working on chimeras

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index d1bc40ea72b096e6ae8ffce9f5488dec31a85000..8a312297cc677ffb78aec597bf8128efbf500a0f 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -26,6 +26,8 @@ EstOutput Weighted::getValues(Tree* t) {
                                //initialize weighted scores
                                WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
                                
+                               vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
+                               
                                D.push_back(0.0000); //initialize a spot in D for each combination
                                
                                /********************************************************/
@@ -52,9 +54,25 @@ EstOutput Weighted::getValues(Tree* t) {
                                        //is this sum from a sequence which is in one of the users groups
                                        if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
                                                //is this sum from a sequence which is in this groupCombo
-                                               if ((t->tree[v].getGroup() == globaldata->Groups[i]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
-                                                       sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-                                                       D[count] += sum; 
+                                               if (inUsersGroups(t->tree[v].getGroup(), groups)) {
+                                                       int numSeqsInGroupI, numSeqsInGroupL;
+                                                       
+                                                       map<string, int>::iterator it;
+                                                       it = t->tree[v].pcount.find(groups[0]);
+                                                       if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
+                                                               numSeqsInGroupI = it->second;
+                                                       }else{ numSeqsInGroupI = 0; }
+                                                       
+                                                       it = t->tree[v].pcount.find(groups[1]);
+                                                       if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
+                                                               numSeqsInGroupL = it->second;
+                                                       }else{ numSeqsInGroupL = 0; }
+                                                       
+                                                       double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+
+                                                       //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+                                                       
+                                                       D[count] += weightedSum; 
                                                }
                                        }
                                }
@@ -125,6 +143,7 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
                WScore[(groupA+groupB)] = 0.0;
                float D = 0.0;
                
+               vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
                                                
                /********************************************************/
                //calculate a D value for the group combo
@@ -147,9 +166,25 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
                                sum += abs(t->tree[index].getBranchLength());
                        }
                                                
-                       if ((t->tree[v].getGroup() == groupA) || (t->tree[v].getGroup() == groupB)) {
-                               sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
-                               D += sum; 
+                       if (inUsersGroups(t->tree[v].getGroup(), groups)) {
+                               int numSeqsInGroupI, numSeqsInGroupL;
+                                                       
+                               map<string, int>::iterator it;
+                               it = t->tree[v].pcount.find(groups[0]);
+                               if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i
+                                       numSeqsInGroupI = it->second;
+                               }else{ numSeqsInGroupI = 0; }
+                               
+                               it = t->tree[v].pcount.find(groups[1]);
+                               if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l
+                                       numSeqsInGroupL = it->second;
+                               }else{ numSeqsInGroupL = 0; }
+                               
+                               double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
+                               
+                               //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+                               
+                               D += weightedSum; 
                        }
                }
                /********************************************************/