finished cluster.split adding classify method.

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 780afe0d485627fb63c3d7265f55b2aee19147fb..35a19f485816c87db85b71c74ca138f00595b180 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -85,23 +85,6 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                }
                m8FileHandle.close();
                
-               string root = dbFileName;
-               string temp = dbFileName + ".nsq";
-               remove(temp.c_str());   
-               temp = dbFileName + ".nsi";
-               remove(temp.c_str());
-               
-               temp = dbFileName + ".nsd";
-               remove(temp.c_str());   
-
-               temp = dbFileName + ".nin";
-               remove(temp.c_str());   
-
-               temp = dbFileName + ".nhr";
-               remove(temp.c_str());   
-       
-
-               
                return topMatches;
        }
        catch(exception& e) {
@@ -167,7 +150,7 @@ void BlastDB::addSequence(Sequence seq) {
                unalignedFastaFile << '>' << count << endl;                                     //      sequences, which will be input to formatdb
                unalignedFastaFile << seq.getUnaligned() << endl;
                unalignedFastaFile.close();
-               
+       
                count++;
        }
        catch(exception& e) {
@@ -194,55 +177,6 @@ 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 
 /**************************************************************************************************/
 
 /**************************************************************************************************/