}
m->runParse = true;
+ m->Groups.clear();
+ m->namesOfGroups.clear();
+ m->Treenames.clear();
+ m->names.clear();
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//randomtree will tell us if user had their own treefile or if they just want the random distribution
//user has entered their own tree
if (randomtree == "") {
+
+ m->setTreeFile(treefile);
+
if (groupfile != "") {
//read in group map info.
tmap = new TreeMap(groupfile);