Examples with HitHsps gov.nih.nlm.ncbi.blast.HitHsps used on opensource projects

Example 1 with HitHsps

use of gov.nih.nlm.ncbi.blast.HitHsps in project jvarkit by lindenb.

the class MergeSplittedBlast method merge.

private Hit merge(List<Hit> hits) {
    Hit first = hits.get(0);
    Split firstSplit = parse(first);
    Hit newHit = new Hit();
    newHit.setHitAccession(first.getHitAccession());
    newHit.setHitDef(firstSplit.chrom);
    newHit.setHitId(first.getHitId());
    newHit.setHitNum(first.getHitNum());
    newHit.setHitLen(String.valueOf(firstSplit.len));
    newHit.setHitHsps(new HitHsps());
    List<Hsp> hsps = new ArrayList<Hsp>();
    for (Hit h0 : hits) {
        /* fix hit_from/hit_to */
        Split split = parse(h0);
        List<Hsp> L = h0.getHitHsps().getHsp();
        for (int i = 0; i < L.size(); ++i) {
            Hsp newHsp = BlastHspAlignment.cloneHsp(L.get(i));
            BlastHspAlignment aln = new BlastHspAlignment(newHsp);
            int h_from = aln.getHitFrom1();
            int h_to = aln.getHitTo1();
            h_from += (split.start1 - 1);
            h_to += (split.start1 - 1);
            newHsp.setHspHitFrom(String.valueOf(h_from));
            newHsp.setHspHitTo(String.valueOf(h_to));
            hsps.add(newHsp);
        }
    }
    boolean done = false;
    while (!done) {
        done = true;
        for (int i = 0; i + 1 < hsps.size(); ++i) {
            Hsp hsp0 = hsps.get(i);
            for (int j = i + 1; j < hsps.size(); ++j) {
                // debug("comparing hsp "+i+" vs "+j+" N="+hsps.size());
                Hsp hsp1 = hsps.get(j);
                Hsp newHitHsp = merge(hsp0, hsp1);
                if (newHitHsp != null) {
                    hsps.set(i, newHitHsp);
                    hsps.remove(j);
                    done = false;
                    break;
                }
            }
            if (!done)
                break;
        }
    }
    for (int i = 0; i < hsps.size(); ++i) hsps.get(i).setHspNum(String.valueOf(i + 1));
    newHit.getHitHsps().getHsp().addAll(hsps);
    return newHit;
}