X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=e76a7b039c4e91afec85c27f375b22f120185f7b;hb=9099173ea17b13be96563c7579ecc8dc2ef65d20;hp=3ef141ed8518eb4ff9a0057152484d2ef85b3968;hpb=06da1833191d5dee7e206f436d9631680f1e7c42;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 3ef141e..e76a7b0 100644
--- 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) {
 
 }
 
+/**************************************************************************************************/
+