X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.cpp;h=ae9ad9a46ef1ce5634c867219904857731bf3d6e;hb=9f4c08cab5a7a9a0e156bd4a5a3a478b476162dc;hp=83d40fe8342558eacb598525862364dba0f7e5ca;hpb=813f0516e9c7533859f57ebe6d7b8854896bf009;p=mothur.git

diff --git a/chimera.cpp b/chimera.cpp
index 83d40fe..ae9ad9a 100644
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -31,6 +31,8 @@ string Chimera::createFilter(vector<Sequence*> seqs, float t) {
 			if (m->control_pressed) { return filterString; }
 		
 			string seqAligned = seqs[i]->getAligned();
+			
+			if (seqAligned.length() != filterString.length()) {  m->mothurOut(seqs[i]->getName() + " is not the same length as the template sequences. Aborting!\n");  exit(1); }
 		
 			for (int j = 0; j < seqAligned.length(); j++) {
 				//if this spot is a gap
@@ -101,30 +103,37 @@ vector<Sequence*> Chimera::readSeqs(string file) {
 		m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
 		
 		#ifdef USE_MPI	
-			int pid;
-			vector<long> positions;
+			int pid, processors;
+			vector<unsigned long int> positions;
 			int numSeqs;
+			int tag = 2001;
 		
 			MPI_Status status; 
 			MPI_File inMPI;
 			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+			MPI_Comm_size(MPI_COMM_WORLD, &processors);
 
-			char* inFileName = new char[file.length()];
-			memcpy(inFileName, file.c_str(), file.length());
+			//char* inFileName = new char[file.length()];
+			//memcpy(inFileName, file.c_str(), file.length());
+			
+			char inFileName[1024];
+			strcpy(inFileName, file.c_str());
 	
 			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
-			delete inFileName;
+			//delete inFileName;
 
 			if (pid == 0) {
-				positions = setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+				positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
 
 				//send file positions to all processes
-				MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-				MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos	
+				for(int i = 1; i < processors; i++) { 
+					MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+					MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+				}
 			}else{
-				MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+				MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 				positions.resize(numSeqs+1);
-				MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+				MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 			}
 			
 			//read file 
@@ -154,17 +163,18 @@ vector<Sequence*> Chimera::readSeqs(string file) {
 			}
 			
 			MPI_File_close(&inMPI);
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 	#else
 
 		ifstream in;
-		openInputFile(file, in);
+		m->openInputFile(file, in);
 		
 		//read in seqs and store in vector
 		while(!in.eof()){
 			
 			if (m->control_pressed) { return container; }
 			
-			Sequence* current = new Sequence(in);  gobble(in);
+			Sequence* current = new Sequence(in);  m->gobble(in);
 			
 			if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
 			else if (length != current->getAligned().length()) {	unaligned = true;	}
@@ -199,13 +209,16 @@ void Chimera::setMask(string filename) {
 			MPI_Offset size;
 			MPI_Status status;
 			
-			char* inFileName = new char[filename.length()];
-			memcpy(inFileName, filename.c_str(), filename.length());
+			//char* inFileName = new char[filename.length()];
+			//memcpy(inFileName, filename.c_str(), filename.length());
+			
+			char inFileName[1024];
+			strcpy(inFileName, filename.c_str());
 	
 			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 			MPI_File_get_size(inMPI, &size);
 
-			delete inFileName;
+			//delete inFileName;
 			
 			char* buffer = new char[size];
 			MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
@@ -228,7 +241,7 @@ void Chimera::setMask(string filename) {
 	#else
 	
 			ifstream infile;
-			openInputFile(filename, infile);
+			m->openInputFile(filename, infile);
 			
 			if (!infile.eof()) {
 				Sequence temp(infile);