changed unifrac.weighted()

diff --git a/weighted.cpp b/weighted.cpp
index a0d2f5ef4117191886cb3abcc078a4620b609abc..c43180d53409cf583ce86f3388dc9a8eb709988a 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -26,17 +26,18 @@ EstOutput Weighted::getValues(Tree* t) {
                
                //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
                int n = 1;
+               int count = 0;
                for (int i=1; i<numGroups; i++) { 
-                       for (int l = n; l < numGroups; l++) {
+                       for (int l = n; l < numGroups; l++) {   
                                //initialize weighted scores
                                if (globaldata->Groups.size() == 0) {
                                        WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0;
-                                       D.push_back(0.0000);  //initialize a spot in D for each combination
                                }else {
                                        WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] = 0.0;
-                                       D.push_back(0.0000); //initialize a spot in D for each combination
                                }
                                
+                               D.push_back(0.0000); //initialize a spot in D for each combination
+                               
                                /********************************************************/
                                //calculate a D value for each group combo
                                for(int v=0;v<t->getNumLeaves();v++){
@@ -64,7 +65,7 @@ EstOutput Weighted::getValues(Tree* t) {
                                                        //is this sum from a sequence which is in this groupCombo
                                                        if ((t->tree[v].getGroup() == tmap->namesOfGroups[i-1]) || (t->tree[v].getGroup() == tmap->namesOfGroups[l])) {
                                                                sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-                                                               D[n-1] += sum; 
+                                                               D[count] += sum; 
                                                        }
                                                }
                                        }else {
@@ -73,16 +74,17 @@ EstOutput Weighted::getValues(Tree* t) {
                                                        //is this sum from a sequence which is in this groupCombo
                                                        if ((t->tree[v].getGroup() == globaldata->Groups[i-1]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
                                                                sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-                                                               D[n-1] += sum; 
+                                                               D[count] += sum; 
                                                        }
                                                }
                                        }
                                }
                                /*********************************************************/
+                               count++;
                        }
+                       n++;
                }
                
-               
                data.clear(); //clear out old values
        
                for(int i=0;i<t->getNumNodes();i++){
@@ -143,22 +145,21 @@ EstOutput Weighted::getValues(Tree* t) {
                //calculate weighted score for each group combination
                double UN;      
                n = 1;
+               count = 0;
                for (int i=1; i<numGroups; i++) { 
                        for (int l = n; l < numGroups; l++) {
                                //the user has not entered specific groups
                                if (globaldata->Groups.size() == 0) {
-                                       UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[n-1]);
-cout << "W score = " << WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] << endl;
+                                       UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[count]);
                                }else {//they have entered specific groups
-                                       UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[n-1]);
-cout << "W score = " << WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] << endl;
+                                       UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[count]);
                                }
-cout << " D = "<< D[n-1] << endl;
                                if (isnan(UN) || isinf(UN)) { UN = 0; } 
                                data.push_back(UN);
+                               count++;
                        }
+                       n++;
                }
-
                return data;
        }
        catch(exception& e) {