 * @author Alexei Drummond
 */
public class Test {

    static final int PROTEIN_REPS = 6000;
    static final int NUCLEOTIDE_REPS = 10;

    public static void main(String[] args) {

        String pep1 = "MRVISRARSACTWTSCTSLSPCSTSCPPSPAAPTLLRRRSLPQQRRRPSSSPNRRVRGVTTSPCPTRSLVYKRRVGAPQRLCAETVATMQAQEANALLLSRMEALEWFKKFTVWLRVYAIFIFQLAFSFGLGSVFWLGFPQNRNFCVENYSFFLTVLVPIVCMFITYTLGNEHPSNATVLFIYLLANSLTAAIFQMCSESRVLVGSYVMTLALFISFTGLAFLGGRDRRRWKCISCVYVVMLLSFLTLALLSDADWLQKIVVTLCAFSISFFLGILAYDSLMVIFFCPPNQCIRHAVCLYLDSMAIFLTLLLMLSGPRWISLSDGVPLDNGTLTAASTTGKS";
        String pep2 = "MPRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVAHLVRVEVVE";

        String nuc1 = "TGGAATGGGTGCTAGGTGAAGGCTTTGTTGAATCAGGATGCTGAGCTGGTGTTTTTACAGGTCCAGATATGATGAGCTGGAGTTTTGGTAGGCCCAGGTACCTCCTCCAAAATTGACCACATAATTGGTCACAAATCAGGCCTCCACAGATACAAAAATATTGAAATTATCCCATGCATCCTGTCTGATCACCACAGACTAAGGCTGATCTTCAATAACAACATAAAAATAGAAAGCCAGGTTCACTGCTGCGGCTGCGCCTCCTTGTTCTCAGCGTCACCACTGCCGCCATGCCCGGAGGGTTGCTTCTCGGGGACGAAGCCCCCAACTTTGAGGCCAATACCACCATCGGCCGCATCCGCTTCCACGATTTCCTGGGAGATTCATGGGGCATTCTCTTTTCCCACCCACGGGACTTTACCCCAGTGTGCACCACAGAACTTGGCAGAGCTGCAAAGCTGGCGCCAGAGTTCGCCAAGAGGAATGTTAAGTTGATTGCTCTTTCAATAGACAGTGTTGAGGATCATCTTGCCTGGAGCAAGGACATCAATGCTTACAATGGTGAAACACCCACGGAAAAGTTGCCATTTCCCATCATTGATGATAAGGGCAGGGACCTTGCCATCCTTTTGGGCATGTTGGATCCAGTCGAGAAGGACGATAACAACATGCCTGTGACGGCCCGTGTGGTGTTCATTTTTGGCCCTGACAAGAAACTGAAGCTGTCTATCCTCTACCCTGCCACCACGAGCAGGAACTTTGATGAGATTCTCAGAGTGGTTGACTCTCTCCAGCTGACAGGCACAAAGCCGGTTGCCACCCCAGTTGACTGGAAGAAGGGAGAGAGCGTGATGGTAGTCCCCACCCTCTCCGAAGAGGAAGCCAAACAATGTTTCCCTAAAGGAGTCTTCACCAAAGAGCTCCCGTCTGGCAAAAAATACCTCCGTTATACACCCCAGCCTTAAGTCTTTGCGGAAATTGGGGCTGCATCTGCACGTCCAGCACTGGGGCCTGAGGACGTCAGCCGGCAGCCGTGGGTCCTTGCAGCAGGTCCGTAGAAAGATCGTGGCATGATCACAGCCGGTCCTGTAGATCGCTCGCTATACTACTGGGTCATTAAATGGAAATGGCACCAAAACCTTCTCGGGATTCTTTACTCTGTGCCTTCGCCAGCATTCTGCCCCTCTGCCTGTCACAGTGCCCTACTGACTGGCTCTCTTTGAAACGAATTATGTATTGAAGATTCCTTAGGTCTCTGCAGGGTCTTTGATCAGCAAGCAAGGTAGTGTCAGTGTGGGCTCTGTGCTAGAATGATGAAACACCTTTTGTAGCTTTCCGAACGGAATCTTCTGTTACCCATTTTGGAGAGCACTGACATGGGGAGAAGCTTTCAATTCTGTATTTTTAGTAAATAAAGTGGGGACAGCCGGGAGAATTCTTACAGGGAATCTATTGTAAGTTTCTATCGAAGTGGGCTCAGAAAGCCTTTCGCCTCCCAAGAGTGCGCATGTACCTCCTAGAGTTTCCACATCTGCTCTCTGGTGATGTCTGCCTGTGAACGCACCTTATAAAAGACGGGCGGTGACAGTGTTTTACCACTCAGTGTCCTAGTAGTGGGTGGCCATTTCTGAATTCTGCTTTTTGAGGTTCAACAAATAAAATCCTGATCAGAAAAAAAAAAAAATAGAAAGCCAACATTCATGTGGAAACTGAACAACACTACTCAATGATTCCTTGGTCAGAGATGAAATAAAGAAAGAAATTAAAGACTTTTTAGAGTTTAATGAAAATGAAGCCACAACATACCCAAACTTATGGGACACAATGAAGGCATTTCTAAGAGGAAAACTCATAGCCCTGAGTGCATCCAAAGGAAAAAAAAAAAAACCTAGAGAGAGTGTACACTAGCAGCCTGACTGCACACTTAGAAGCTCTGCAAAAAAAGGAATCAAATTCACCCAAGAGGAATAGACAGCAGGAAATAATCAAACTTAGGGCTGAAATCAACCAAATGGAAACAAAAAGAACTATTCAAAGAGTGGGCCAAACCAGGAGCTAGTTCTTTGAGAAAATCAACAAGATAGATAAACCCTTAGCCAGACTCACTAGAGGGCACAGGGACAGCATCCTAATTAACAAAATCAGAACTGAAAAGGGAGACATAACAACAGATCCTGAAGAAATCCAAAACACCACCAGATCCTCTACAAAAGGCTATACTCAACAAAACTGGAAAACCTGGATGAAAGGAAAAGCTTCTAGACAGA";
