X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=19a320afa409e9e7be546b69c85f8c3c99e05fa6;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=892010839f519495744e0d68518124ffa1778fae;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 8920108..19a320a 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -24,8 +24,7 @@ vector<string> HeatMapCommand::getValidParameters(){
 //**********************************************************************************************************************
 HeatMapCommand::HeatMapCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["svg"] = tempOutNames;
 	}
@@ -62,12 +61,12 @@ vector<string> HeatMapCommand::getRequiredFiles(){
 HeatMapCommand::HeatMapCommand(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
@@ -183,7 +182,7 @@ HeatMapCommand::~HeatMapCommand(){
 int HeatMapCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir);
 		format = globaldata->getFormat();