added [ERROR] flag if command aborts

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index cb377273ebf711d1c7ef41363178a30a4add2e31..4ab81ea4ae3186265ce08286008fc48fcbac4881 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -62,8 +62,7 @@ vector<string> RareFactCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 RareFactCommand::RareFactCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["rarefaction"] = tempOutNames;
                outputTypes["r_chao"] = tempOutNames;
@@ -90,13 +89,13 @@ RareFactCommand::RareFactCommand(){
 RareFactCommand::RareFactCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                Estimators.clear();
                                
                //allow user to run help
-               if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+               if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -214,7 +213,7 @@ RareFactCommand::~RareFactCommand(){}
 int RareFactCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                string hadShared = "";
                if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }