queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
blastFileName = toString(randNumber) + ".blast";
+}
+/**************************************************************************************************/
+
+BlastDB::BlastDB() : Database() {
+
+ globaldata = GlobalData::getInstance();
+ count = 0;
+
+ int randNumber = rand();
+ dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = toString(randNumber) + ".blast";
+
}
/**************************************************************************************************/
return topMatches;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "findClosestSequences");
+ m->errorOut(e, "BlastDB", "findClosestSequences");
exit(1);
}
return topMatches;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "findClosest");
+ m->errorOut(e, "BlastDB", "findClosest");
exit(1);
}
}
count++;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "addSequence");
+ m->errorOut(e, "BlastDB", "addSequence");
exit(1);
}
}
void BlastDB::generateDB() {
try {
- //mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+ //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
- //mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
+ //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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "MPISend");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int BlastDB::MPIRecv(int sender) {
+ try {
+ MPI_Status status;
+
+ //receive gapOpen - float
+ MPI_Recv(&gapOpen, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive gapExtend - float
+ MPI_Recv(&gapExtend, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive match - float
+ MPI_Recv(&match, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive mismatch - float
+ MPI_Recv(&misMatch, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "generateDB");
+ m->errorOut(e, "BlastDB", "MPIRecv");
exit(1);
}
}
+#endif
+/**************************************************************************************************/
/**************************************************************************************************/