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

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 4b5667584a07fd1ca5f6832efd16c192e04c5f1c..19adf796b5d1d26f3a681144c6c801cdb4b4f63d 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -443,5 +443,65 @@ void Sequence::reverseComplement(){
        aligned = temp;
        
 }
-
+#ifdef USE_MPI 
 //********************************************************************************************************************
+int Sequence::MPISend(int receiver) {
+       try {
+               //send name - string
+               int length = name.length();
+               char buf[name.length()];
+               strcpy(buf, name.c_str()); 
+               
+               MPI_Send(&length, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); 
+
+               MPI_Send(&buf, length, MPI_CHAR, receiver, 2001, MPI_COMM_WORLD);
+       
+               //send aligned - string
+               length = aligned.length();
+               char buf2[aligned.length()];
+               strcpy(buf2, aligned.c_str()); 
+       
+               MPI_Send(&length, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); 
+       
+               MPI_Send(&buf2, length, MPI_CHAR, receiver, 2001, MPI_COMM_WORLD);
+       
+               return 0;
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "MPISend");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+int Sequence::MPIRecv(int sender) {
+       try {
+               MPI_Status status;
+       
+               //receive name - string
+               int length;
+               MPI_Recv(&length, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
+       
+               char buf[length];
+               MPI_Recv(&buf, length, MPI_CHAR, sender, 2001, MPI_COMM_WORLD, &status);
+               name = buf;
+               
+               //receive aligned - string
+               MPI_Recv(&length, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
+       
+               char buf2[length];
+               MPI_Recv(&buf2, length, MPI_CHAR, sender, 2001, MPI_COMM_WORLD, &status);
+               aligned = buf2;
+               
+               setAligned(aligned);
+               
+               return 0;
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "MPIRecv");
+               exit(1);
+       }
+}
+#endif
+/**************************************************************************************************/