added [ERROR] flag if command aborts

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 9cf5a73a56802b65bae10d1c28187f214ebcfb56..fdacc3a58fb799ba9b1fcff2497d9ba5ab562ccd 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -25,8 +25,7 @@ vector<string> ParseListCommand::getValidParameters(){
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["list"] = tempOutNames;
        }
@@ -61,11 +60,11 @@ vector<string> ParseListCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                        
                //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
@@ -170,7 +169,7 @@ ParseListCommand::~ParseListCommand(){}
 int ParseListCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //set fileroot
                string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));