X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.cpp;h=28b0221ba8458cb1a760fade14426ea6a7123568;hb=edad2fa8defaa6856b3606a215bf64b91340eeb4;hp=1eb3ceedb228220f8e8d86231866c1606a50b196;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 1eb3cee..28b0221 100644
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -34,7 +34,7 @@ vector<string> HeatMapSimCommand::getValidParameters(){
 //**********************************************************************************************************************
 HeatMapSimCommand::HeatMapSimCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["svg"] = tempOutNames;
 	}
@@ -70,14 +70,14 @@ vector<string> HeatMapSimCommand::getRequiredFiles(){
 HeatMapSimCommand::HeatMapSimCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 		Groups.clear();
 		Estimators.clear();
 			
 		//allow user to run help
-		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -272,7 +272,7 @@ HeatMapSimCommand::~HeatMapSimCommand(){}
 int HeatMapSimCommand::execute(){
 	try {
 	
-		if (abort == true)  { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		heatmap = new HeatMapSim(outputDir);