X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=amovacommand.cpp;h=0a9b53b8af07ea837553355328aa6d00230c29f8;hp=c0b9aec10e4f8695f040e61e80910a8efeb310af;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3

diff --git a/amovacommand.cpp b/amovacommand.cpp
index c0b9aec..0a9b53b 100644
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -66,8 +66,7 @@ vector<string> AmovaCommand::getValidParameters(){
 //**********************************************************************************************************************
 AmovaCommand::AmovaCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["amova"] = tempOutNames;
 	}
@@ -105,12 +104,12 @@ vector<string> AmovaCommand::getRequiredFiles(){
 AmovaCommand::AmovaCommand(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
@@ -349,7 +348,7 @@ AmovaCommand::~AmovaCommand(){}
 int AmovaCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//read design file
 		designMap = new GroupMap(designfile);