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 #include "mothur.h"
  11 #include "sequence.hpp"
  12 #include "database.hpp"
  13
  14 /**************************************************************************************************/
  15
  16 Database::Database(string fastaFileName){               //      This assumes that the template database is in fasta format, may
  17                                                                                                 //      need to alter this in the future?
  18
  19         ifstream fastaFile;
  20         openInputFile(fastaFileName, fastaFile);
  21
  22         cout << endl << "Reading in the " << fastaFileName << " template sequences...\t";       cout.flush();
  23
  24         //all of this is elsewhere already!
  25         numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');   //      count the number of
  26         fastaFile.seekg(0);                                                                                                                                             //      sequences
  27
  28         templateSequences.resize(numSeqs);
  29
  30         string seqName, sequence;
  31         for(int i=0;i<numSeqs;i++){
  32                 fastaFile >> seqName;
  33                 seqName = seqName.substr(1);
  34                 char letter;
  35                 string aligned;
  36
  37                 while(fastaFile && (letter=fastaFile.get()) != '>'){
  38                         if(isprint(letter)){
  39                                 letter = toupper(letter);
  40                                 if(letter == 'U'){letter = 'T';}
  41                                 aligned += letter;
  42                         }
  43                 }
  44                 templateSequences[i] = new Sequence(seqName, aligned);
  45                 fastaFile.putback(letter);
  46         }
  47
  48         fastaFile.close();
  49         //all of this is elsewhere already!
  50
  51         cout << "DONE." << endl;        cout.flush();
  52
  53 }
  54
  55 /**************************************************************************************************/
  56
  57 float Database::getSearchScore()        {       return searchScore;             }       //      we're assuming that the search is already done
  58
  59 /**************************************************************************************************/