added [ERROR] flag if command aborts

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 3ed9bf2131a45ac7a4b0ac44d959b16bfe28cd36..4809964db6f2e3a65bd30f72d8f157fd7bc1fa44 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -25,8 +25,7 @@ vector<string> MGClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 MGClusterCommand::MGClusterCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
                outputTypes["rabund"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> MGClusterCommand::getRequiredFiles(){
 MGClusterCommand::MGClusterCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
-               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 {
                        //valid paramters for this command
@@ -202,7 +201,7 @@ MGClusterCommand::~MGClusterCommand(){}
 int MGClusterCommand::execute(){
        try {
                
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read names file
                if (namefile != "") {