added distance option to summary.shared

[mothur.git] / unweighted.cpp

diff --git a/unweighted.cpp b/unweighted.cpp
index a9515d160a93c50813f61f5a54c1da6423cd4da3..2afc4a71486617b61308b651fef413895ba05b54 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -24,7 +24,7 @@ EstOutput Unweighted::getValues(Tree* t, int p, string o) {
                int numComp = 0;
                vector< vector<string> > namesOfGroupCombos;
                for (int r=0; r<numGroups; r++) { 
-                       for (int l = r+1; l < numGroups; l++) {
+                       for (int l = 0; l < r; l++) {
                                numComp++;
                                vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
                                namesOfGroupCombos.push_back(groups);
@@ -241,7 +241,7 @@ EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, st
                int numComp = 0;
                vector< vector<string> > namesOfGroupCombos;
                for (int r=0; r<numGroups; r++) { 
-                       for (int l = r+1; l < numGroups; l++) {
+                       for (int l = 0; l < r; l++) {
                                numComp++;
                                vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
                                namesOfGroupCombos.push_back(groups);
@@ -401,7 +401,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                        double totalBL = 0.00;  //all branch lengths
                        double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
                                
-                       for(int i=0;i<t->getNumNodes();i++){
+                       for(int i=0;i<copyTree->getNumNodes();i++){
                        
                                if (m->control_pressed) {  return data; }
                                
@@ -411,15 +411,15 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                
                                int pcountSize = 0;
                                for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
-                                       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; } } 
+                                       map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
+                                       if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } 
                                }
                                
                                if (pcountSize == 0) { }
-                               else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());   }
+                               else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());     }
                                        
-                               if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
-                                       totalBL += abs(t->tree[i].getBranchLength()); 
+                               if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
+                                       totalBL += abs(copyTree->tree[i].getBranchLength()); 
                                }
                        }