X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=875628d85d8dbcb4caf6d712b41be517eefef733;hb=5e5253ff472de3c6349e562d2580873287be0c65;hp=be287a05069c394def3f1cf48257f25b863db3be;hpb=6f4b9401f7deb8aaf0d87659298308f4138cc3b0;p=mothur.git diff --git a/classify.cpp b/classify.cpp index be287a0..875628d 100644 --- a/classify.cpp +++ b/classify.cpp @@ -27,12 +27,14 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me m->mothurOut("Generating search database... "); cout.flush(); #ifdef USE_MPI - int pid; - vector positions; + int pid, processors; + vector positions; + 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[tempFile.length()]; //memcpy(inFileName, tempFile.c_str(), tempFile.length()); @@ -44,15 +46,17 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me //delete inFileName; if (pid == 0) { //only one process needs to scan file - positions = setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs + positions = m->setFilePosFasta(tempFile, 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 - positions.resize(numSeqs); - MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + positions.resize(numSeqs+1); + MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); } //create database @@ -86,13 +90,14 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me database->generateDB(); MPI_File_close(&inMPI); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else //need to know number of template seqs for suffixdb if (method == "suffix") { ifstream inFASTA; - openInputFile(tempFile, inFASTA); - numSeqs = count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + m->openInputFile(tempFile, inFASTA); + m->getNumSeqs(inFASTA, numSeqs); inFASTA.close(); } @@ -103,7 +108,10 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer"; ifstream kmerFileTest(kmerDBName.c_str()); - if(kmerFileTest){ needToGenerate = false; } + if(kmerFileTest){ + bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion()); + if (GoodFile) { needToGenerate = false; } + } } else if(method == "suffix") { database = new SuffixDB(numSeqs); } else if(method == "blast") { database = new BlastDB(gapOpen, gapExtend, match, misMatch); } @@ -116,14 +124,14 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me if (needToGenerate) { ifstream fastaFile; - openInputFile(tempFile, fastaFile); + m->openInputFile(tempFile, fastaFile); while (!fastaFile.eof()) { Sequence temp(fastaFile); - gobble(fastaFile); + m->gobble(fastaFile); names.push_back(temp.getName()); - + database->addSequence(temp); } fastaFile.close(); @@ -133,21 +141,27 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me }else if ((method == "kmer") && (!needToGenerate)) { ifstream kmerFileTest(kmerDBName.c_str()); database->readKmerDB(kmerFileTest); - + ifstream fastaFile; - openInputFile(tempFile, fastaFile); + m->openInputFile(tempFile, fastaFile); while (!fastaFile.eof()) { Sequence temp(fastaFile); - gobble(fastaFile); + m->gobble(fastaFile); names.push_back(temp.getName()); } fastaFile.close(); } -#endif +#endif + database->setNumSeqs(names.size()); + //sanity check + bool okay = phyloTree->ErrorCheck(names); + + if (!okay) { m->control_pressed = true; } + m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine(); @@ -171,12 +185,14 @@ int Classify::readTaxonomy(string file) { m->mothurOut("Reading in the " + file + " taxonomy...\t"); cout.flush(); #ifdef USE_MPI - int pid, num; - vector positions; + int pid, num, processors; + vector positions; + 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()); @@ -188,15 +204,17 @@ int Classify::readTaxonomy(string file) { //delete inFileName; if (pid == 0) { - positions = setFilePosEachLine(file, num); + positions = m->setFilePosEachLine(file, num); //send file positions to all processes - MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs - MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos + for(int i = 1; i < processors; i++) { + MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } }else{ - MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs - positions.resize(num); - MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions + MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + positions.resize(num+1); + MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); } //read file @@ -218,9 +236,10 @@ int Classify::readTaxonomy(string file) { } MPI_File_close(&inMPI); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else ifstream inTax; - openInputFile(file, inTax); + m->openInputFile(file, inTax); //read template seqs and save while (!inTax.eof()) { @@ -230,13 +249,15 @@ int Classify::readTaxonomy(string file) { phyloTree->addSeqToTree(name, taxInfo); - gobble(inTax); + m->gobble(inTax); } inTax.close(); #endif phyloTree->assignHeirarchyIDs(0); + phyloTree->setUp(file); + m->mothurOut("DONE."); m->mothurOutEndLine(); cout.flush();