reversecommand.cpp

   1 /*
   2  *  reversecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/6/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "reversecommand.h"
  11 #include "sequence.hpp"
  12
  13
  14 //***************************************************************************************************************
  15
  16 ReverseSeqsCommand::ReverseSeqsCommand(){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19                 if(globaldata->getFastaFile() == "")            {       cout << "you need to at least enter a fasta file name" << endl; }
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. 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 SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30
  31 //***************************************************************************************************************
  32
  33 ReverseSeqsCommand::~ReverseSeqsCommand(){      /*      do nothing      */      }
  34
  35 //***************************************************************************************************************
  36
  37
  38 int ReverseSeqsCommand::execute(){
  39         try{
  40
  41                 ifstream inFASTA;
  42                 openInputFile(globaldata->getFastaFile(), inFASTA);
  43
  44                 ofstream outFASTA;
  45                 string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile());
  46                 openOutputFile(reverseFile, outFASTA);
  47
  48                 while(!inFASTA.eof()){
  49                         Sequence currSeq(inFASTA);
  50                         currSeq.reverseComplement();
  51                         currSeq.printSequence(outFASTA);
  52                 }
  53                 inFASTA.close();
  54                 outFASTA.close();
  55
  56                 return 0;
  57
  58         }
  59         catch(exception& e) {
  60                 cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  61                 exit(1);
  62         }
  63         catch(...) {
  64                 cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67 }
  68
  69 //***************************************************************************************************************