readotucommand.cpp

   1 /*
   2  *  readotu.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readotucommand.h"
  11
  12 //**********************************************************************************************************************
  13 ReadOtuCommand::ReadOtuCommand(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 filename = globaldata->inputFileName;
  17                 read = new ReadPhilFile(filename);
  18                 if (globaldata->getFormat() == "shared") {
  19                         //read in group map info.
  20                         groupMap = new GroupMap(globaldata->getGroupFile());
  21                 }
  22         }
  23         catch(exception& e) {
  24                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  25                 exit(1);
  26         }
  27         catch(...) {
  28                 cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  29                 exit(1);
  30         }
  31 }
  32
  33 //**********************************************************************************************************************
  34
  35 ReadOtuCommand::~ReadOtuCommand(){
  36         delete read;
  37 }
  38
  39 //**********************************************************************************************************************
  40
  41 int ReadOtuCommand::execute(){
  42         try {
  43                 read->read(&*globaldata);
  44                 if (globaldata->getFormat() == "shared") {
  45                         groupMap->readMap();
  46
  47                         //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
  48                         globaldata->gGroupmap = groupMap;
  49
  50                         shared = new SharedCommand();
  51                         shared->execute();
  52                         parselist = new ParseListCommand();
  53                         parselist->execute();
  54                 }
  55                 return 0;
  56         }
  57         catch(exception& e) {
  58                 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  59                 exit(1);
  60         }
  61         catch(...) {
  62                 cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************