From 9daea1c357d32c6a7b34c5cbec122b7cfc5c92e3 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Fri, 6 Mar 2009 12:50:31 +0000
Subject: [PATCH] fixed bug in read tree

---
 readtree.cpp | 31 +++++++++++++++----------------
 tree.cpp     | 39 +--------------------------------------
 tree.h       |  1 -
 3 files changed, 16 insertions(+), 55 deletions(-)

diff --git a/readtree.cpp b/readtree.cpp
index 59239c8..a253741 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -336,25 +336,24 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 			if(n1 == -1) {
 				cerr << "Name: " << name << " not found in your groupfile.. \n"; exit(1);
 				
-				globaldata->gTreemap->namesOfSeqs.push_back(name);
-				globaldata->gTreemap->treemap[name].groupname = "xxx";
-				globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+				//globaldata->gTreemap->namesOfSeqs.push_back(name);
+				//globaldata->gTreemap->treemap[name].groupname = "xxx";
+				//globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
 				
-				map<string, int>::iterator it;
-				it = globaldata->gTreemap->seqsPerGroup.find("xxx");
-				if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
-					globaldata->gTreemap->namesOfGroups.push_back("xxx");
-					globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
-				}else {
-					globaldata->gTreemap->seqsPerGroup["xxx"]++;
-				}
+				//map<string, int>::iterator it;
+				//it = globaldata->gTreemap->seqsPerGroup.find("xxx");
+				//if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
+				//	globaldata->gTreemap->namesOfGroups.push_back("xxx");
+				//	globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+				//}else {
+				//	globaldata->gTreemap->seqsPerGroup["xxx"]++;
+				//}
 				
 				//find index in tree of name
-				n1 = T->getIndex(name);
-				group = "xxx";
-				numLeaves++;
-				numNodes = 2*numLeaves - 1;
-				//T->resetTree();
+				//n1 = T->getIndex(name);
+				//group = "xxx";
+				//numLeaves++;
+				//numNodes = 2*numLeaves - 1;
 			}
 			
 			T->tree[n1].setGroup(group);
diff --git a/tree.cpp b/tree.cpp
index e34253d..2cd9cba 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -49,43 +49,6 @@ Tree::Tree() {
 	}		
 }
 
-/*****************************************************************/
-void Tree::resetTree(){
-try {
-		numLeaves = globaldata->gTreemap->getNumSeqs();
-		numNodes = 2*numLeaves - 1;
-		
-		tree.resize(numNodes);
-
-		//initialize tree with correct number of nodes, name and group info.
-		for (int i = 0; i < numNodes; i++) {
-			//initialize leaf nodes
-			if (i <= (numLeaves-1)) {
-				tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
-				tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
-				//set pcount and pGroup for groupname to 1.
-				tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
-				tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
-				//Treemap knows name, group and index to speed up search
-				globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
-	
-			//intialize non leaf nodes
-			}else if (i > (numLeaves-1)) {
-				tree[i].setName("");
-				tree[i].setGroup("");
-			}
-		}
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function resetTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Tree class function resetTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
-
-}
 /*****************************************************************/
 int Tree::getIndex(string searchName) {
 	try {
@@ -189,7 +152,7 @@ map<string, int> Tree::mergeGroups(int i) {
 	try {
 		int lc = tree[i].getLChild();
 		int rc = tree[i].getRChild();
-cout << i << lc << rc << endl;
+
 		//set parsimony groups to left child
 		map<string,int> parsimony = tree[lc].pGroups;
 		
diff --git a/tree.h b/tree.h
index 828b038..d6a3b55 100644
--- a/tree.h
+++ b/tree.h
@@ -24,7 +24,6 @@ public:
 	
 	
 	void getCopy(Tree*);  //makes tree a copy of the one passed in.
-	void resetTree(); //this is needed to allow user to omit names from the group file
 	void assembleRandomTree();
 	void assembleRandomUnifracTree(vector<string>);
 	void assembleRandomUnifracTree(string, string);
-- 
2.39.2