5 * Created by Pat Schloss on 12/16/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 #include "sequence.hpp"
12 #include "database.hpp"
14 /**************************************************************************************************/
16 Database::Database(string fastaFileName){ // This assumes that the template database is in fasta format, may
17 // need to alter this in the future?
21 openInputFile(fastaFileName, fastaFile);
24 mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
26 //all of this is elsewhere already!
27 numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>'); // count the number of
28 fastaFile.seekg(0); // sequences
30 templateSequences.resize(numSeqs);
32 string seqName, sequence;
33 for(int i=0;i<numSeqs;i++){
35 seqName = seqName.substr(1);
39 while(fastaFile && (letter=fastaFile.get()) != '>'){
41 letter = toupper(letter);
42 if(letter == 'U'){letter = 'T';}
46 templateSequences[i] = Sequence(seqName, aligned);
48 //necessary because Sequence constructor by default sets whatever it reads to unaligned
49 //the setUnaligned function remove gap char.
50 templateSequences[i].setUnaligned(templateSequences[i].getUnaligned());
52 if (templateSequences[i].getUnaligned().length() > longest) { longest = templateSequences[i].getUnaligned().length(); }
54 fastaFile.putback(letter);
58 //all of this is elsewhere already!
61 mothurOutEndLine(); cout.flush();
64 /**************************************************************************************************/
66 Database::~Database(){
68 templateSequences.clear();
71 /**************************************************************************************************/
73 float Database::getSearchScore() { return searchScore; } // we're assuming that the search is already done
76 /**************************************************************************************************/
78 int Database::getLongestBase() { return longest+1; }
80 /**************************************************************************************************/