added [ERROR] flag if command aborts

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d3d574e470c352d046c07d52a7f1a30d02d4a902..8d9f177941549b62742f76e0b38c5337ab5b3922 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -26,8 +26,7 @@ vector<string> ClassifyOtuCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClassifyOtuCommand::ClassifyOtuCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["constaxonomy"] = tempOutNames;
                outputTypes["taxsummary"] = tempOutNames;
@@ -63,13 +62,13 @@ vector<string> ClassifyOtuCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
        try{
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                                
                //allow user to run help
                if (option == "help") { 
-                       help(); abort = true;
+                       help(); abort = true; calledHelp = true;
                } else {
                        //valid paramters for this command
                        string Array[] =  {"list","label","name","taxonomy","cutoff","probs","basis","reftaxonomy","group","outputdir","inputdir"};
@@ -229,7 +228,7 @@ ClassifyOtuCommand::~ClassifyOtuCommand(){}
 int ClassifyOtuCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //if user gave a namesfile then use it
                if (namefile != "") {   readNamesFile();        }