TreeReader* reader = new TreeReader(treefile, "", namefile);
vector<Tree*> T = reader->getTrees();
- map<string, string> nameMap = reader->getNameMap();
+ map<string, string> nameMap;
+ m->readNames(namefile, nameMap);
delete reader;
//print new Tree
T[0]->print(out, nameMap);
out.close();
- delete (T[0]->getTreeMap());
+ delete (T[0]->getCountTable());
for (int i = 0; i < T.size(); i++) { delete T[i]; }
//set phylip file as new current phylipfile