added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 17db069cdedb8a019d980c32fc4b6e7767fab27b..780afe0d485627fb63c3d7265f55b2aee19147fb 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -25,6 +25,19 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        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";
+
 }
 
 /**************************************************************************************************/
@@ -181,6 +194,56 @@ void 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) {
+               m->errorOut(e, "BlastDB", "MPIRecv");
+               exit(1);
+       }
+}
+#endif 
+/**************************************************************************************************/
 
 /**************************************************************************************************/