-
- assertEquals(integrationTestFile.hmm.getSymbols(), symbols);
-
- List<Double> averages = new ArrayList<>();
- averages.add(1.24257);
- averages.add(1.59430);
- averages.add(1.62906);
- averages.add(1.16413);
-
- assertEquals(integrationTestFile.hmm
- .getAverageMatchStateEmissionProbabilities(), averages);
-
- assertEquals(integrationTestFile.hmm.getInsertZeroEmissions().get(2),
- 1.38629);
- assertEquals(integrationTestFile.hmm.getInsertZeroEmissions().get(3),
- 1.38629);
-
- assertEquals(integrationTestFile.hmm.getBeginStateTransitions().get(1),
- 3.94183);
- assertEquals(integrationTestFile.hmm.getBeginStateTransitions().get(4),
- 0.26236);
-
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(1).get(1),
- 2.37873);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(8).get(0),
- 2.16916);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(12).get(2),
- 2.32214);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(43).get(3),
- 2.60783);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(54).get(2),
- 2.46442);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(23).get(2),
- 2.50691);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(56).get(1),
- 2.32720);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(65).get(0),
- 2.79349);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(21).get(0),
- 2.54484);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(79).get(3),
- 2.88183);
- assertEquals(integrationTestFile.hmm.getMatchEmissions().get(76).get(3),
- 1.84373);
-
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(23).get(0),
- 1.35803);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(54).get(3),
- 1.46331);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(65).get(3),
- 1.39101);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(57).get(2),
- 1.38112);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(42).get(1),
- 1.58747);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(12).get(3),
- 1.38740);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(6).get(1),
- 1.38524);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(59).get(0),
- 1.03649);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(78).get(0),
- 1.38629);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(17).get(2),
- 1.39937);
- assertEquals(integrationTestFile.hmm.getInsertEmissions().get(0).get(2),
- 1.38629);
-
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(13).get(1),
- 4.02482);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(64).get(2),
- 4.03073);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(45).get(6),
- 0.42814);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(71).get(4),
- 0.28542);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(32).get(5),
- 1.18729);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(9).get(0),
- 0.03536);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(0).get(3),
- 1.46634);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(31).get(6),
- 0.44749);
- assertNull(
- integrationTestFile.hmm.getStateTransitions().get(79).get(2));
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(3).get(1),
- 4.05203);
- assertEquals(
- integrationTestFile.hmm.getStateTransitions().get(16).get(4),
- 0.26771);
-
- assertEquals(integrationTestFile.hmm.getAlignmentColumnIndexes().get(0)
- .intValue(), 1);
- assertEquals(integrationTestFile.hmm.getAlignmentColumnIndexes().get(9)
- .intValue(), 18);
- assertEquals(integrationTestFile.hmm.getAlignmentColumnIndexes().get(12)
- .intValue(), 28);
- assertEquals(integrationTestFile.hmm.getAlignmentColumnIndexes().get(56)
- .intValue(), 999);
- assertEquals(integrationTestFile.hmm.getAlignmentColumnIndexes().get(79)
- .intValue(), 1112);
