readseqscommand.cpp

   1 /*
   2  *  readseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/13/09.
   6  *  Copyright 2009 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "readseqscommand.h"
  11
  12 //**********************************************************************************************************************
  13 ReadSeqsCommand::ReadSeqsCommand(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16
  17         }
  18         catch(exception& e) {
  19                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. 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 ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26 }
  27
  28 //**********************************************************************************************************************
  29
  30 ReadSeqsCommand::~ReadSeqsCommand(){
  31         //delete readFasta->getDB();
  32 //      delete readNexus->getDB();
  33 //      delete readClustal->getDB();
  34 //      delete readPhylip->getDB();
  35 }
  36
  37 //**********************************************************************************************************************
  38
  39 int ReadSeqsCommand::execute(){
  40         try {
  41                 filebuf fb;
  42
  43                 //fb.open ("fasta.txt",ios::out);
  44 //              readFasta->read();
  45 //              SequenceDB* db = readFasta->getDB();
  46
  47                 //fb.open("nexus.txt",ios::out);
  48 //              readNexus->read();
  49 //              SequenceDB* db = readNexus->getDB();
  50
  51                 //fb.open("clustal.txt",ios::out);
  52 //              readClustal->read();
  53 //              SequenceDB* db = readClustal->getDB();
  54
  55                 //fb.open("phylip.txt",ios::out);
  56 //              readPhylip->read();
  57 //              SequenceDB* db = readPhylip->getDB();
  58
  59
  60
  61                 //for(int i = 0; i < db->size(); i++) {
  62 //                      cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getUnaligned() << "\n\n";
  63 //              }
  64
  65                 //ostream os(&fb);
  66 //              db->print(os);
  67 //              fb.close();
  68
  69                 return 0;
  70         }
  71         catch(exception& e) {
  72                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  73                 exit(1);
  74         }
  75         catch(...) {
  76                 cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************