5 * Created by Pat Schloss on 12/16/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
13 #include "sequence.hpp"
14 #include "database.hpp"
16 /**************************************************************************************************/
18 Database::Database(string fastaFileName){
20 ifstream fastaFile(fastaFileName.c_str());
22 cerr << "Error: Could not open " << fastaFileName << endl;
25 cout << endl << "Reading in the " << fastaFileName << " template sequences...\t"; cout.flush();
27 numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');
30 templateSequences.resize(numSeqs);
32 string seqName, sequence;
33 for(int i=0;i<numSeqs;i++){
34 templateSequences[i] = new Sequence();
37 templateSequences[i]->setName(seqName);
42 while(fastaFile && (letter=fastaFile.get()) != '>'){
44 letter = toupper(letter);
48 templateSequences[i]->setAligned(aligned);
49 templateSequences[i]->setUnaligned(aligned);
50 fastaFile.putback(letter);
54 cout << "DONE." << endl; cout.flush();
58 /**************************************************************************************************/