X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=634bf0caff8d279e259c64fb76f28737aaaa8219;hb=0486bc2eed084ac387d2f59b6d23d13b2382daf7;hp=b80a3abb4bb76bd0a5da3afa5548df0771797e45;hpb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index b80a3ab..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++) {
@@ -406,7 +405,7 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
 		//flip it so you can print it
 		int count = 0;
 		for (int r=0; r<globaldata->Groups.size(); r++) { 
-			for (int l = r+1; l < globaldata->Groups.size(); l++) {
+			for (int l = 0; l < r; l++) {
 				dists[r][l] = utreeScores[count][0];
 				dists[l][r] = utreeScores[count][0];
 				count++;