+vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db, int num) {
+ try {
+
+ vector<Sequence*> refResults;
+
+ //get parts of query
+ 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;
+ vector<int> smaller;
+ vector<int> larger;
+
+ if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; larger = tempIndexesLeft; }
+ else { smaller = tempIndexesLeft; larger = tempIndexesRight; }
+
+ //merge results
+ map<int, int> seen;
+ map<int, int>::iterator it;
+ vector<int> mergedResults;
+ for (int i = 0; i < smaller.size(); i++) {
+ if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+
+ //add left if you havent already
+ it = seen.find(smaller[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(smaller[i]);
+ seen[smaller[i]] = smaller[i];
+ }
+
+ //add right if you havent already
+ it = seen.find(larger[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(larger[i]);
+ seen[larger[i]] = larger[i];
+ }
+ }
+
+ for (int i = smaller.size(); i < larger.size(); i++) {
+ if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+
+ //add right if you havent already
+ it = seen.find(larger[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(larger[i]);
+ seen[larger[i]] = larger[i];
+ }
+ }
+
+ for (int i = 0; i < mergedResults.size(); i++) {
+ //cout << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl;
+ if (db[mergedResults[i]]->getName() != q->getName()) {
+ Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
+ refResults.push_back(temp);
+
+ }
+ }
+
+
+// for(int i=0;i<refResults.size();i++){
+// cout << refResults[i]->getName() << endl;
+// }
+
+ delete queryRight;
+ delete queryLeft;
+
+ return refResults;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getBlastSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db, int num) {
+ try {
+ vector<Sequence*> refResults;
+
+ //get parts of query
+ 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
+
+ Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
+ Sequence* queryRight = new Sequence(q->getName(), rightQuery);
+
+ vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, num);
+ vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, num);
+
+ //merge results
+ map<int, int> seen;
+ map<int, int>::iterator it;
+ vector<int> mergedResults;
+ for (int i = 0; i < tempIndexesLeft.size(); i++) {
+
+ if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+
+ //add left if you havent already
+ it = seen.find(tempIndexesLeft[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(tempIndexesLeft[i]);
+ seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
+ }
+
+ //add right if you havent already
+ it = seen.find(tempIndexesRight[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(tempIndexesRight[i]);
+ seen[tempIndexesRight[i]] = tempIndexesRight[i];
+ }
+ }
+
+ //numWanted = mergedResults.size();
+
+ //cout << q->getName() << endl;
+
+ for (int i = 0; i < mergedResults.size(); i++) {
+ //cout << db[mergedResults[i]]->getName() << endl;
+ if (db[mergedResults[i]]->getName() != q->getName()) {
+ Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
+ refResults.push_back(temp);
+ }
+ }
+ //cout << endl;
+ delete queryRight;
+ delete queryLeft;
+
+ return refResults;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getKmerSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+