readseqscommand.cpp

   1 /*
   2  *  readseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/13/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readseqscommand.h"
  11
  12 //**********************************************************************************************************************
  13 ReadSeqsCommand::ReadSeqsCommand(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 filename = globaldata->inputFileName;
  17                 if(globaldata->getFastaFile().compare("") != 0) {
  18                         readFasta = new ReadFasta(filename);
  19                         readFasta->read();
  20                         globaldata->gSequenceDB = readFasta->getDB();
  21                 }
  22                 else if(globaldata->getNexusFile().compare("") != 0) {
  23                         readNexus = new ReadNexus(filename);
  24                         readNexus->read();
  25                         globaldata->gSequenceDB = readNexus->getDB();
  26                 }
  27                 else if(globaldata->getClustalFile().compare("") != 0) {
  28                         readClustal = new ReadClustal(filename);
  29                         readClustal->read();
  30                         globaldata->gSequenceDB = readClustal->getDB();
  31                 }
  32                 else if(globaldata->getPhylipFile().compare("") != 0) {
  33                         readPhylip = new ReadPhylip(filename);
  34                         readPhylip->read();
  35                         globaldata->gSequenceDB = readPhylip->getDB();
  36                 }
  37         }
  38         catch(exception& e) {
  39                 cout << "Standard Error: " << e.what() << " has occurred in the ReadSeqsCommand class Function ReadSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  40                 exit(1);
  41         }
  42         catch(...) {
  43                 cout << "An unknown error has occurred in the ReadSeqsCommand class function ReadSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46 }
  47
  48 //**********************************************************************************************************************
  49
  50 ReadSeqsCommand::~ReadSeqsCommand(){
  51         //delete readFasta->getDB();
  52 //      delete readNexus->getDB();
  53 //      delete readClustal->getDB();
  54 //      delete readPhylip->getDB();
  55 }
  56
  57 //**********************************************************************************************************************
  58
  59 int ReadSeqsCommand::execute(){
  60         try {
  61                 filebuf fb;
  62
  63                 //fb.open ("fasta.txt",ios::out);
  64                 //readFasta->read();
  65 //              SequenceDB* db = readFasta->getDB();
  66
  67                 //fb.open("nexus.txt",ios::out);
  68 //              readNexus->read();
  69 //              SequenceDB* db = readNexus->getDB();
  70
  71                 //fb.open("clustal.txt",ios::out);
  72 //              readClustal->read();
  73 //              SequenceDB* db = readClustal->getDB();
  74
  75                 //fb.open("phylip.txt",ios::out);
  76 //              readPhylip->read();
  77 //              SequenceDB* db = readPhylip->getDB();
  78
  79
  80
  81                 //for(int i = 0; i < db->size(); i++) {
  82 //                      cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getAligned() << "\n\n";
  83 //              }
  84
  85                 //ostream os(&fb);
  86 //              db->print(os);
  87 //              fb.close();
  88
  89                 return 0;
  90         }
  91         catch(exception& e) {
  92                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95         catch(...) {
  96                 cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99 }
 100 //**********************************************************************************************************************