added [ERROR] flag if command aborts

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 143135f18f7cd61d68f9750944dd70a8493e803c..239a4bc65d7d80ddf6322eca0188550068cf758f 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -37,8 +37,7 @@ vector<string> IndicatorCommand::getRequiredParameters(){
 //**********************************************************************************************************************
 IndicatorCommand::IndicatorCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;
                outputTypes["summary"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> IndicatorCommand::getRequiredFiles(){
 IndicatorCommand::IndicatorCommand(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
@@ -199,7 +198,7 @@ IndicatorCommand::~IndicatorCommand(){}
 int IndicatorCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                //read designfile if given and set up globaldatas groups for read of sharedfiles
                if (designfile != "") {