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"
16 /**************************************************************************************************/
17 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
18 try { // need to alter this in the future?
22 openInputFile(fastaFileName, fastaFile);
25 mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
27 while (!fastaFile.eof()) {
28 Sequence temp(fastaFile); gobble(fastaFile);
30 if (temp.getName() != "") {
31 templateSequences.push_back(temp);
33 if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length(); }
37 numSeqs = templateSequences.size();
40 //all of this is elsewhere already!
43 mothurOutEndLine(); cout.flush();
45 //in case you delete the seqs and then ask for them
46 emptySequence = Sequence();
47 emptySequence.setName("no_match");
48 emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
49 emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
51 bool needToGenerate = true;
53 if(method == "kmer") {
54 search = new KmerDB(fastaFileName, kmerSize);
56 kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
57 ifstream kmerFileTest(kmerDBName.c_str());
59 if(kmerFileTest){ needToGenerate = false; }
61 else if(method == "suffix") { search = new SuffixDB(numSeqs); }
62 else if(method == "blast") { search = new BlastDB(gapOpen, gapExtend, match, misMatch); }
64 mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
66 search = new KmerDB(fastaFileName, 8);
71 //add sequences to search
72 for (int i = 0; i < templateSequences.size(); i++) {
73 search->addSequence(templateSequences[i]);
77 }else if ((method == "kmer") && (!needToGenerate)) {
78 ifstream kmerFileTest(kmerDBName.c_str());
79 search->readKmerDB(kmerFileTest);
82 search->setNumSeqs(numSeqs);
85 errorOut(e, "AlignmentDB", "AlignmentDB");
89 /**************************************************************************************************/
90 AlignmentDB::~AlignmentDB() { delete search; }
91 /**************************************************************************************************/
92 Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
95 vector<int> spot = search->findClosestSequences(seq, 1);
97 if (spot.size() != 0) { return templateSequences[spot[0]]; }
98 else { return emptySequence; }
101 catch(exception& e) {
102 errorOut(e, "AlignmentDB", "findClosestSequence");
106 /**************************************************************************************************/