added [ERROR] flag if command aborts

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 14138de30355151035a7ddca66f5bd928e534bc5..b49af32a76c1cbb2d65ab2a5bf32555a171c5de7 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -24,8 +24,7 @@ vector<string> OtuHierarchyCommand::getValidParameters(){
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["otuheirarchy"] = tempOutNames;
        }
@@ -60,10 +59,10 @@ vector<string> OtuHierarchyCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(string option) {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //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
@@ -157,7 +156,7 @@ OtuHierarchyCommand::~OtuHierarchyCommand(){}
 int OtuHierarchyCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
                vector<ListVector> lists = getListVectors();