X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=2a673b0cb622bd97b8f91dc4f1c2e9c69de19e8d;hb=692e0c1f69a78b568dc85cbdcea9fb6c189e2e6c;hp=6c184701e2a4d3054ddd8bb74e6d586afee4ccd4;hpb=fb5a52d8d7896ba00c9ccc6add22ed89c5fb2ad7;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 6c18470..2a673b0 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -12,6 +12,8 @@
 /**************************************************************************************************/
 EstOutput Parsimony::getValues(Tree* t) {
 	try {
+		globaldata = GlobalData::getInstance();
+		
 		data.resize(1,0);
 			
 		int score = 0;
@@ -20,8 +22,42 @@ EstOutput Parsimony::getValues(Tree* t) {
 			int lc = t->tree[i].getLChild();
 			int rc = t->tree[i].getRChild();
 			
-			 if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
+			int iSize = 0;
+			int rcSize = 0;
+			int lcSize = 0;
+
+			//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) == 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) == 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) == true) {  lcSize++;  }
+			}
+			
+			//if that leaves no groups give it 1 so it will cause no change to parent
+			if (lcSize == 0) { lcSize++; }
+
+
+			//if you have more groups than either of your kids then theres been a change.
+			 if(iSize > rcSize || iSize > lcSize){
 				score++;
+
 			}
 		} 
 		
@@ -40,3 +76,21 @@ EstOutput Parsimony::getValues(Tree* t) {
 
 }
 /**************************************************************************************************/
+
+bool Parsimony::inUsersGroups(string groupname) {
+	try {
+		for (int i = 0; i < globaldata->Groups.size(); i++) {
+			if (groupname == globaldata->Groups[i]) { return true; }
+		}
+		return false;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the Parsimony class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/**************************************************************************************************/