changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index fe919dea41de925a5d27227f3805de3e156f9128..4947dc97939b6b147718968bb70e544ca262cc00 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -167,17 +167,23 @@ int ChimeraCheckCommand::execute(){
                        int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                        int inMode=MPI_MODE_RDONLY; 
                        
-                       char* outFilename = new char[outputFileName.length()];\r
-                       memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+                       //char* outFilename = new char[outputFileName.length()];
+                       //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+                       
+                       char outFilename[1024];
+                       strcpy(outFilename, outputFileName.c_str());
 
-                       char* inFileName = new char[fastafile.length()];\r
-                       memcpy(inFileName, fastafile.c_str(), fastafile.length());
+                       //char* inFileName = new char[fastafile.length()];
+                       //memcpy(inFileName, fastafile.c_str(), fastafile.length());
+                       
+                       char inFileName[1024];
+                       strcpy(inFileName, fastafile.c_str());
 
                        MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                        MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
                        
-                       delete outFilename;
-                       delete inFileName;
+                       //delete outFilename;
+                       //delete inFileName;
 
                        if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  delete chimera; return 0;  }
                        
@@ -185,13 +191,16 @@ int ChimeraCheckCommand::execute(){
                                MPIPos = setFilePosFasta(fastafile, 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(&MPIPos[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(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+                               }       
                                
                                //figure out how many sequences you have to align
                                numSeqsPerProcessor = numSeqs / processors;
-                               if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
                                int startIndex =  pid * numSeqsPerProcessor;
+                               if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
+                               
                        
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
@@ -204,14 +213,15 @@ int ChimeraCheckCommand::execute(){
                                        MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
                                }
                        }else{ //you are a child process
-                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+                               MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                MPIPos.resize(numSeqs+1);
-                               MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+                               MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
                                
                                //figure out how many sequences you have to align
                                numSeqsPerProcessor = numSeqs / processors;
-                               if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
                                int startIndex =  pid * numSeqsPerProcessor;
+                               if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
+                               
                                
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
@@ -227,6 +237,7 @@ int ChimeraCheckCommand::execute(){
                        //close files 
                        MPI_File_close(&inMPI);
                        MPI_File_close(&outMPI);
+                       MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
        #else
                
                //break up file
@@ -234,7 +245,7 @@ int ChimeraCheckCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(fastafile, inFASTA);
-                               numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numSeqs));
@@ -298,7 +309,7 @@ int ChimeraCheckCommand::execute(){
                #else
                        ifstream inFASTA;
                        openInputFile(fastafile, inFASTA);
-                       numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numSeqs);
                        inFASTA.close();
                        lines.push_back(new linePair(0, numSeqs));