}
m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->setTreeFile(treefile);
+
if (groupfile != "") {
//read in group map info.
tmap = new TreeMap(groupfile);