Big tree query that the RDB handled just fine

gistfile1.txt

                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) ";