From dbc9352256135d7b3e2b17dddc5c506770e2df92 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Fri, 6 Mar 2009 14:58:27 +0000
Subject: [PATCH] fixed parsimony bug

---
 ace.cpp       |  2 --
 parsimony.cpp | 16 +++++++++++++++-
 tree.cpp      | 10 +++-------
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/ace.cpp b/ace.cpp
index d074310..17049bd 100644
--- a/ace.cpp
+++ b/ace.cpp
@@ -13,9 +13,7 @@
 
 EstOutput Ace::getValues(SAbundVector* rank) {
 	try {
-		cout << "abund = " << abund << "\n";
 		data.resize(3,0);
-	//	vector<double> aceData(3,0);
 		double ace, acelci, acehci;
 	
 		int nrare = 0;
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;
diff --git a/tree.cpp b/tree.cpp
index 2cd9cba..1e115bd 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -178,7 +178,7 @@ map<string, int> Tree::mergeGroups(int i) {
 			for(it=parsimony.begin();it!=parsimony.end();it++){
 				if(it->second == 1){
 					parsimony.erase(it->first);
-					it--;
+//					it--;
 				}
 			}
 			//set one remaining groups to 1
@@ -240,24 +240,20 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
 				maxPars = parsimony[it->first];
 			}
 		}
-	
+			
 		// this is true if right child had a greater parsimony for a certain group
 		if(maxPars > 1){
 			//erase all the groups that are only 1 because you found something with 2.
 			for(it=parsimony.begin();it!=parsimony.end();it++){
 				if(it->second == 1){
 					parsimony.erase(it->first);
-					it--;
 				}
 			}
-			//set one remaining groups to 1
-			//so with our above example p[white] = 2 would be left and it would become p[white] = 1
 			for(it=parsimony.begin();it!=parsimony.end();it++){
 				parsimony[it->first] = 1;
 			}
+		}		
 		
-		}
-	
 		return parsimony;
 	}
 	catch(exception& e) {
-- 
2.39.2