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         longest = 0;
  19
  20         ifstream fastaFile;
  21         openInputFile(fastaFileName, fastaFile);
  22
  23         mothurOutEndLine();
  24         mothurOut("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] = Sequence(seqName, aligned);
  47
  48                 //necessary because Sequence constructor by default sets whatever it reads to unaligned
  49                 //the setUnaligned function remove gap char.
  50                 templateSequences[i].setUnaligned(templateSequences[i].getUnaligned());
  51
  52                 if (templateSequences[i].getUnaligned().length() > longest)  { longest = templateSequences[i].getUnaligned().length(); }
  53
  54                 fastaFile.putback(letter);
  55         }*/
  56
  57         while (!fastaFile.eof()) {
  58                 Sequence temp(fastaFile);
  59
  60                 templateSequences.push_back(temp);
  61
  62                 //save longest base
  63                 if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length(); }
  64
  65                 gobble(fastaFile);
  66         }
  67
  68         numSeqs = templateSequences.size();
  69
  70         fastaFile.close();
  71         //all of this is elsewhere already!
  72
  73         mothurOut("DONE.");
  74         mothurOutEndLine();     cout.flush();
  75
  76 }
  77 /**************************************************************************************************/
  78
  79 Database::~Database(){
  80
  81                 templateSequences.clear();
  82 }
  83
  84 /**************************************************************************************************/
  85
  86 float Database::getSearchScore()        {       return searchScore;             }       //      we're assuming that the search is already done
  87
  88
  89 /**************************************************************************************************/
  90
  91 int Database::getLongestBase()  {       return longest+1;               }
  92
  93 /**************************************************************************************************/
  94
  95