new_m->set_window(window->value());
new_m->set_threshold(threshold->value());
new_m->analyze();
-
+ // FIXME: why isn't the nway_paths refined_pathz structure just initialized
+ // FIXME: with the contents of pathz?
+ new_m->set_soft_threshold(threshold->value());
// copy over motifs
std::vector<Sequence> motifs_copy;
std::vector<Color> color_copy;