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         mothurOutEndLine();
  23         mothurOut("Reading in the " + fastaFileName + " template sequences...\t");      cout.flush();
  24
  25         //all of this is elsewhere already!
  26         numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');   //      count the number of
  27         fastaFile.seekg(0);                                                                                                                                             //      sequences
  28
  29         templateSequences.resize(numSeqs);
  30
  31         string seqName, sequence;
  32         for(int i=0;i<numSeqs;i++){
  33                 fastaFile >> seqName;
  34                 seqName = seqName.substr(1);
  35                 char letter;
  36                 string aligned;
  37
  38                 while(fastaFile && (letter=fastaFile.get()) != '>'){
  39                         if(isprint(letter)){
  40                                 letter = toupper(letter);
  41                                 if(letter == 'U'){letter = 'T';}
  42                                 aligned += letter;
  43                         }
  44                 }
  45                 templateSequences[i] = Sequence(seqName, aligned);
  46                 fastaFile.putback(letter);
  47         }
  48
  49         fastaFile.close();
  50         //all of this is elsewhere already!
  51
  52         mothurOut("DONE.");
  53         mothurOutEndLine();     cout.flush();
  54
  55 }
  56 /**************************************************************************************************/
  57
  58 Database::~Database(){
  59
  60                 templateSequences.clear();
  61 }
  62
  63 /**************************************************************************************************/
  64
  65 float Database::getSearchScore()        {       return searchScore;             }       //      we're assuming that the search is already done
  66
  67 /**************************************************************************************************/