+ // generating a fasta file with unaligned template
+ unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
+ unalignedFastaFile << seq.getUnaligned() << endl;
+ unalignedFastaFile.close();
+
+ count++;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "addSequence");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void BlastDB::generateDB() {
+ try {
+
+ //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+
+ path = globaldata->argv;
+ path = path.substr(0, (path.find_last_of('m')));
+
+ string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
+ // option tells formatdb that seqs are DNA, not prot
+ //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "generateDB");
+ exit(1);
+ }
+}
+#ifdef USE_MPI
+/**************************************************************************************************/
+int BlastDB::MPISend(int receiver) {
+ try {
+
+ //send gapOpen - float
+ MPI_Send(&gapOpen, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send gapExtend - float
+ MPI_Send(&gapExtend, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send match - float
+ MPI_Send(&match, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send mismatch - float
+ MPI_Send(&misMatch, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ return 0;