-
- assertEquals(testHMM.getMatchEmission(0, 2), 1.62906);
- assertEquals(testHMM.getMatchEmission(2, 1), 2.37873);
- assertEquals(testHMM.getMatchEmission(12, 2), 2.61355);
- assertEquals(testHMM.getMatchEmission(26, 0), 1.86925);
- assertEquals(testHMM.getMatchEmission(32, 3), 2.58263);
- assertEquals(testHMM.getMatchEmission(59, 3), 2.20507);
- assertEquals(testHMM.getMatchEmission(63, 0), 0.41244);
- assertEquals(testHMM.getMatchEmission(69, 1), 3.17398);
- assertEquals(testHMM.getMatchEmission(76, 2), 2.65861);
-
- assertEquals(testHMM.getInsertEmission(0, 1), 1.38629);
- assertEquals(testHMM.getInsertEmission(1, 2), 1.38629);
- assertEquals(testHMM.getInsertEmission(31, 3), 1.28150);
- assertEquals(testHMM.getInsertEmission(43, 0), 1.32290);
- assertEquals(testHMM.getInsertEmission(48, 2), 1.52606);
- assertEquals(testHMM.getInsertEmission(52, 1), 1.62259);
- assertEquals(testHMM.getInsertEmission(67, 0), 1.38141);
- assertEquals(testHMM.getInsertEmission(70, 3), 1.38629);
- assertEquals(testHMM.getInsertEmission(80, 3), 1.38629);
-
- assertEquals(testHMM.getStateTransition(2, 0), 0.03725);
- assertEquals(testHMM.getStateTransition(6, 1), 3.89715);
- assertEquals(testHMM.getStateTransition(9, 3), 1.38021);
- assertEquals(testHMM.getStateTransition(20, 4), 0.23815);
- assertEquals(testHMM.getStateTransition(34, 6), 0.33363);
- assertEquals(testHMM.getStateTransition(46, 5), 1.05474);
- assertEquals(testHMM.getStateTransition(57, 6), 0.31164);
- assertEquals(testHMM.getStateTransition(68, 2), 3.99242);
- assertEquals(testHMM.getStateTransition(80, 6),
+
+ assertEquals(getMatchEmission(0, 2, testHMM), 1.62906);
+ assertEquals(getMatchEmission(2, 1, testHMM), 2.37873);
+ assertEquals(getMatchEmission(12, 2, testHMM), 2.61355);
+ assertEquals(getMatchEmission(26, 0, testHMM), 1.86925);
+ assertEquals(getMatchEmission(32, 3, testHMM), 2.58263);
+ assertEquals(getMatchEmission(59, 3, testHMM), 2.20507);
+ assertEquals(getMatchEmission(63, 0, testHMM), 0.41244);
+ assertEquals(getMatchEmission(69, 1, testHMM), 3.17398);
+ assertEquals(getMatchEmission(76, 2, testHMM), 2.65861);
+
+ assertEquals(getInsertEmission(0, 1, testHMM), 1.38629);
+ assertEquals(getInsertEmission(1, 2, testHMM), 1.38629);
+ assertEquals(getInsertEmission(31, 3, testHMM), 1.28150);
+ assertEquals(getInsertEmission(43, 0, testHMM), 1.32290);
+ assertEquals(getInsertEmission(48, 2, testHMM), 1.52606);
+ assertEquals(getInsertEmission(52, 1, testHMM), 1.62259);
+ assertEquals(getInsertEmission(67, 0, testHMM), 1.38141);
+ assertEquals(getInsertEmission(70, 3, testHMM), 1.38629);
+ assertEquals(getInsertEmission(80, 3, testHMM), 1.38629);
+
+ assertEquals(getStateTransition(2, 0, testHMM), 0.03725);
+ assertEquals(getStateTransition(6, 1, testHMM), 3.89715);
+ assertEquals(getStateTransition(9, 3, testHMM), 1.38021);
+ assertEquals(getStateTransition(20, 4, testHMM), 0.23815);
+ assertEquals(getStateTransition(34, 6, testHMM), 0.33363);
+ assertEquals(getStateTransition(46, 5, testHMM), 1.05474);
+ assertEquals(getStateTransition(57, 6, testHMM), 0.31164);
+ assertEquals(getStateTransition(68, 2, testHMM), 3.99242);
+ assertEquals(getStateTransition(80, 6, testHMM),