added [ERROR] flag if command aborts

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 1ecef653e11fe15d206b41fd958834be194455ff..78f26047e0debdf3e620b2e0179bfab12fe93354 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetListCountCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["otu"] = tempOutNames;
        }
@@ -61,12 +60,12 @@ vector<string> GetListCountCommand::getRequiredFiles(){
 GetListCountCommand::GetListCountCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                                
                //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
@@ -168,7 +167,7 @@ GetListCountCommand::~GetListCountCommand(){}
 
 int GetListCountCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                globaldata->setFormat("list");