added [ERROR] flag if command aborts

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 7b58162d20d8ac1910323c2946f7f8b4c05299af..d20f4af0acd4861cea64688e6e05460e42cbaf75 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -25,8 +25,7 @@ vector<string> ReverseSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ReverseSeqsCommand::ReverseSeqsCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
        }
@@ -62,10 +61,10 @@ vector<string> ReverseSeqsCommand::getRequiredFiles(){
 
 ReverseSeqsCommand::ReverseSeqsCommand(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
@@ -144,7 +143,7 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){  /*      do nothing      */      }
 int ReverseSeqsCommand::execute(){
        try{
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ifstream inFASTA;
                m->openInputFile(fasta, inFASTA);