createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
- //run filter on template
- for (int i = 0; i < templateSeqs.size(); i++) { if (m->control_pressed) { break; } runFilter(templateSeqs[i]); }
-
-
+ if (searchMethod == "distance") {
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+
+ //run filter on template copying templateSeqs into filteredTemplateSeqs
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
+ runFilter(newSeq);
+ filteredTemplateSeqs.push_back(newSeq);
+ }
+ }
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
}
-
+ //cout << endl << endl;
return 0;
}
catch(exception& e) {
string queryUnAligned = q->getUnaligned();
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
-
+//cout << "whole length = " << queryUnAligned.length() << '\t' << "left length = " << leftQuery.length() << '\t' << "right length = "<< rightQuery.length() << endl;
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;
+ //cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl;
vector<int> smaller;
vector<int> larger;