added [ERROR] flag if command aborts

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index e67659f50db215490313062d442336afbd2f25e1..fbe7964e67f7eb52600bbab1bde5dc28d3ef3a1f 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -49,8 +49,7 @@ vector<string> SummaryCommand::getValidParameters(){
 //**********************************************************************************************************************
 SummaryCommand::SummaryCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;
        }
@@ -87,13 +86,13 @@ vector<string> SummaryCommand::getRequiredFiles(){
 SummaryCommand::SummaryCommand(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
@@ -194,7 +193,7 @@ SummaryCommand::~SummaryCommand(){}
 int SummaryCommand::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);  }