systemcommand.cpp

   1 /*
   2  *  systemcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "systemcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 SystemCommand::SystemCommand(string option){
  15         try {
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
  23                         else {
  24                                 //check for outputdir and inputdir parameters
  25                                 int commaPos = option.find_first_of(',');
  26
  27                                 //if there is a comma then grab string up to that pos
  28                                 if (commaPos != option.npos) {
  29                                         option = option.substr(0, commaPos);
  30                                 }
  31
  32                                 command = option;
  33                         }
  34                 }
  35
  36         }
  37         catch(exception& e) {
  38                 errorOut(e, "SystemCommand", "SystemCommand");
  39                 exit(1);
  40         }
  41 }
  42 //**********************************************************************************************************************
  43
  44 void SystemCommand::help(){
  45         try {
  46                 mothurOut("The system command allows you to execute a system command from within mothur.\n");
  47                 mothurOut("The system has no parameters.\n");
  48                 mothurOut("The system command should be in the following format: system(yourCommand).\n");
  49                 mothurOut("Example system(clear).\n");
  50         }
  51         catch(exception& e) {
  52                 errorOut(e, "SystemCommand", "help");
  53                 exit(1);
  54         }
  55 }
  56
  57 //**********************************************************************************************************************
  58
  59 int SystemCommand::execute(){
  60         try {
  61
  62                 if (abort == true) { return 0; }
  63
  64                 system(command.c_str());
  65
  66                 return 0;
  67         }
  68
  69         catch(exception& e) {
  70                 errorOut(e, "SystemCommand", "execute");
  71                 exit(1);
  72         }
  73 }
  74
  75 //**********************************************************************************************************************