//align each peice to correct parent from results
for (int i = 0; i < queryParts.size(); i++) {
alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
Nast nast(alignment, queryParts[i], parentParts[i]);
delete alignment;
}
//align each peice to correct parent from results
for (int i = 0; i < queryParts.size(); i++) {
alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
Nast nast(alignment, queryParts[i], parentParts[i]);
delete alignment;
}