added [ERROR] flag if command aborts

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 4eb652c9b951f0e1384eafeae722b6ea583b5790..a987594815b00a2e2aa40e177a794a99014bbe33 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -24,8 +24,7 @@ vector<string> PhyloDiversityCommand::getValidParameters(){
 //**********************************************************************************************************************
 PhyloDiversityCommand::PhyloDiversityCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["phylodiv"] = tempOutNames;
                outputTypes["rarefy"] = tempOutNames;
@@ -63,10 +62,10 @@ vector<string> PhyloDiversityCommand::getRequiredFiles(){
 PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               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
@@ -169,7 +168,7 @@ PhyloDiversityCommand::~PhyloDiversityCommand(){}
 int PhyloDiversityCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
                for (int i = 0; i < globaldata->Groups.size(); i++) { if (globaldata->Groups[i] == "xxx") { globaldata->Groups.erase(globaldata->Groups.begin()+i);  break; }  }