From f3edf14c46814ca437960f0e1070abfbea582c26 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 28 Feb 2011 12:08:07 +0000
Subject: [PATCH] fixed unweighted command

---
 Mothur.xcodeproj/project.pbxproj |  5 +++--
 readtree.cpp                     |  2 +-
 unweighted.cpp                   | 11 ++++++-----
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 8caeba7..ccb5aa2 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1625,7 +1625,7 @@
 			attributes = {
 				ORGANIZATIONNAME = "Schloss Lab";
 			};
-			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
 			compatibilityVersion = "Xcode 3.1";
 			developmentRegion = English;
 			hasScannedForEncodings = 1;
@@ -1950,6 +1950,7 @@
 				GCC_OPTIMIZATION_LEVEL = 0;
 				INSTALL_PATH = /usr/local/bin;
 				PRODUCT_NAME = Mothur;
+				SDKROOT = macosx10.6;
 			};
 			name = Debug;
 		};
@@ -2048,7 +2049,7 @@
 			defaultConfigurationIsVisible = 0;
 			defaultConfigurationName = Release;
 		};
-		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
 				1DEB928A08733DD80010E9CD /* Debug */,
diff --git a/readtree.cpp b/readtree.cpp
index e8aeacc..308115d 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -217,7 +217,7 @@ string ReadNewickTree::nexusTranslation() {
 			
 			if (lastChar == ',') {  name.erase(name.end()-1); } //erase the comma
 			*/	
-		cout << "numseqs = " << numSeqs << endl;
+		
 		string number, name;
 		for(int i=0;i<numSeqs;i++){
 			
diff --git a/unweighted.cpp b/unweighted.cpp
index 08e83ec..a75ddc5 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -199,14 +199,14 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 				m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
 				m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
 			}else{
-				
+				//cout << "trying to get root" << endl;	
 				//if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
 				getRoot(t, nodeBelonging, namesOfGroupCombos[h]);
-				
+				//cout << "here" << endl;	
 				for(int i=0;i<t->getNumNodes();i++){
 					
 					if (m->control_pressed) {  return data; }
-					
+					//cout << i << endl;	
 					//pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 					//pcountSize = 2, not unique to one group
 					//pcountSize = 1, unique to one group
@@ -497,17 +497,18 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) { 
 	try {
 		//you are a leaf so get your parent
-		int index = t->tree[index].getParent();
+		int index = t->tree[v].getParent();
 		
 		if (includeRoot) { 
 			rootForGrouping[grouping].clear();
 		}else {
+			
 			//my parent is a potential root
 			rootForGrouping[grouping].insert(index);
 			
 			//while you aren't at root
 			while(t->tree[index].getParent() != -1){
-				
+				//cout << index << endl;	
 				if (m->control_pressed) {  return 0; }
 				
 				//am I the root for this grouping? if so I want to stop "early"
-- 
2.39.2