added [ERROR] flag if command aborts

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 7edb717853461ba4cd23f9845b36880dd9ce38ae..7da424c1ce0520fb8125915abb006126e93eeeec 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -25,8 +25,7 @@ vector<string> SeqSummaryCommand::getValidParameters(){
 //**********************************************************************************************************************
 SeqSummaryCommand::SeqSummaryCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;
        }
@@ -62,10 +61,10 @@ vector<string> SeqSummaryCommand::getRequiredFiles(){
 
 SeqSummaryCommand::SeqSummaryCommand(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
@@ -148,7 +147,7 @@ SeqSummaryCommand::~SeqSummaryCommand(){    /*      do nothing      */      }
 int SeqSummaryCommand::execute(){
        try{
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";