added order=A or order=B to trim.flows and shhh.flows commands. added load balancing...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 0df53d5649881c924be60140338e5fff7c2bc840..b793dc885ef9213f290f118be55066a0e2837086 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -644,6 +644,7 @@ int TreeGroupCommand::makeSimsShared() {
             }else {
                 m->clearGroups();
                 Groups.clear();
+                m->Treenames.clear();
                 vector<SharedRAbundVector*> temp;
                 for (int i = 0; i < lookup.size(); i++) {
                     if (lookup[i]->getNumSeqs() < subsampleSize) { 
@@ -652,6 +653,7 @@ int TreeGroupCommand::makeSimsShared() {
                     }else { 
                         Groups.push_back(lookup[i]->getGroup()); 
                         temp.push_back(lookup[i]);
+                        m->Treenames.push_back(lookup[i]->getGroup());
                     }
                 } 
                 lookup = temp;
@@ -917,11 +919,15 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
             }
                }
-               
+        
+               if (m->debug) {  m->mothurOut("[DEBUG]: done with iters.\n"); }
+            
         if (iters != 1) {
             //we need to find the average distance and standard deviation for each groups distance
             vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals);  
             
+            if (m->debug) {  m->mothurOut("[DEBUG]: found averages.\n"); }
+            
             //create average tree for each calc
             for (int i = 0; i < calcDists.size(); i++) {
                 vector< vector<double> > matrix; //square matrix to represent the distance
@@ -951,6 +957,8 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 if (newTree != NULL) { writeTree(outputFile, newTree); }                
             }
             
+            if (m->debug) {  m->mothurOut("[DEBUG]: done averages trees.\n"); }
+            
             //create all trees for each calc and find their consensus tree
             for (int i = 0; i < calcDists.size(); i++) {
                 if (m->control_pressed) { break; }
@@ -982,7 +990,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                         int row = calcDistsTotals[myIter][i][j].seq1;
                         int column = calcDistsTotals[myIter][i][j].seq2;
                         double dist = calcDistsTotals[myIter][i][j].dist;
-                        
+                       
                         matrix[row][column] = dist;
                         matrix[column][row] = dist;
                     }
@@ -997,11 +1005,15 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 outAll.close();
                 if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
                 
+                if (m->debug) {  m->mothurOut("[DEBUG]: done all trees.\n"); }
+                
                 Consensus consensus;
                 //clear old tree names if any
                 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
                 Tree* conTree = consensus.getTree(trees);
                 
+                if (m->debug) {  m->mothurOut("[DEBUG]: done cons tree.\n"); }
+                
                 //create a new filename
                 variables["[tag]"] = "cons";
                 string conFile = getOutputFileName("tree",variables);