prov.getEntry(0).addParam(new Param());
prov.getEntry(0).getParam(0).setName("treeType");
prov.getEntry(0).getParam(0).setType("utf8");
- prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
- // general parameter
+ prov.getEntry(0).getParam(0).setContent(NJTree.NEIGHBOUR_JOINING);
+ // TODO: type of tree is a general parameter
int ranges[] = tp.getTree().seqData.getVisibleContigs();
// VisibleContigs are with respect to alignment coordinates. Still need
// offsets