added [ERROR] flag if command aborts

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 26cdcda0178bcfdbfc8c89fbbbced8866edb796c..58fb3649887afbd9e6e6b3441650c336688c0168 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -47,8 +47,7 @@ vector<string> CorrAxesCommand::getRequiredParameters(){
 //**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["corr.axes"] = tempOutNames;
        }
@@ -72,11 +71,11 @@ vector<string> CorrAxesCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                globaldata = GlobalData::getInstance();
                
                //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
@@ -221,7 +220,7 @@ CorrAxesCommand::~CorrAxesCommand(){}
 int CorrAxesCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                /*************************************************************************************/
                // use smart distancing to get right sharedRabund and convert to relabund if needed  //