weightedcommand

[mothur.git] / weighted.cpp

diff --git a/weighted.cpp b/weighted.cpp
index c43180d53409cf583ce86f3388dc9a8eb709988a..915cf368353dcdbb1617b9d239ce17ff6890450b 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -173,4 +173,97 @@ EstOutput Weighted::getValues(Tree* t) {
 
 }
 
-/**************************************************************************************************/
\ No newline at end of file
+/**************************************************************************************************/
+EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) { 
+ try {
+               globaldata = GlobalData::getInstance();
+               
+               data.clear(); //clear out old values
+               
+               //initialize weighted score
+               WScore[(groupA+groupB)] = 0.0;
+               float D = 0.0;
+               
+                                               
+               /********************************************************/
+               //calculate a D value for the group combo
+               for(int v=0;v<t->getNumLeaves();v++){
+                       int index = v;
+                       double sum = 0.0000;
+               
+                       //while you aren't at root
+                       while(t->tree[index].getParent() != -1){
+                                                       
+                               //if you have a BL
+                               if(t->tree[index].getBranchLength() != -1){
+                                       sum += t->tree[index].getBranchLength();
+                               }
+                               index = t->tree[index].getParent();
+                       }
+                                               
+                       //get last breanch length added
+                       if(t->tree[index].getBranchLength() != -1){
+                               sum += 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; 
+                       }
+               }
+               /********************************************************/                              
+               
+               //calculate u for the group comb 
+               for(int i=0;i<t->getNumNodes();i++){
+                       double u;
+                       //does this node have descendants from groupA
+                       it = t->tree[i].pcount.find(groupA);
+                       //if it does u = # of its descendants with a certain group / total number in tree with a certain group
+                       if (it != t->tree[i].pcount.end()) {
+                               u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA];
+                       }else { u = 0.00; }
+               
+                                               
+                       //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];
+                       }
+                                               
+                       u = abs(u) * t->tree[i].getBranchLength();
+                                       
+                       //save groupcombs u value
+                       WScore[(groupA+groupB)] += u;
+               }
+               
+               /********************************************************/
+               
+               //calculate weighted score for the group combination
+               double UN;      
+               UN = (WScore[(groupA+groupB)] / D);
+               
+               if (isnan(UN) || isinf(UN)) { UN = 0; } 
+               data.push_back(UN);
+                               
+               return data; 
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
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