X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtree.cpp;h=6fa4c3da814347cc60c0807bd16cb373fff8c962;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=be7dc79509abbc78aeeb0a66ab45ca57b0d1324a;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/readtree.cpp b/readtree.cpp
index be7dc79..6fa4c3d 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -20,12 +20,12 @@ ReadTree::ReadTree() {
 	}
 }
 /***********************************************************************/
-int ReadTree::AssembleTrees() {
+int ReadTree::AssembleTrees(map<string, string> nameMap) {
 	 try {
 		 //assemble users trees
 		 for (int i = 0; i < Trees.size(); i++) {
 			 if (m->control_pressed) { return 0;  }
-			 Trees[i]->assembleTree();
+			 Trees[i]->assembleTree(nameMap);
 		 }
 		 return 0;
 	 }
@@ -425,7 +425,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) {
 				map<string, int>::iterator it;
 				it = tmap->seqsPerGroup.find("xxx");
 				if (it == tmap->seqsPerGroup.end()) { //its a new group
-					tmap->namesOfGroups.push_back("xxx");
+					tmap->addGroup("xxx");
 					tmap->seqsPerGroup["xxx"] = 1;
 				}else {
 					tmap->seqsPerGroup["xxx"]++;