RNASpecificTree t = new RNASpecificTree();
t.buildFromViennaFormat(
"CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
"...((((...))...(((...)))..))....".toCharArray());
SizeRelatedTreePruning cost = new SizeRelatedTreePruning(1);
cost.calculateCost(t);
Assert.assertEquals(17, t.getWeight(10, t.getNeighborIx(10, 5)),0.01);
Assert.assertEquals(3, t.getWeight(6, t.getNeighborIx(6, 7)),0.01);
}