Biggish SQL query

gistfile1.java

	public Set<PhyloTree> findByTopology3(TaxonVariant a, TaxonVariant b, TaxonVariant c) {
		Set<PhyloTree> returnVal = new HashSet<PhyloTree>();
				
		Set<TaxonVariant> aTV = getTaxonLabelHome().expandTaxonVariant(a);
		Set<TaxonVariant> bTV = getTaxonLabelHome().expandTaxonVariant(b);
		Set<TaxonVariant> cTV = getTaxonLabelHome().expandTaxonVariant(c);
		
		if (aTV.isEmpty() || bTV.isEmpty() || cTV.isEmpty()) {
			// XXX This avoids a query syntax error later on but maybe isn't
			// the best behavior.
			return new HashSet<PhyloTree> ();
		}
		
		String query = "select distinct a.tree.rootNode "
			+
			// Find the trees with three nodes a, b, and c, such that...
			"from PhyloTreeNode as a, PhyloTreeNode as b, PhyloTreeNode as c, "
			+
			// There's a node "ab" (which will be an ancestor of both a and b)
			"PhyloTreeNode as ab "
			+
			// All four nodes are in the same tree
			"where a.tree = b.tree " + "and a.tree = c.tree " + "and a.tree = ab.tree "
			+
			"and a.taxonLabel.taxonVariant in (:a) " +
			"and b.taxonLabel.taxonVariant in (:b) " +
			"and c.taxonLabel.taxonVariant in (:c) " +
						// ab is an ancestor of a
			"and ab.leftNode < a.leftNode and ab.rightNode > a.rightNode " +
			// ab is an ancestor of b
			"and ab.leftNode < b.leftNode and ab.rightNode > b.rightNode " +
			// ab is NOT an ancestor of c
			"and (ab.leftNode >= c.leftNode or ab.rightNode <= c.rightNode) ";
		
		Query q = getSession().createQuery(query);

		q.setParameterList("a", aTV);
		q.setParameterList("b", bTV);
		q.setParameterList("c", cTV);
		List<PhyloTreeNode> rootNodes = q.list();

		if (rootNodes.isEmpty()) {
			return returnVal;
		}

		Query t = getSession().createQuery("from PhyloTree where rootNode in (:roots)");
		t.setParameterList("roots", rootNodes);

		returnVal.addAll(t.list());
		return returnVal;
	}