X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=1e115bddad1a451c181c4c26b90b758788df1155;hb=dbc9352256135d7b3e2b17dddc5c506770e2df92;hp=e34253d8cf90fc17b5ca72b0465a6d16a502da4b;hpb=8f92612d5a69f5245e63a20657e7d93519c0769e;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index e34253d..1e115bd 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;
 		
@@ -215,7 +178,7 @@ cout << i << lc << rc << endl;
 			for(it=parsimony.begin();it!=parsimony.end();it++){
 				if(it->second == 1){
 					parsimony.erase(it->first);
-					it--;
+//					it--;
 				}
 			}
 			//set one remaining groups to 1
@@ -277,24 +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) {