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);
30 templateSequences.push_back(temp);
33 if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length(); }
38 numSeqs = templateSequences.size();
41 //all of this is elsewhere already!
44 mothurOutEndLine(); cout.flush();
46 //in case you delete the seqs and then ask for them
47 emptySequence = Sequence();
48 emptySequence.setName("no_match");
49 emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
50 emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
52 bool needToGenerate = true;
54 if(method == "kmer") {
55 search = new KmerDB(fastaFileName, kmerSize);
57 kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
58 ifstream kmerFileTest(kmerDBName.c_str());
60 if(kmerFileTest){ needToGenerate = false; }
62 else if(method == "suffix") { search = new SuffixDB(numSeqs); }
63 else if(method == "blast") { search = new BlastDB(gapOpen, gapExtend, match, misMatch); }
65 mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
67 search = new KmerDB(fastaFileName, 8);
72 //add sequences to search
73 for (int i = 0; i < templateSequences.size(); i++) {
74 search->addSequence(templateSequences[i]);
78 }else if ((method == "kmer") && (!needToGenerate)) {
79 ifstream kmerFileTest(kmerDBName.c_str());
80 search->readKmerDB(kmerFileTest);
83 search->setNumSeqs(numSeqs);
86 errorOut(e, "AlignmentDB", "AlignmentDB");
90 /**************************************************************************************************/
91 AlignmentDB::~AlignmentDB() { delete search; }
92 /**************************************************************************************************/
93 Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
96 vector<int> spot = search->findClosestSequences(seq, 1);
98 if (spot.size() != 0) { return templateSequences[spot[0]]; }
99 else { return emptySequence; }
102 catch(exception& e) {
103 errorOut(e, "AlignmentDB", "findClosestSequence");
107 /**************************************************************************************************/