+ bool needToGenerate = true;
+ string kmerDBName;
+ if(method == "kmer") {
+ database = new KmerDB(tempFile, kmerSize);
+
+ kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTest(kmerDBName.c_str());
+ if(kmerFileTest){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
+ if (GoodFile) { needToGenerate = false; }
+ }
+ }
+ else if(method == "suffix") { database = new SuffixDB(numSeqs); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
+ else if(method == "distance") { database = new DistanceDB(); }
+ else {
+ m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
+ m->mothurOutEndLine();
+ database = new KmerDB(tempFile, 8);
+ }
+
+ if (needToGenerate) {
+ for (int k = 0; k < rdb->referenceSeqs.size(); k++) {
+ Sequence temp(rdb->referenceSeqs[k].getName(), rdb->referenceSeqs[k].getAligned());
+ names.push_back(temp.getName());
+ database->addSequence(temp);
+ }
+ database->generateDB();
+ }else if ((method == "kmer") && (!needToGenerate)) {
+ ifstream kmerFileTest(kmerDBName.c_str());
+ database->readKmerDB(kmerFileTest);
+
+ for (int k = 0; k < rdb->referenceSeqs.size(); k++) {
+ names.push_back(rdb->referenceSeqs[k].getName());
+ }
+ }
+
+ database->setNumSeqs(numSeqs);
+
+ //sanity check
+ bool okay = phyloTree->ErrorCheck(names);
+
+ if (!okay) { m->control_pressed = true; }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences and generate the search databases.");m->mothurOutEndLine();
+
+ }else {
+
+ templateFile = tempFile;
+
+ int start = time(NULL);
+
+ m->mothurOut("Generating search database... "); cout.flush();
+ #ifdef USE_MPI
+ int pid, processors;
+ vector<unsigned long long> positions;
+ int tag = 2001;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);