X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=0df53d5649881c924be60140338e5fff7c2bc840;hb=1f0e54b53b714781f3f2fee7d01177fade98a625;hp=90d336da38f57f70fa0f5ddb59125cc2099ec346;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 90d336d..0df53d5 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;
@@ -889,6 +890,9 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 
                 //Close all thread handles and free memory allocations.
                 for(int i=0; i < pDataArray.size(); i++){
+                    if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+                        m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
+                    }
                     for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) {  delete pDataArray[i]->thisLookup[j];  } 
                     
                     for (int k = 0; k < calcDists.size(); k++) {
@@ -916,31 +920,7 @@ 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++) {