database.cpp

   1 /*
   2  *  database.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/16/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 using namespace std;
  11
  12 #include <string>
  13 #include <vector>
  14 #include <fstream>
  15 #include <iostream>
  16
  17 #include "sequence.hpp"
  18 #include "database.hpp"
  19
  20 /**************************************************************************************************/
  21
  22 Database::Database(string fastaFileName){
  23
  24         ifstream fastaFile(fastaFileName.c_str());
  25         if(!fastaFile) {
  26                 cerr << "Error: Could not open " << fastaFileName << endl;
  27                 exit(1);
  28         }
  29         cout << endl << "Reading in the " << fastaFileName << " template sequences...\t";       cout.flush();
  30
  31         numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');
  32         fastaFile.seekg(0);
  33
  34         templateSequences.resize(numSeqs);
  35
  36         string seqName, sequence;
  37         for(int i=0;i<numSeqs;i++){
  38                 templateSequences[i] = new Sequence();
  39
  40                 fastaFile >> seqName;
  41                 templateSequences[i]->setName(seqName);
  42
  43                 char letter;
  44                 string aligned;
  45
  46                 while(fastaFile && (letter=fastaFile.get()) != '>'){
  47                         if(isprint(letter)){
  48                                 letter = toupper(letter);
  49                                 aligned += letter;
  50                         }
  51                 }
  52                 templateSequences[i]->setAligned(aligned);
  53                 templateSequences[i]->setUnaligned(aligned);
  54                 fastaFile.putback(letter);
  55         }
  56
  57         fastaFile.close();
  58         cout << "DONE." << endl;        cout.flush();
  59
  60 }
  61
  62 /**************************************************************************************************/