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

[mothur.git] / kmerdb.cpp

diff --git a/kmerdb.cpp b/kmerdb.cpp
index 7f7f26589cf6a5c8a566393db9ec76939eb7c0a9..77d93daf4b6c8cf18a8be546fcd4eb41c0dc7301 100644 (file)
--- a/kmerdb.cpp
+++ b/kmerdb.cpp
@@ -48,6 +48,8 @@ KmerDB::KmerDB(string fastaFileName, int kSize) : Database(), kmerSize(kSize) {
 
 }
 /**************************************************************************************************/
+KmerDB::KmerDB() : Database() {}
+/**************************************************************************************************/
 
 KmerDB::~KmerDB(){}
 
@@ -204,6 +206,44 @@ vector<int> KmerDB::getSequencesWithKmer(int kmer) {
                exit(1);
        }       
 }
+#ifdef USE_MPI 
+/**************************************************************************************************/
+int KmerDB::MPISend(int receiver) {
+       try {
+               
+               //send kmerSize - int
+               MPI_Send(&kmerSize, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); 
+               
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KmerDB", "MPISend");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+int KmerDB::MPIRecv(int sender) {
+       try {
+               MPI_Status status;
+               
+               //receive kmerSize - int
+               MPI_Recv(&kmerSize, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
+               
+               //set maxKmer 
+               int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
+               count = 0;
+               maxKmer = power4s[kmerSize];
+               kmerLocations.resize(maxKmer+1);
+               
+               return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "KmerDB", "MPIRecv");
+               exit(1);
+       }
+}
+#endif
+/**************************************************************************************************/
 
 
 /**************************************************************************************************/