        String nuc2 = "GTTAACCCTTTAAGGGTGCTGGCTCTTTTGCTTTAAAATTCAACATGTGTTCTTTTGAAGGATATTAATTCCAAAGCAGGCCGTTTGTTCTATACGTTCCCGGAACTCAGGTTCTTCAAGGAAATAGGGTTTTAATTGGGTGGGTTAATTATCATGAGCCTGCCCCCACAAAGGGGGTTTGGGCAGTTAATAAATAGTAGCCATTTCAAAAGGTTAAATTCCCTCTCATTTCAGAGGAGGCACAACTCCCACAGTTTGATCTGATGTTGTCTTGTCAGTCGTATCCATTGGTTCATGTGACAATAAATCCTTCTTTATTTGAACCCATTCTAAATCTCTAGTTATTTGTAATATTCCTTGAGTGAGTAATGGCTTAGGTAGGAGTACCGTTCAGCTTTATTAAGATCCCTTGAGGGCTTGTGATGGTGGTTCCTTGGCTTGCAGAGTGGTATTCTCAGCTTGGTGAGATGCAGAGACAGACCCGTGTCAGCTTTAAGAGTCCATCCCCTTTTCTCTTGTTTAAGGACATCAATGCTTACAATGGTGAAACACCCACGGAAAAGTTGCCATTTCCCATCATTGATGATAAGGGCAGGGACCTTGCCATCCTTTTGGGCATGTTGGATCCAGTCGAGAAGGACGATAACAACATGCCTGTGACGGCCCGTGTGGTGAGTCGGAAGGCTGTGTGAATGCTTGAGCCAATACAAGAGGAATATGTACAGTTGTGCATGTTAGAGCAGTGGTTCTCAGCCTTTGGGGTCATGACCCCTTTGGGGGGGGTCAAACAACCTTTTCACAGGGGTCACACACAGAATATTCTTCCTATCAGTATTTACATCATGATTCATAACAGTAGCAAAATTACAGTTATGAAGTAGCAATAAAATAACTTGGGGGAATCACATGAGGGTCGCAGCATTGGGAAGGTTGAGGACCCCTCTGTGTTAGAGGAAGGGTGGACAGACTAGGAGGAGTCTTTCCCTCCCTCCTTTGGCTACCTAGTAATAAACTCCATTTTCCTCTGCCAGTTCTGTTTTCTTCCCTGGACTAAGGGGAAAAGAGGTGTATAGAGCTCATGATGCTGAGTGTCAGAAGCAGCTTTACCGTCATGTACTAACGAAGGCCTCCTGTGTGCTTTACAGGTGTTCATTTTTGGCCCTGACAAGAAACTGAAGCTGTCTATCCTCTACCCTGCCACCACGGGCAGGAACTTTGATGAGATTCTCAGAGTGGTTGACTCTCTCCAGCTGACAGGCACAAAGCCGGTTGCCACCCCAGTTGACAGGAAGGTAAAACTGCTCTTAAGAACTGGATGCCCAGCTTGCCAGAAAGATCCAAAGGACAGTCTCTCATGGCCACTTTCAGGATGTGGGTTTCTTGGGCCTTTATCTATTGTCCCAGTAGAGTGTCCCAGGAGGATTTGTTTAAGAGTTCATTCACACTGATTTGTATAAAACACAAACTGTGGTTTTTGCTAACCCTACATAATTCCAACAGATATAGGTCACAGTGATCCCAGAAGTTAAACATTCGTAACCCCAAAATCCCAGCTCCAAAGCGCTCCAAAATCCAAGACTTCTTGGTTTTTCTTTA";


        long startTime = System.currentTimeMillis();

        HitCounter counter = new MyHitCounter();

        ScoreMatrix matrix = new Blosum62();

        int count = 0;

        for (int i = 0; i < PROTEIN_REPS; i++) {

            count = counter.countHits(pep1, pep2, matrix, 3, 10);
        }

        long stopTime = System.currentTimeMillis();
        System.out.println("Protein test:");
        System.out.println("  hit count = " + count);
        System.out.println("  " +PROTEIN_REPS + " reps performed in " + (stopTime-startTime) + " ms");

        startTime = System.currentTimeMillis();

        counter = new MyHitCounter();

        matrix = new NucleotideScores(5,-4);

        count = 0;

        for (int i = 0; i < NUCLEOTIDE_REPS; i++) {

            count = counter.countHits(nuc1, nuc2, matrix, 11, 55);
        }

        stopTime = System.currentTimeMillis();
        System.out.println("Nucleotide test:");
        System.out.println("  hit count = " + count);
        System.out.println("  " +NUCLEOTIDE_REPS + " reps performed in " + (stopTime-startTime) + " ms");

    }
}