+//assumes you have added all the template sequences using the addSequence function and run generateDB.
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
+ try{
+ vector<int> topMatches;
+ float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score;
+ Scores.clear();
+
+ ofstream queryFile;
+
+ m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ queryFile << '>' << seq->getName() << endl;
+ queryFile << seq->getUnaligned() << endl;
+ queryFile.close();
+
+ // the goal here is to quickly survey the database to find the closest match. To do this we are using the default
+ // wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+//7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
+ string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+ system(blastCommand.c_str());
+
+ ifstream m8FileHandle;
+ m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+
+ string dummy, eScore;
+ int templateAccession;
+ m->gobble(m8FileHandle);
+
+ while(!m8FileHandle.eof()){
+ m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
+ //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t';
+
+ //get rest of junk in line
+ //while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; }else{ cout << c; } } //
+ //cout << endl;
+ m->gobble(m8FileHandle);
+ if (score >= minPerID) {
+ topMatches.push_back(templateAccession);
+ Scores.push_back(searchScore);
+ }
+//cout << templateAccession << endl;
+ }
+ m8FileHandle.close();
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
+//cout << "\n" ;
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosestMegaBlast");
+ exit(1);
+ }
+}
+/**************************************************************************************************/