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

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index a0d593c803f691821afdb680e79be80f179b0afa..b158815f90f266e07d64d4efa173fb7c4edaa0a0 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -183,7 +183,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                        
                                D[count] += weightedSum;
                        }
-
+                       
                        //adding the wieghted sums from group l
                        for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l
                                map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
@@ -194,15 +194,13 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                        
                                D[count] += weightedSum;
                        }
-                       
                        count++;
                }
-               
+        
                //calculate u for the group comb 
-               
                for (int h = start; h < (start+num); h++) {     
                        //report progress
-                       m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
+                       //m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
                                                
                        string groupA = namesOfGroupCombos[h][0]; 
                        string groupB = namesOfGroupCombos[h][1];
@@ -224,6 +222,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                                
                                //does this node have descendants from group l
                                it = t->tree[i].pcount.find(groupB);
+                               
                                //if it does subtract their percentage from u
                                if (it != t->tree[i].pcount.end()) {
                                        u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB];
@@ -236,9 +235,8 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                                                WScore[(groupA+groupB)] += u; 
                                        }
                                }
-                               
-                               
                        }
+                       
                }
                
                /********************************************************/
@@ -372,7 +370,7 @@ double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) {
                        
                        int sib = lc;
                        if (lc == index) { sib = rc; }
-                       
+                                               
                        map<string, int>::iterator itGroup;
                        int pcountSize = 0;
                        itGroup = t->tree[sib].pcount.find(groupA);
@@ -402,12 +400,12 @@ double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) {
                
                //get all nodes above the root to add so we don't add their u values above
                index = *(rootForGrouping[grouping].begin());
+               
                while(t->tree[index].getParent() != -1){
                        int parent = t->tree[index].getParent();
                        rootForGrouping[grouping].insert(parent);
                        index = parent;
                }
-               
                return sum;
        }
        catch(exception& e) {