a few meaningless changes that are commented out

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index fb250d7fe96cb4ed38df8c0ce33d1c7e17911945..6b0a6d06474809f16fae1a0c17338ef1f7458dc7 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,47 +9,14 @@
 
 #include "systemcommand.h"
 
-//**********************************************************************************************************************
-vector<string> SystemCommand::getValidParameters(){    
-       try {
-               vector<string> myArray;
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SystemCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> SystemCommand::getRequiredParameters(){ 
-       try {
-               vector<string> myArray;
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SystemCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> SystemCommand::getRequiredFiles(){      
-       try {
-               vector<string> myArray;
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SystemCommand", "getRequiredFiles");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
 
+//**********************************************************************************************************************
 SystemCommand::SystemCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
@@ -74,12 +41,14 @@ SystemCommand::SystemCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void SystemCommand::help(){
+string SystemCommand::getHelpString(){
        try {
-               m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
-               m->mothurOut("The system has no parameters.\n");
-               m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
-               m->mothurOut("Example system(clear).\n");
+               string helpString = "";
+               helpString += "The system command allows you to execute a system command from within mothur.\n";
+               helpString += "The system has no parameters.\n";
+               helpString += "The system command should be in the following format: system(yourCommand).\n";
+               helpString += "Example system(clear).\n";
+               return helpString;
        }
        catch(exception& e) {
                m->errorOut(e, "SystemCommand", "help");
@@ -92,7 +61,7 @@ void SystemCommand::help(){
 int SystemCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                system(command.c_str());