added primer.design command. fixed bug with linux unifrac subsampling, metastats...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 90d336da38f57f70fa0f5ddb59125cc2099ec346..7803d89497a7fface1856dff7d374cb563a6328d 100644 (file)
--- 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;
@@ -916,31 +917,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                
         if (iters != 1) {
             //we need to find the average distance and standard deviation for each groups distance
-            
-            vector< vector<seqDist>  > calcAverages; calcAverages.resize(treeCalculators.size()); 
-            for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
-                calcAverages[i].resize(calcDistsTotals[0][i].size());
-                
-                for (int j = 0; j < calcAverages[i].size(); j++) {
-                    calcAverages[i][j].seq1 = calcDists[i][j].seq1;
-                    calcAverages[i][j].seq2 = calcDists[i][j].seq2;
-                    calcAverages[i][j].dist = 0.0;
-                }
-            }
-            
-            for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
-                for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
-                    for (int j = 0; j < calcAverages[i].size(); j++) {
-                        calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
-                    }
-                }
-            }
-            
-            for (int i = 0; i < calcAverages.size(); i++) {  //finds average.
-                for (int j = 0; j < calcAverages[i].size(); j++) {
-                    calcAverages[i][j].dist /= (float) iters;
-                }
-            }
+            vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals);  
             
             //create average tree for each calc
             for (int i = 0; i < calcDists.size(); i++) {