+++ /dev/null
-/*
- * alignmentdb.cpp
- * Mothur
- *
- * Created by westcott on 11/4/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "alignmentdb.h"
-#include "kmerdb.hpp"
-#include "suffixdb.hpp"
-#include "blastdb.hpp"
-#include "referencedb.h"
-
-/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){ // This assumes that the template database is in fasta format, may
- try { // need to alter this in the future?
- m = MothurOut::getInstance();
- longest = 0;
- method = s;
- bool needToGenerate = true;
- ReferenceDB* rdb = ReferenceDB::getInstance();
- bool silent = false;
- threadID = tid;
-
- if (fastaFileName == "saved-silent") {
- fastaFileName = "saved"; silent = true;
- }
-
- if (fastaFileName == "saved") {
- int start = time(NULL);
-
- if (!silent) { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
-
- for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
- templateSequences.push_back(rdb->referenceSeqs[i]);
- //save longest base
- if (rdb->referenceSeqs[i].getUnaligned().length() >= longest) { longest = (rdb->referenceSeqs[i].getUnaligned().length()+1); }
- }
- fastaFileName = rdb->getSavedReference();
-
- numSeqs = templateSequences.size();
- if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine(); }
-
- }else {
- int start = time(NULL);
- m->mothurOutEndLine();
- m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
-
- #ifdef USE_MPI
- int pid, processors;
- vector<unsigned long long> positions;
-
- 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);
- int tag = 2001;
-
- char inFileName[1024];
- 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 = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
-
- //send file positions to all processes
- 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_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);
- }
-
- //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 = new char[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); }
- delete buf4;
-
- istringstream iss (tempBuf,istringstream::in);
-
- Sequence temp(iss);
- if (temp.getName() != "") {
- templateSequences.push_back(temp);
-
- if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
-
- //save longest base
- if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
- }
- }
-
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-
- MPI_File_close(&inMPI);
-
- #else
- ifstream fastaFile;
- m->openInputFile(fastaFileName, fastaFile);
-
- while (!fastaFile.eof()) {
- Sequence temp(fastaFile); m->gobble(fastaFile);
-
- if (m->control_pressed) { templateSequences.clear(); break; }
-
- if (temp.getName() != "") {
- templateSequences.push_back(temp);
-
- if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
-
- //save longest base
- if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
- }
- }
- fastaFile.close();
- #endif
-
- numSeqs = templateSequences.size();
- //all of this is elsewhere already!
-
- m->mothurOut("DONE.");
- m->mothurOutEndLine(); cout.flush();
- m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine();
-
- }
-
-
- //in case you delete the seqs and then ask for them
- emptySequence = Sequence();
- emptySequence.setName("no_match");
- emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
-
-
- string kmerDBName;
- if(method == "kmer") {
- search = new KmerDB(fastaFileName, kmerSize);
-
- #ifdef USE_MPI
- #else
- kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
- ifstream kmerFileTest(kmerDBName.c_str());
-
- if(kmerFileTest){
- bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
- if (GoodFile) { needToGenerate = false; }
- }
- #endif
- }
- else if(method == "suffix") { search = new SuffixDB(numSeqs); }
- else if(method == "blast") { search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
- else {
- method = "kmer";
- m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
- m->mothurOutEndLine();
- search = new KmerDB(fastaFileName, 8);
- }
-
- if (!(m->control_pressed)) {
- if (needToGenerate) {
- //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)) {
- ifstream kmerFileTest(kmerDBName.c_str());
- search->readKmerDB(kmerFileTest);
- }
-
- search->setNumSeqs(numSeqs);
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "AlignmentDB");
- exit(1);
- }
-}
-/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string s){
- try {
- m = MothurOut::getInstance();
- method = s;
-
- if(method == "suffix") { search = new SuffixDB(); }
- else if(method == "blast") { search = new BlastDB("", 0); }
- 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) {
- try{
-
- vector<int> spot = search->findClosestSequences(seq, 1);
-
- if (spot.size() != 0) { return templateSequences[spot[0]]; }
- else { return emptySequence; }
-
- }
- catch(exception& e) {
- m->errorOut(e, "AlignmentDB", "findClosestSequence");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-
-
-
-
-
projects / mothur.git / blobdiff