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
  13 #include "sequence.hpp"
  14 #include "database.hpp"
  15
  16 /**************************************************************************************************/
  17
  18 Database::Database(string fastaFileName){               //      This assumes that the template database is in fasta format, may
  19                                                                                                 //      need to alter this in the future?
  20
  21         ifstream fastaFile;
  22         openInputFile(fastaFileName, fastaFile);
  23
  24         cout << endl << "Reading in the " << fastaFileName << " template sequences...\t";       cout.flush();
  25
  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
  29
  30         templateSequences.resize(numSeqs);
  31
  32         string seqName, sequence;
  33         for(int i=0;i<numSeqs;i++){
  34                 fastaFile >> seqName;
  35                 seqName = seqName.substr(1);
  36                 char letter;
  37                 string aligned;
  38
  39                 while(fastaFile && (letter=fastaFile.get()) != '>'){
  40                         if(isprint(letter)){
  41                                 letter = toupper(letter);
  42                                 if(letter == 'U'){letter = 'T';}
  43                                 aligned += letter;
  44                         }
  45                 }
  46                 templateSequences[i] = new Sequence(seqName, aligned);
  47                 fastaFile.putback(letter);
  48         }
  49
  50         fastaFile.close();
  51         //all of this is elsewhere already!
  52
  53         cout << "DONE." << endl;        cout.flush();
  54
  55 }
  56
  57 /**************************************************************************************************/
  58
  59 float Database::getSearchScore()        {       return searchScore;             }       //      we're assuming that the search is already done
  60
  61 /**************************************************************************************************/