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[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 3ef141ed8518eb4ff9a0057152484d2ef85b3968..e76a7b039c4e91afec85c27f375b22f120185f7b 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 +30,7 @@ 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();
-                       
-                       //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--;  }
-                       }
-                       //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--;  }
-                       }
-                       
-                       //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 isize are 0 then that branch is to be ignored
                        if (iSize == 0) { }
                        else if ((rcSize == 0) || (lcSize == 0)) { }
@@ -47,8 +38,13 @@ EstOutput Parsimony::getValues(Tree* t) {
                        else if(iSize > rcSize || iSize > lcSize){
                                score++;
                        }
+                       cout << i << ' ' << score << ": ";
+                       t->tree[i].printNode();
                } 
                
+               string hold;
+               cin >> hold;
+               
                data[0] = score;
                
                return data;
@@ -64,3 +60,5 @@ EstOutput Parsimony::getValues(Tree* t) {
 
 }
 
+/**************************************************************************************************/
+