readfasta.cpp

   1 /*
   2  *  readfasta.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/21/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readfasta.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 ReadFasta::ReadFasta(string file) : ReadSeqs(file) {
  16         try {
  17         }
  18         catch(exception& e) {
  19                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  20                 exit(1);
  21         }
  22         catch(...) {
  23                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26 }
  27 /*******************************************************************************/
  28 ReadFasta::~ReadFasta(){
  29         //for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  30                 //delete sequencedb.get(i);
  31 }
  32 /*******************************************************************************/
  33 void ReadFasta::read() {
  34         string name = "";
  35         string sequence = "";
  36         string temp;
  37         int count = 0;
  38
  39         while(!filehandle.eof()){
  40                 if(count == 0)
  41                         filehandle >> temp;
  42                 if(temp.substr(0,1).compare(">") == 0) {
  43                         if(count != 0) {
  44                                 Sequence newSequence(name, sequence);
  45                                 sequencedb.add(newSequence);
  46                                 sequence = "";
  47                         }
  48                         else
  49                                 count++;
  50                         name = temp.substr(1,temp.length()-1);
  51                 }
  52                 else {
  53                         sequence += temp;
  54                 }
  55
  56                 filehandle >> temp;
  57                 gobble(filehandle);
  58
  59                 if(filehandle.eof())
  60                         sequence += temp;
  61
  62         }
  63         Sequence newSequence(name, sequence);
  64         sequencedb.add(newSequence);
  65
  66         filehandle.close();
  67 }
  68
  69 /*********************************************************************************/
  70 SequenceDB* ReadFasta::getDB() {
  71         return &sequencedb;
  72 }