changes while testing

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 90d336da38f57f70fa0f5ddb59125cc2099ec346..80698f1b4b0317719421dbe9c4af3c0583bd9d97 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; }
                        
@@ -455,7 +458,7 @@ int TreeGroupCommand::execute(){
                 readMatrix->read(nameMap);
             }else if (countfile != "") {
                 ct = new CountTable();
-                ct->readTable(countfile);
+                ct->readTable(countfile, true);
                 readMatrix->read(ct);
             }else {
                 readMatrix->read(nameMap);
@@ -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;
@@ -643,6 +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) { 
@@ -651,6 +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;
@@ -659,8 +662,18 @@ int TreeGroupCommand::makeSimsShared() {
             
             if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
         }
-        
         numGroups = lookup.size();
+        
+        //sanity check to make sure processors < numComparisions
+        int numDists = 0;
+        for(int i=0;i<numGroups;i++){
+            for(int j=0;j<i;j++){
+                numDists++;
+                if (numDists > processors) { break; }
+            }
+        }
+        if (numDists < processors) { processors = numDists; }
+        
                lines.resize(processors);
                for (int i = 0; i < processors; i++) {
                        lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
@@ -889,6 +902,9 @@ 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++) {
@@ -912,35 +928,17 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 thisItersLookup.clear();
                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
             }
+            
+            if (m->debug) {  m->mothurOut("[DEBUG]: iter = " + toString(thisIter) + ".\n"); }
                }
-               
+        
+               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);  
             
-            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;
-                }
-            }
+            if (m->debug) {  m->mothurOut("[DEBUG]: found averages.\n"); }
             
             //create average tree for each calc
             for (int i = 0; i < calcDists.size(); i++) {
@@ -971,6 +969,8 @@ 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; }
@@ -1002,7 +1002,7 @@ 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;
                     }
@@ -1017,11 +1017,15 @@ 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);