readfasta.cpp

   1 /*
   2  *  readfasta.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/21/09.
   6  *  Copyright 2009 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "readfasta.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 ReadFasta::ReadFasta(string file) {
  16         try {
  17                 openInputFile(file, filehandle);
  18                 fastaFile = file;
  19                 globaldata = GlobalData::getInstance();
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 /*******************************************************************************/
  31 ReadFasta::~ReadFasta(){
  32         //for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  33                 //delete sequencedb.get(i);
  34 }
  35 /*******************************************************************************/
  36 void ReadFasta::read() {
  37         string name = "";
  38         string sequence = "";
  39         string temp;
  40         int count = 0;
  41         while(!filehandle.eof()){
  42                 if(count == 0)
  43                         filehandle >> temp;
  44                 if(temp.substr(0,1).compare(">") == 0) {
  45                         if(count != 0) {
  46                                 Sequence newSequence(name, sequence);
  47                                 sequencedb.add(newSequence);
  48                                 sequence = "";
  49                         }
  50                         else
  51                                 count++;
  52                         name = temp.substr(1,temp.length()-1);
  53                 }
  54                 else
  55                         sequence += temp;
  56
  57                 filehandle >> temp;
  58         }
  59         Sequence newSequence(name, sequence);
  60         sequencedb.add(newSequence);
  61
  62         filehandle.close();
  63 }
  64
  65 /*********************************************************************************/
  66 SequenceDB* ReadFasta::getDB() {
  67         return &sequencedb;
  68 }