made get.oturep more memory efficient by breaking the work into 2 pieces.

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 396a6b4b91c4496b80dfc3009cdda4a0f34b12e6..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";
+
 }
 
 /**************************************************************************************************/
@@ -92,7 +105,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosestSequences");
+               m->errorOut(e, "BlastDB", "findClosestSequences");
                exit(1);
        }
 
@@ -139,7 +152,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosest");
+               m->errorOut(e, "BlastDB", "findClosest");
                exit(1);
        }
 }
@@ -158,7 +171,7 @@ void BlastDB::addSequence(Sequence seq) {
                count++;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "addSequence");
+               m->errorOut(e, "BlastDB", "addSequence");
                exit(1);
        }
 }
@@ -166,7 +179,7 @@ void BlastDB::addSequence(Sequence seq) {
 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')));
@@ -174,13 +187,63 @@ void BlastDB::generateDB() {
                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 
+/**************************************************************************************************/
 
 /**************************************************************************************************/