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         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 //              templateSequences[i] = new Sequence();          //      We're storing the aligned template sequences as a vector of
  34                                                                                                         //      pointers to Sequence objects
  35                 fastaFile >> seqName;
  36 //              templateSequences[i]->setName(seqName);
  37
  38                 char letter;
  39                 string aligned;
  40
  41                 while(fastaFile && (letter=fastaFile.get()) != '>'){
  42                         if(isprint(letter)){
  43                                 letter = toupper(letter);
  44                                 if(letter == 'U'){letter = 'T';}
  45                                 aligned += letter;
  46                         }
  47                 }
  48                 templateSequences[i] = new Sequence(seqName, aligned);
  49 //              templateSequences[i]->setAligned(aligned);      //      Obviously, we need the fully aligned template sequence
  50 //              templateSequences[i]->setUnaligned(aligned);//  We will also need the unaligned sequence for pairwise alignments
  51                 fastaFile.putback(letter);                                      //      and database searches
  52         }
  53
  54         fastaFile.close();
  55         cout << "DONE." << endl;        cout.flush();
  56
  57 }
  58
  59 /**************************************************************************************************/
  60
  61 float Database::getSearchScore()        {       return searchScore;             }       //      we're assuming that the search is already done
  62
  63 /**************************************************************************************************/