X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=634bf0caff8d279e259c64fb76f28737aaaa8219;hb=0486bc2eed084ac387d2f59b6d23d13b2382daf7;hp=79ee042a9ac883ddadbfef057dff813a4e51cf2a;hpb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 79ee042..634bf0c 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -25,8 +25,7 @@ vector<string> UnifracUnweightedCommand::getValidParameters(){
 UnifracUnweightedCommand::UnifracUnweightedCommand(){	
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["unweighted"] = tempOutNames;
 		outputTypes["uwsummary"] = tempOutNames;
@@ -66,11 +65,11 @@ vector<string> UnifracUnweightedCommand::getRequiredFiles(){
 UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		Groups.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
@@ -191,7 +190,7 @@ void UnifracUnweightedCommand::help(){
 int UnifracUnweightedCommand::execute() {
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		int start = time(NULL);
 		
@@ -260,7 +259,7 @@ int UnifracUnweightedCommand::execute() {
 				}
 				
 				//report progress
-				m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();	
+//				m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();	
 			}
 	
 			for(int a = 0; a < numComp; a++) {