/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){ // This assumes that the template database is in fasta format, may
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){ // This assumes that the template database is in fasta format, may
try { // need to alter this in the future?
m = MothurOut::getInstance();
longest = 0;
-
- ifstream fastaFile;
- openInputFile(fastaFileName, fastaFile);
+ method = s;
+ bool needToGenerate = true;
m->mothurOutEndLine();
m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
+ #ifdef USE_MPI
+ int pid;
+ vector<long> positions;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ char inFileName[fastaFileName.length()];
+ strcpy(inFileName, fastaFileName.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (pid == 0) {
+ positions = setFilePosFasta(fastaFileName, 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
+ }else{
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ positions.resize(numSeqs+1);
+ MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ }
+
+ //read file
+ for(int i=0;i<numSeqs;i++){
+
+ if (m->control_pressed) { templateSequences.clear(); break; }
+
+ //read next sequence
+ int length = positions[i+1] - positions[i];
+ char buf4[length];
+ MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence temp(iss);
+ if (temp.getName() != "") {
+ templateSequences.push_back(temp);
+ //save longest base
+ if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
+ }
+ }
+
+ MPI_File_close(&inMPI);
+ #else
+ ifstream fastaFile;
+ openInputFile(fastaFileName, fastaFile);
+
while (!fastaFile.eof()) {
Sequence temp(fastaFile); gobble(fastaFile);
if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
}
}
+ fastaFile.close();
+ #endif
+
numSeqs = templateSequences.size();
-
- fastaFile.close();
//all of this is elsewhere already!
m->mothurOut("DONE.");
emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- bool needToGenerate = true;
+
string kmerDBName;
if(method == "kmer") {
search = new KmerDB(fastaFileName, kmerSize);
- kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
- ifstream kmerFileTest(kmerDBName.c_str());
+ #ifdef USE_MPI
+ #else
+ kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTest(kmerDBName.c_str());
- if(kmerFileTest){ needToGenerate = false; }
+ if(kmerFileTest){ needToGenerate = false; }
+ #endif
}
else if(method == "suffix") { search = new SuffixDB(numSeqs); }
else if(method == "blast") { search = new BlastDB(gapOpen, gapExtend, match, misMatch); }
//add sequences to search
for (int i = 0; i < templateSequences.size(); i++) {
search->addSequence(templateSequences[i]);
+
+ if (m->control_pressed) { templateSequences.clear(); break; }
}
+
+ if (m->control_pressed) { templateSequences.clear(); }
+
search->generateDB();
}else if ((method == "kmer") && (!needToGenerate)) {
}
}
/**************************************************************************************************/
+AlignmentDB::AlignmentDB(string s){
+ try {
+ m = MothurOut::getInstance();
+ method = s;
+
+ if(method == "suffix") { search = new SuffixDB(); }
+ else if(method == "blast") { search = new BlastDB(); }
+ else { search = new KmerDB(); }
+
+
+ //in case you delete the seqs and then ask for them
+ emptySequence = Sequence();
+ emptySequence.setName("no_match");
+ emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+ emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignmentDB", "AlignmentDB");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
AlignmentDB::~AlignmentDB() { delete search; }
/**************************************************************************************************/
Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
exit(1);
}
}
+#ifdef USE_MPI
/**************************************************************************************************/
+int AlignmentDB::MPISend(int receiver) {
+ try {
+
+ //send numSeqs - int
+ MPI_Send(&numSeqs, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send longest - int
+ MPI_Send(&longest, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send templateSequences
+ for (int i = 0; i < templateSequences.size(); i++) {
+ templateSequences[i].MPISend(receiver);
+ }
+
+ //send Database
+ search->MPISend(receiver);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignmentDB", "MPISend");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int AlignmentDB::MPIRecv(int sender) {
+ try {
+ MPI_Status status;
+ //receive numSeqs - int
+ MPI_Recv(&numSeqs, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive longest - int
+ MPI_Recv(&longest, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive templateSequences
+ templateSequences.resize(numSeqs);
+ for (int i = 0; i < templateSequences.size(); i++) {
+ templateSequences[i].MPIRecv(sender);
+ }
+
+ //receive Database
+ search->MPIRecv(sender);
+
+ for (int i = 0; i < templateSequences.size(); i++) {
+ search->addSequence(templateSequences[i]);
+ }
+ search->generateDB();
+ search->setNumSeqs(numSeqs);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignmentDB", "MPIRecv");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
+
+
projects / mothur.git / blobdiff