Exemple #1
0
void process_tree(struct rooted_tree *tree, struct parameters params)
{
	struct llist *outgroup_nodes = get_outgroup_nodes(tree, params.labels);
	if (! params.deroot) {
		/* re-root according to outgroup nodes */
		enum reroot_status result = reroot(tree, outgroup_nodes, 
				params.i_node_lbl_as_support);
		switch (result) {
		case REROOT_OK:
			dump_newick(tree->root);
			break;
		case LCA_IS_TREE_ROOT:
			if (params.try_ingroup)
				try_ingroup(tree, params);
			else {
				fprintf (stderr,
					"ERROR: Outgroup's LCA is tree's root "
					"- cannot reroot. Try -l.\n");
			}
			break;
		case NOT_PHYLOGRAM:
			fprintf (stderr, 
				"ERROR: Tree must be a phylogram, but some "
				"branch lengths are not defined - aborting.\n");
			break;
		default:
			assert(0);
		}
		destroy_all_rnodes(NULL);
		destroy_tree(tree);
	} else {
		enum deroot_status result = deroot(tree);
		switch (result) {
		case DEROOT_OK:
			dump_newick(tree->root);
			break;
		case NOT_BIFURCATING:
			fprintf (stderr,
				"ERROR: tree is already unrooted, or root"
				" has only 1 child - cannot deroot.\n");
			break;
		case BALANCED:
			fprintf (stderr,
				"ERROR: can't decide which of root's "
				"children is the outgroup.\n");
			break;
		case MEM_PROB:
			perror(NULL);
			break;
		default:
			assert(0);
		}
		destroy_all_rnodes(NULL);
		destroy_tree(tree);
	}
	destroy_llist(outgroup_nodes);
}
Exemple #2
0
void process_tree(struct rooted_tree *tree, struct parameters params)
{
	struct llist *outgroup_nodes = get_outgroup_nodes(tree, params.labels);
	if (! params.deroot) {
		/* re-root according to outgroup nodes */
		enum reroot_status result = reroot(tree, outgroup_nodes);
		switch (result) {
		case REROOT_OK:
			dump_newick(tree->root);
			break;
		case LCA_IS_TREE_ROOT:
			if (params.try_ingroup)
				try_ingroup(tree, params);
			else {
				fprintf (stderr,
					"Outgroup's LCA is tree's root "
					"- cannot reroot. Try -l.\n");
			}
			break;
		default:
			assert(0);
		}
		destroy_tree_cb(tree, NULL);
	} else {
		enum deroot_status result = deroot(tree);
		switch (result) {
		case DEROOT_OK:
			dump_newick(tree->root);
			break;
		case NOT_BIFURCATING:
			fprintf (stderr,
				"WARNING: tree is already unrooted, or root"
				" has only 1 child - cannot deroot.\n");
			break;
		case BALANCED:
			fprintf (stderr,
				"WARNING: can't decide which of root's "
				"children is the outgroup.\n");
			break;
		default:
			assert(0);
		}
		destroy_tree_cb(tree, NULL);
	}
	destroy_llist(outgroup_nodes);
}