mods to trim.seqs

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 708724a4e5cd46643e7ec29464b61c1f34c7cd41..abc07d0743a0a3e8f7172c27fe4094571abb3d5c 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,14 +9,47 @@
 
 #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; }
@@ -59,7 +92,7 @@ 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());