fixed parsimony for groups

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 3ef141ed8518eb4ff9a0057152484d2ef85b3968..54960cc516047f0f43ff8cde28f697512d9d6c91 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -17,7 +17,12 @@ EstOutput Parsimony::getValues(Tree* t) {
                data.resize(1,0);
                        
                int score = 0;
-                                       
+               
+               //create pgroups that reflect the groups the user want to use
+               for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+                       t->tree[i].pGroups = (t->mergeUserGroups(i));
+               }
+
                for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
                        int lc = t->tree[i].getLChild();
                        int rc = t->tree[i].getRChild();
@@ -25,21 +30,25 @@ EstOutput Parsimony::getValues(Tree* t) {
                        int iSize = t->tree[i].pGroups.size();
                        int rcSize = t->tree[rc].pGroups.size();
                        int lcSize = t->tree[lc].pGroups.size();
-                       
+cout << " i groups ";                  
                        //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--;  }
+cout << it->first << " ";
+                       //      if (inUsersGroups(it->first, globaldata->Groups) != true) {  iSize--;  }
                        }
+cout << endl << " rc groups ";
                        //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--;  }
+cout << it->first << " ";
+                               //if (inUsersGroups(it->first, globaldata->Groups) != true) {  rcSize--;  }
                        }
-                       
+cout << endl << " lc groups ";                 
                        //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--;  }
+cout << it->first << " ";
+                               //if (inUsersGroups(it->first, globaldata->Groups) != true) {  lcSize--;  }
                        }
-                       
+cout << endl;                  
                        //if isize are 0 then that branch is to be ignored
                        if (iSize == 0) { }
                        else if ((rcSize == 0) || (lcSize == 0)) { }