added [ERROR] flag if command aborts

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index e7fb357b9bd3028fcbd32bf388af9bbb9b4c2847..129c9700c4f945813cbb639f028d71a57b88d7b1 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -33,8 +33,7 @@ vector<string> LibShuffCommand::getValidParameters(){
 //**********************************************************************************************************************
 LibShuffCommand::LibShuffCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["coverage"] = tempOutNames;
                outputTypes["libshuffsummary"] = tempOutNames;
@@ -72,11 +71,11 @@ vector<string> LibShuffCommand::getRequiredFiles(){
 LibShuffCommand::LibShuffCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                Groups.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
@@ -189,7 +188,7 @@ void LibShuffCommand::help(){
 int LibShuffCommand::execute(){
        try {
                
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                savedDXYValues = form->evaluateAll();
                savedMinValues = form->getSavedMins();