string qAligned = query->getAligned();
string newQuery = "";
-
+
//sort parents by region start
sort(parents.begin(), parents.end(), compareRegionStart);
//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;
}
//set query to new aligned string
query->setAligned(newQuery);
-
+
//free memory
for (int i = 0; i < queryParts.size(); i++) { delete queryParts[i]; }
for (int i = 0; i < parentParts.size(); i++) { delete parentParts[i]; }