fixed bug in unifrac commands with nexus translation if files don't match

diff --git a/unweighted.cpp b/unweighted.cpp
index 312d549b11a1a4a7a4e7960d5a0689885e9a52d2..d0eea3dc2b9f1f507213627e6d18df9a4e6afe68 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -168,7 +168,8 @@ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfG
 /**************************************************************************************************/
 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) { 
  try {
-               
+       
+        
                EstOutput results; results.resize(num);
                
                int count = 0;
@@ -178,7 +179,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
         
                        
                for (int h = start; h < (start+num); h++) {
-       //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;         
+                               
                        if (m->control_pressed) { return results; }
                
                        double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
@@ -214,7 +215,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                                map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
                                                if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } 
                                        }
-                                       //
+                                                                               
                                        //unique calc
                                        if (pcountSize == 0) { }
                                        else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root 
@@ -228,7 +229,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                        }
                                        
                                }
-       cout << UniqueBL << '\t' << totalBL << endl;            
+       //cout << UniqueBL << '\t' << totalBL << endl;          
                                UW = (UniqueBL / totalBL);  
        
                                if (isnan(UW) || isinf(UW)) { UW = 0; }
@@ -238,11 +239,11 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                        count++;
 
                        //report progress
-                       if((count % twentyPercent) == 0) {      float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
+                       //if((count % twentyPercent) == 0) {    float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
                }
                
                //report progress
-               if((count % twentyPercent) != 0) {      float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
+               //if((count % twentyPercent) != 0) {    float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
                
                return results; 
        }
@@ -536,7 +537,7 @@ int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) {
                while(t->tree[index].getParent() != -1){
                        int parent = t->tree[index].getParent();
                        rootForGrouping[grouping].insert(parent);
-                       cout << parent << " in root" << endl;
+                       //cout << parent << " in root" << endl;
                        index = parent;
                }