fixed bug in nast:removeextragaps

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index b52c82e58d0bb7c441e9b9df324461b4b9a8df60..760824dbb23f9b2a9d680ace769ccc1c6ffab96c 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -54,21 +54,22 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               openOutputFile(queryFileName, queryFile);
+               openOutputFile((queryFileName+seq->getName()), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
+
                                
                //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
                //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
                
                string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
-               blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+               blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
-               openInputFile(blastFileName, m8FileHandle);
+               openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
                
                string dummy;
                int templateAccession;
@@ -84,7 +85,9 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                        topMatches.push_back(templateAccession);
                }
                m8FileHandle.close();
-               
+               remove((queryFileName+seq->getName()).c_str());
+               remove((blastFileName+seq->getName()).c_str());
+
                return topMatches;
        }
        catch(exception& e) {
@@ -100,7 +103,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               openOutputFile(queryFileName, queryFile);
+               openOutputFile((queryFileName+seq->getName()), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -110,11 +113,11 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
        
                string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
-               blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+               blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
                system(blastCommand.c_str());
-               
+
                ifstream m8FileHandle;
-               openInputFile(blastFileName, m8FileHandle, "no error");
+               openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
        
                string dummy;
                int templateAccession;
@@ -131,6 +134,8 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 //cout << templateAccession << endl;
                }
                m8FileHandle.close();
+               remove((queryFileName+seq->getName()).c_str());
+               remove((blastFileName+seq->getName()).c_str());
 //cout << "\n\n" ;             
                return topMatches;
        }
@@ -177,55 +182,6 @@ 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 
 /**************************************************************************************************/
 
 /**************************************************************************************************/