X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.cpp;h=fc1a8b6f48821a3d66aa1fb9c70799260c56c241;hb=dbc9352256135d7b3e2b17dddc5c506770e2df92;hp=0dea64e99a5f7bbe3adfe3dbd648ab8fb5365acf;hpb=ed04a159be4f1fab2850fa4dd2f40bf51e94e974;p=mothur.git

diff --git a/parsimony.cpp b/parsimony.cpp
index 0dea64e..fc1a8b6 100644
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -89,9 +89,12 @@ EstOutput Parsimony::getValues(Tree* t) {
 		
 			//create pgroups that reflect the groups the user want to use
 			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+//				cout << i << "..." << endl;
 				copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 			}
 		
+//			map<string,int>::iterator it;
+			
 			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 				int lc = copyTree->tree[i].getLChild();
 				int rc = copyTree->tree[i].getRChild();
@@ -99,7 +102,15 @@ EstOutput Parsimony::getValues(Tree* t) {
 				int iSize = copyTree->tree[i].pGroups.size();
 				int rcSize = copyTree->tree[rc].pGroups.size();
 				int lcSize = copyTree->tree[lc].pGroups.size();
-		
+				
+//				cout << i+1 << '\t' << lc+1 << '\t' << rc+1 << ":\t";
+				
+//				for(it=copyTree->tree[i].pGroups.begin();it!=copyTree->tree[i].pGroups.end();it++){
+//					cout << it->first << '\t';
+//				}
+				
+//				cout << " : " << iSize << '\t' << rcSize << '\t' << lcSize << '\t';
+					
 				//if isize are 0 then that branch is to be ignored
 				if (iSize == 0) { }
 				else if ((rcSize == 0) || (lcSize == 0)) { }
@@ -107,9 +118,12 @@ EstOutput Parsimony::getValues(Tree* t) {
 				else if(iSize > rcSize || iSize > lcSize){
 					score++;
 				}
+//				cout << score << endl;
 			} 
 		
 			data[count] = score;
+			string hold;
+//			cin >> hold;
 		}
 		
 		return data;