added merge.groups command

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 489a2f11f7c3a13df14bedf42a05339e86fcaeb2..fb250d7fe96cb4ed38df8c0ce33d1c7e17911945 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,9 +9,42 @@
 
 #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){
+SystemCommand::SystemCommand(string option)  {
        try {
                abort = false;
                
@@ -19,7 +52,7 @@ SystemCommand::SystemCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
+                       if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
                        else { 
                                //check for outputdir and inputdir parameters
                                int commaPos = option.find_first_of(',');
@@ -35,7 +68,7 @@ SystemCommand::SystemCommand(string option){
 
        }
        catch(exception& e) {
-               errorOut(e, "SystemCommand", "SystemCommand");
+               m->errorOut(e, "SystemCommand", "SystemCommand");
                exit(1);
        }
 }
@@ -43,13 +76,13 @@ SystemCommand::SystemCommand(string option){
 
 void SystemCommand::help(){
        try {
-               mothurOut("The system command allows you to execute a system command from within mothur.\n");
-               mothurOut("The system has no parameters.\n");
-               mothurOut("The system command should be in the following format: system(yourCommand).\n");
-               mothurOut("Example system(clear).\n");
+               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");
        }
        catch(exception& e) {
-               errorOut(e, "SystemCommand", "help");
+               m->errorOut(e, "SystemCommand", "help");
                exit(1);
        }
 }
@@ -67,7 +100,7 @@ int SystemCommand::execute(){
        }
 
        catch(exception& e) {
-               errorOut(e, "SystemCommand", "execute");
+               m->errorOut(e, "SystemCommand", "execute");
                exit(1);
        }
 }