added [ERROR] flag if command aborts

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 2a3d138d77497d545a04c259f55dae41d3191413..6b0e4f991f01f7d3a6e323f2670819e00ded79f9 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -25,8 +25,7 @@ vector<string> SubSampleCommand::getValidParameters(){
 //**********************************************************************************************************************
 SubSampleCommand::SubSampleCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["shared"] = tempOutNames;
                outputTypes["list"] = tempOutNames;
@@ -68,12 +67,12 @@ vector<string> SubSampleCommand::getRequiredFiles(){
 SubSampleCommand::SubSampleCommand(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
@@ -279,7 +278,7 @@ SubSampleCommand::~SubSampleCommand(){}
 int SubSampleCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (sharedfile != "")   {   getSubSampleShared();       }
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }