//find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
Sequence* newSeq = new Sequence(q->getName(), q->getAligned());
runFilter(newSeq);
- refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted);
+ refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted, minSim);
delete newSeq;
}else if (searchMethod == "blast") {
refSeqs = getBlastSeqs(q, thisTemplate, numWanted); //fills indexes
string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
- Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
- Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
-
- vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
- vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+ Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
+ Sequence* queryRight = new Sequence(q->getName(), rightQuery);
+ vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim);
+ vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim);
+ cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl;
vector<int> smaller;
vector<int> larger;