- alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+ if ((queryParts[i]->getUnaligned() == "") || (parentParts[i]->getUnaligned() == "")) {;}
+ else {
+ alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase