Пример #1
0
 private AbstractSequence cutRegion(
     AbstractSequence s, BlastAnalysis.Result blastResult, BlastAnalysis.Region region) {
   int rs = Math.max(0, region.getBegin() - blastResult.getStart());
   int re = Math.min(s.getLength(), s.getLength() - (blastResult.getEnd() - region.getEnd()));
   AbstractSequence s2 = re > rs ? new SubSequence(s.getName(), s.getDescription(), s, rs, re) : s;
   return s2;
 }
Пример #2
0
  private List<Region> findOverlappingRegions(Result blastResult) {
    List<Region> result = new ArrayList<Region>();
    for (BlastAnalysis.Region region : blastResult.getReference().getRegions())
      if (region.overlaps(blastResult.getStart(), blastResult.getEnd(), MINIMUM_REGION_OVERLAP))
        result.add(region);

    return result;
  }