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;
}
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;
}