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 vector<string> SystemCommand::getValidParameters(){
  14         try {
  15                 vector<string> myArray;
  16                 return myArray;
  17         }
  18         catch(exception& e) {
  19                 m->errorOut(e, "SystemCommand", "getValidParameters");
  20                 exit(1);
  21         }
  22 }
  23 //**********************************************************************************************************************
  24 vector<string> SystemCommand::getRequiredParameters(){
  25         try {
  26                 vector<string> myArray;
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "SystemCommand", "getRequiredParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 vector<string> SystemCommand::getRequiredFiles(){
  36         try {
  37                 vector<string> myArray;
  38                 return myArray;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "SystemCommand", "getRequiredFiles");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46
  47 SystemCommand::SystemCommand(string option)  {
  48         try {
  49                 abort = false; calledHelp = false;
  50
  51                 //allow user to run help
  52                 if(option == "help") { help(); abort = true; calledHelp = true; }
  53
  54                 else {
  55                         if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
  56                         else {
  57                                 //check for outputdir and inputdir parameters
  58                                 int commaPos = option.find_first_of(',');
  59
  60                                 //if there is a comma then grab string up to that pos
  61                                 if (commaPos != option.npos) {
  62                                         option = option.substr(0, commaPos);
  63                                 }
  64
  65                                 command = option;
  66                         }
  67                 }
  68
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "SystemCommand", "SystemCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76
  77 void SystemCommand::help(){
  78         try {
  79                 m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
  80                 m->mothurOut("The system has no parameters.\n");
  81                 m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
  82                 m->mothurOut("Example system(clear).\n");
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "SystemCommand", "help");
  86                 exit(1);
  87         }
  88 }
  89
  90 //**********************************************************************************************************************
  91
  92 int SystemCommand::execute(){
  93         try {
  94
  95                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  96
  97                 system(command.c_str());
  98
  99                 return 0;
 100         }
 101
 102         catch(exception& e) {
 103                 m->errorOut(e, "SystemCommand", "execute");
 104                 exit(1);
 105         }
 106 }
 107
 108 //**********************************************************************************************************************