assertNull(sm.getDescription());
assertTrue(sm.isDNA());
assertFalse(sm.isProtein());
+ assertEquals(sm.getMinimumScore(), 1.1f);
assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
assertEquals(sm.getPairwiseScore('a', 't'), 1.4f);
assertEquals(sm.getPairwiseScore('U', 'x'), 3.5f);
assertEquals(sm.getPairwiseScore('u', 'x'), 3.5f);
- assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
- assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
+ // X (upper) and '.' unmapped - get minimum score
+ assertEquals(sm.getPairwiseScore('U', 'X'), 1.1f);
+ assertEquals(sm.getPairwiseScore('A', '.'), 1.1f);
assertEquals(sm.getPairwiseScore('-', '-'), 7.6f);
assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
}