5 * Created by westcott on 11/4/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "alignmentdb.h"
12 #include "suffixdb.hpp"
13 #include "blastdb.hpp"
14 #include "referencedb.h"
16 /**************************************************************************************************/
17 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
18 try { // need to alter this in the future?
19 m = MothurOut::getInstance();
22 bool needToGenerate = true;
23 ReferenceDB* rdb = ReferenceDB::getInstance();
27 if (fastaFileName == "saved-silent") {
28 fastaFileName = "saved"; silent = true;
31 if (fastaFileName == "saved") {
32 int start = time(NULL);
34 if (!silent) { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
36 for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
37 templateSequences.push_back(rdb->referenceSeqs[i]);
39 if (rdb->referenceSeqs[i].getUnaligned().length() >= longest) { longest = (rdb->referenceSeqs[i].getUnaligned().length()+1); }
41 fastaFileName = rdb->getSavedReference();
43 numSeqs = templateSequences.size();
44 if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine(); }
47 int start = time(NULL);
48 m->mothurOutEndLine();
49 m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
53 vector<unsigned long long> positions;
57 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
58 MPI_Comm_size(MPI_COMM_WORLD, &processors);
61 char inFileName[1024];
62 strcpy(inFileName, fastaFileName.c_str());
64 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
67 positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
69 //send file positions to all processes
70 for(int i = 1; i < processors; i++) {
71 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
72 MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
75 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
76 positions.resize(numSeqs+1);
77 MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
81 for(int i=0;i<numSeqs;i++){
83 if (m->control_pressed) { templateSequences.clear(); break; }
86 int length = positions[i+1] - positions[i];
87 char* buf4 = new char[length];
89 MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
91 string tempBuf = buf4;
92 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
95 istringstream iss (tempBuf,istringstream::in);
98 if (temp.getName() != "") {
99 templateSequences.push_back(temp);
101 if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
104 if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
108 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
110 MPI_File_close(&inMPI);
114 m->openInputFile(fastaFileName, fastaFile);
116 while (!fastaFile.eof()) {
117 Sequence temp(fastaFile); m->gobble(fastaFile);
119 if (m->control_pressed) { templateSequences.clear(); break; }
121 if (temp.getName() != "") {
122 templateSequences.push_back(temp);
124 if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
127 if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
133 numSeqs = templateSequences.size();
134 //all of this is elsewhere already!
136 m->mothurOut("DONE.");
137 m->mothurOutEndLine(); cout.flush();
138 m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine();
143 //in case you delete the seqs and then ask for them
144 emptySequence = Sequence();
145 emptySequence.setName("no_match");
146 emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
147 emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
151 if(method == "kmer") {
152 search = new KmerDB(fastaFileName, kmerSize);
156 kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
157 ifstream kmerFileTest(kmerDBName.c_str());
160 bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
161 if (GoodFile) { needToGenerate = false; }
165 else if(method == "suffix") { search = new SuffixDB(numSeqs); }
166 else if(method == "blast") { search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
169 m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
170 m->mothurOutEndLine();
171 search = new KmerDB(fastaFileName, 8);
174 if (!(m->control_pressed)) {
175 if (needToGenerate) {
176 //add sequences to search
177 for (int i = 0; i < templateSequences.size(); i++) {
178 search->addSequence(templateSequences[i]);
180 if (m->control_pressed) { templateSequences.clear(); break; }
183 if (m->control_pressed) { templateSequences.clear(); }
185 search->generateDB();
187 }else if ((method == "kmer") && (!needToGenerate)) {
188 ifstream kmerFileTest(kmerDBName.c_str());
189 search->readKmerDB(kmerFileTest);
192 search->setNumSeqs(numSeqs);
196 catch(exception& e) {
197 m->errorOut(e, "AlignmentDB", "AlignmentDB");
201 /**************************************************************************************************/
202 AlignmentDB::AlignmentDB(string s){
204 m = MothurOut::getInstance();
207 if(method == "suffix") { search = new SuffixDB(); }
208 else if(method == "blast") { search = new BlastDB("", 0); }
209 else { search = new KmerDB(); }
212 //in case you delete the seqs and then ask for them
213 emptySequence = Sequence();
214 emptySequence.setName("no_match");
215 emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
216 emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
219 catch(exception& e) {
220 m->errorOut(e, "AlignmentDB", "AlignmentDB");
224 /**************************************************************************************************/
225 AlignmentDB::~AlignmentDB() { delete search; }
226 /**************************************************************************************************/
227 Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
230 vector<int> spot = search->findClosestSequences(seq, 1);
232 if (spot.size() != 0) { return templateSequences[spot[0]]; }
233 else { return emptySequence; }
236 catch(exception& e) {
237 m->errorOut(e, "AlignmentDB", "findClosestSequence");
241 /**************************************************************************************************/