added [ERROR] flag if command aborts

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 7ab15df6db6eb276c9ab2e8696d3de56dd4a6c85..21695e328c90590572a9efebc7caf562c2525c75 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -88,8 +88,7 @@ vector<string> CollectSharedCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CollectSharedCommand::CollectSharedCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["sharedchao"] = tempOutNames;
                outputTypes["sharedsobs"] = tempOutNames;
@@ -141,14 +140,14 @@ CollectSharedCommand::CollectSharedCommand(){
 CollectSharedCommand::CollectSharedCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                Estimators.clear();
                Groups.clear();
                
                //allow user to run help
-               if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+               if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -439,7 +438,7 @@ CollectSharedCommand::~CollectSharedCommand(){
 int CollectSharedCommand::execute(){
        try {
                
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //if the users entered no valid calculators don't execute command
                if (cDisplays.size() == 0) { return 0; }