mods to amova command

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index b80a3abb4bb76bd0a5da3afa5548df0771797e45..634bf0caff8d279e259c64fb76f28737aaaa8219 100644 (file)
--- 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++;