fixed parsimony for groups

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 6239f75f08a59c9a5f690401e15ef93c19fe8f50..3ef141ed8518eb4ff9a0057152484d2ef85b3968 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -17,47 +17,35 @@ EstOutput Parsimony::getValues(Tree* t) {
                data.resize(1,0);
                        
                int score = 0;
-                       
+                                       
                for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
                        int lc = t->tree[i].getLChild();
                        int rc = t->tree[i].getRChild();
                        
-                       int iSize = 0;
-                       int rcSize = 0;
-                       int lcSize = 0;
-
+                       int iSize = t->tree[i].pGroups.size();
+                       int rcSize = t->tree[rc].pGroups.size();
+                       int lcSize = t->tree[lc].pGroups.size();
+                       
                        //add in all the groups the users wanted
                        for (it = t->tree[i].pGroups.begin(); it != t->tree[i].pGroups.end(); it++) {
-                               if (inUsersGroups(it->first, globaldata->Groups) == true) {  iSize++;  }
+                               if (inUsersGroups(it->first, globaldata->Groups) != true) {  iSize--;  }
                        }
-
-                       //if that leaves no groups give it 1 so it will cause no change to parent
-                       if (iSize == 0) { iSize++; }
-                       
                        //add in all the groups the users wanted
                        for (it = t->tree[rc].pGroups.begin(); it != t->tree[rc].pGroups.end(); it++) {
-
-                               if (inUsersGroups(it->first, globaldata->Groups) == true) {  rcSize++;  }
+                               if (inUsersGroups(it->first, globaldata->Groups) != true) {  rcSize--;  }
                        }
                        
-                       //if that leaves no groups give it 1 so it will cause no change to parent
-                       if (rcSize == 0) { rcSize++; }
-
-                               
                        //add in all the groups the users wanted
                        for (it = t->tree[lc].pGroups.begin(); it != t->tree[lc].pGroups.end(); it++) {
-
-                               if (inUsersGroups(it->first, globaldata->Groups) == true) {  lcSize++;  }
+                               if (inUsersGroups(it->first, globaldata->Groups) != true) {  lcSize--;  }
                        }
                        
-                       //if that leaves no groups give it 1 so it will cause no change to parent
-                       if (lcSize == 0) { lcSize++; }
-
-
+                       //if isize are 0 then that branch is to be ignored
+                       if (iSize == 0) { }
+                       else if ((rcSize == 0) || (lcSize == 0)) { }
                        //if you have more groups than either of your kids then theres been a change.
-                        if(iSize > rcSize || iSize > lcSize){
+                       else if(iSize > rcSize || iSize > lcSize){
                                score++;
-
                        }
                }