-
- assertEquals(integrationTestFile.hmm.getAnnotations().get(0).get("RF")
- .charValue(), 'x');
- assertEquals(integrationTestFile.hmm.getAnnotations().get(3).get("CS")
- .charValue(), '-');
- assertEquals(integrationTestFile.hmm.getAnnotations().get(65)
- .get("CONS").charValue(), 't');
- assertEquals(integrationTestFile.hmm.getAnnotations().get(23).get("MM")
- .charValue(), '-');
- assertEquals(integrationTestFile.hmm.getAnnotations().get(56).get("MM")
- .charValue(), '-');
- assertEquals(integrationTestFile.hmm.getAnnotations().get(76).get("RF")
- .charValue(), 'x');
- assertEquals(integrationTestFile.hmm.getAnnotations().get(79)
- .get("CONS").charValue(), 'a');
+ symbols.add('V');
+ symbols.add('W');
+ symbols.add('Y');
+
+ assertEquals(pKinase.hmm.getSymbols(), symbols);
+
+ assertEquals(pKinase.hmm.getMatchEmission(0, 19), 3.43274);
+ assertEquals(pKinase.hmm.getMatchEmission(12, 12), 4.33979);
+ assertEquals(pKinase.hmm.getMatchEmission(23, 7), 3.65600);
+ assertEquals(pKinase.hmm.getMatchEmission(54, 1), 4.76187);
+ assertEquals(pKinase.hmm.getMatchEmission(79, 0), 2.81579);
+ assertEquals(pKinase.hmm.getMatchEmission(100, 0), 1.86496);
+ assertEquals(pKinase.hmm.getMatchEmission(112, 14), 2.77179);
+ assertEquals(pKinase.hmm.getMatchEmission(143, 17), 5.10478);
+ assertEquals(pKinase.hmm.getMatchEmission(156, 4), 4.69372);
+ assertEquals(pKinase.hmm.getMatchEmission(178, 3), 2.52594);
+ assertEquals(pKinase.hmm.getMatchEmission(210, 2), 4.23598);
+ assertEquals(pKinase.hmm.getMatchEmission(260, 19), 3.81122);
+
+ assertEquals(pKinase.hmm.getInsertEmission(2, 1), 4.42225);
+ assertEquals(pKinase.hmm.getInsertEmission(15, 6), 3.72501);
+ assertEquals(pKinase.hmm.getInsertEmission(22, 9), 2.69355);
+ assertEquals(pKinase.hmm.getInsertEmission(57, 2), 2.77519);
+ assertEquals(pKinase.hmm.getInsertEmission(62, 14), 2.89801);
+ assertEquals(pKinase.hmm.getInsertEmission(95, 17), 2.98532);
+ assertEquals(pKinase.hmm.getInsertEmission(105, 4), 3.46354);
+ assertEquals(pKinase.hmm.getInsertEmission(134, 1), 4.42225);
+ assertEquals(pKinase.hmm.getInsertEmission(143, 0), 2.68618);
+ assertEquals(pKinase.hmm.getInsertEmission(152, 16), 2.77519);
+ assertEquals(pKinase.hmm.getInsertEmission(203, 16), 2.77519);
+ assertEquals(pKinase.hmm.getInsertEmission(255, 12), 2.73739);
+
+ assertEquals(pKinase.hmm.getStateTransition(0, 6),
+ Double.NEGATIVE_INFINITY);
+ assertEquals(pKinase.hmm.getStateTransition(3, 6), 0.95510);
+ assertEquals(pKinase.hmm.getStateTransition(29, 3), 0.61958);
+ assertEquals(pKinase.hmm.getStateTransition(46, 4), 0.77255);
+ assertEquals(pKinase.hmm.getStateTransition(53, 1), 5.01631);
+ assertEquals(pKinase.hmm.getStateTransition(79, 2), 5.73865);
+ assertEquals(pKinase.hmm.getStateTransition(101, 2), 5.73865);
+ assertEquals(pKinase.hmm.getStateTransition(120, 5), 0.48576);
+ assertEquals(pKinase.hmm.getStateTransition(146, 5), 0.70219);
+ assertEquals(pKinase.hmm.getStateTransition(169, 3), 1.23224);
+ assertEquals(pKinase.hmm.getStateTransition(209, 0), 0.01003);
+ assertEquals(pKinase.hmm.getStateTransition(243, 1), 5.01631);
+
+ assertEquals(pKinase.hmm.getNodeAlignmentColumn(3).intValue(), 3);
+ assertEquals(pKinase.hmm.getReferenceAnnotation(7), '-');
+ assertEquals(pKinase.hmm.getConsensusResidue(23), 't');
+ assertEquals(pKinase.hmm.getMaskedValue(30), '-');
+ assertEquals(pKinase.hmm.getConsensusStructure(56), 'S');
+
+ assertEquals(pKinase.hmm.getNodeAlignmentColumn(78).intValue(), 136);
+ assertEquals(pKinase.hmm.getReferenceAnnotation(93), '-');
+ assertEquals(pKinase.hmm.getConsensusResidue(145), 'a');
+ assertEquals(pKinase.hmm.getMaskedValue(183), '-');
+ assertEquals(pKinase.hmm.getConsensusStructure(240), 'H');