From 4542a79d20176ff0ee830b0f9d4f4c92637439d9 Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Mon, 17 Dec 2012 13:07:31 -0500
Subject: [PATCH] fixed issue in tree.shared when shared file was not sorted

---
 sharedutilities.cpp   |  4 +++-
 treegroupscommand.cpp | 17 +++++++++--------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 71d7782..d9891db 100644
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -22,7 +22,9 @@ void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVect
 		}
 		
 		lookup.clear();
-		
+        
+		sort(Groups.begin(), Groups.end());
+        
 		//create and initialize vector of sharedvectors, one for each group
 		for (int i = 0; i < Groups.size(); i++) { 
 			SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 90d336d..0d01459 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -429,7 +429,10 @@ int TreeGroupCommand::execute(){
 			m->Treenames.clear();
 			
 			//fills globaldatas tree names
-			m->Treenames = m->getGroups();
+			//m->Treenames = m->getGroups();
+            for (int k = 0; k < lookup.size(); k++) {
+                m->Treenames.push_back(lookup[k]->getGroup());
+            }
 		
 			if (m->control_pressed) { return 0; }
 			
@@ -463,7 +466,10 @@ int TreeGroupCommand::execute(){
 
 			list = readMatrix->getListVector();
 			SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
-
+            
+            //clear globaldatas old tree names if any
+			m->Treenames.clear();
+            
 			//make treemap
             if (ct != NULL) { delete ct; }
 			ct = new CountTable();
@@ -475,17 +481,12 @@ int TreeGroupCommand::execute(){
                 nameMap.insert(bin); 
                 gps.insert(bin); 
                 groupMap[bin] = bin;
+                m->Treenames.push_back(bin);
             }
             ct->createTable(nameMap, groupMap, gps);
 			
 			vector<string> namesGroups = ct->getNamesOfGroups();
 			m->setGroups(namesGroups);
-		
-			//clear globaldatas old tree names if any
-			m->Treenames.clear();
-            
-			//fills globaldatas tree names
-			m->Treenames = m->getGroups();
 			
 			//used in tree constructor 
 			m->runParse = false;
-- 
2.39.2