Merge remote-tracking branch 'origin/master'

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index be7dc79509abbc78aeeb0a66ab45ca57b0d1324a..6fa4c3da814347cc60c0807bd16cb373fff8c962 100644 (file)
--- 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"]++;