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 "mothur.h"
  13 #include "sequence.hpp"
  14 #include "database.hpp"
  15
  16 /**************************************************************************************************/
  17
  18 Database::Database(string fastaFileName){
  19
  20         ifstream fastaFile(fastaFileName.c_str());
  21         if(!fastaFile) {
  22                 cerr << "Error: Could not open " << fastaFileName << endl;
  23                 exit(1);
  24         }
  25         cout << endl << "Reading in the " << fastaFileName << " template sequences...\t";       cout.flush();
  26
  27         numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');
  28         fastaFile.seekg(0);
  29
  30         templateSequences.resize(numSeqs);
  31
  32         string seqName, sequence;
  33         for(int i=0;i<numSeqs;i++){
  34                 templateSequences[i] = new Sequence();
  35
  36                 fastaFile >> seqName;
  37                 templateSequences[i]->setName(seqName);
  38
  39                 char letter;
  40                 string aligned;
  41
  42                 while(fastaFile && (letter=fastaFile.get()) != '>'){
  43                         if(isprint(letter)){
  44                                 letter = toupper(letter);
  45                                 aligned += letter;
  46                         }
  47                 }
  48                 templateSequences[i]->setAligned(aligned);
  49                 templateSequences[i]->setUnaligned(aligned);
  50                 fastaFile.putback(letter);
  51         }
  52
  53         fastaFile.close();
  54         cout << "DONE." << endl;        cout.flush();
  55
  56 }
  57
  58 /**************************************************************************************************/