Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HiddenMarkovModelTest	17	57	6	1.0100%	Show methods

Class HiddenMarkovModelTest

Class HiddenMarkovModelTest	Line # 17	Total Statements 57	Complexity 6	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	2323	4.04	1.01	1.0 1.0100%
testGetMatchEmissionProbabilities() : void   testGetMatchEmissionProbabilities() : void	4040	11.011	1.01	1.0 1.0100%
testGetInsertEmissionProbabilities() : void   testGetInsertEmissionProbabilities() : void	6565	9.09	1.01	1.0 1.0100%
testGetStateTransitionProbabilities() : void   testGetStateTransitionProbabilities() : void	8484	14.014	1.01	1.0 1.0100%
testGetConsensusSequence() : void   testGetConsensusSequence() : void	118118	9.09	1.01	1.0 1.0100%
testGetInformationContent() : void   testGetInformationContent() : void	140140	10.010	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.23809524	jalview.datamodel.HiddenMarkovModelTest.testGetStateTransitionProbabilitiesjalview.datamodel.HiddenMarkovModelTest.testGetStateTransitionProbabilities	1PASS
	0.1904762	jalview.datamodel.HiddenMarkovModelTest.testGetMatchEmissionProbabilitiesjalview.datamodel.HiddenMarkovModelTest.testGetMatchEmissionProbabilities	1PASS
	0.17460318	jalview.datamodel.HiddenMarkovModelTest.testGetInformationContentjalview.datamodel.HiddenMarkovModelTest.testGetInformationContent	1PASS
	0.15873016	jalview.datamodel.HiddenMarkovModelTest.testGetConsensusSequencejalview.datamodel.HiddenMarkovModelTest.testGetConsensusSequence	1PASS
	0.15873016	jalview.datamodel.HiddenMarkovModelTest.testGetInsertEmissionProbabilitiesjalview.datamodel.HiddenMarkovModelTest.testGetInsertEmissionProbabilities	1PASS

 

Source view

1		package jalview.datamodel;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.io.DataSourceType;
6		import jalview.io.FileParse;
7		import jalview.io.HMMFile;
8		import jalview.schemes.ResidueProperties;
9
10		import java.io.IOException;
11		import java.net.MalformedURLException;
12		import java.util.Map;
13
14		import org.testng.annotations.BeforeClass;
15		import org.testng.annotations.Test;
16
		100% Uncovered Elements: 0 (63) Complexity: 6 Complexity Density: 0.11
17		public class HiddenMarkovModelTest {
18
19		HiddenMarkovModel hmm;
20
21		HiddenMarkovModel alignmentHmm;
22
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
23	1	@BeforeClass(alwaysRun = true)...
24		public void setUp() throws MalformedURLException, IOException
25		{
26		/*
27		* load hmm model of a Kinase domain to a HiddenMarkovModel
28		*/
29	1	HMMFile file = new HMMFile(new FileParse(
30		"test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
31	1	hmm = file.getHMM();
32
33		// used to check if consensus sequence is automatically aligned with alignment
34	1	HMMFile alignmentTest = new HMMFile(
35		new FileParse("test/jalview/io/HMMAlignmentTestHMM.hmm",
36		DataSourceType.FILE));
37	1	alignmentHmm = alignmentTest.getHMM();
38		}
39
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
40	1	@Test(groups = "Functional")...
41		public void testGetMatchEmissionProbabilities()
42		throws MalformedURLException, IOException
43		{
44		/*
45		* raw value in file is 3.67403
46		* saved as probability e^-X = 0.05259
47		*/
48	1	double mep = hmm.getMatchEmissionProbability(0, 'R');
49	1	assertEquals(mep, 0.02537400637, 0.0001d);
50	1	assertEquals(mep, Math.pow(Math.E, -3.67403), 0.0001d);
51
52	1	mep = hmm.getMatchEmissionProbability(19, 'W');
53	1	assertEquals(mep, 0.00588228492, 0.0001d);
54	1	assertEquals(mep, Math.pow(Math.E, -5.13581), 0.0001d);
55
56		// column 160 is a gapped region of the model
57	1	mep = hmm.getMatchEmissionProbability(160, 'G');
58	1	assertEquals(mep, 0D, 0.0001d);
59
60	1	mep = hmm.getMatchEmissionProbability(475, 'A');
61	1	assertEquals(mep, 0.04995163708, 0.0001d);
62	1	assertEquals(mep, Math.pow(Math.E, -2.99670), 0.0001d);
63		}
64
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
65	1	@Test(groups = "Functional")...
66		public void testGetInsertEmissionProbabilities()
67		{
68	1	double iep = hmm.getInsertEmissionProbability(2, 'A');
69	1	assertEquals(iep, Math.pow(Math.E, -2.68618), 0.0001d);
70		// symbol is not case-sensitive
71	1	assertEquals(iep, hmm.getInsertEmissionProbability(2, 'a'));
72
73	1	iep = hmm.getInsertEmissionProbability(5, 'T');
74	1	assertEquals(iep, Math.pow(Math.E, -2.77519), 0.0001d);
75
76		// column 161 is gapped in the hmm
77	1	iep = hmm.getInsertEmissionProbability(161, 'K');
78	1	assertEquals(iep, 0D, 0.0001d);
79
80	1	iep = hmm.getInsertEmissionProbability(472, 'L');
81	1	assertEquals(iep, Math.pow(Math.E, -2.69355), 0.0001d);
82		}
83
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
84	1	@Test(groups = "Functional")...
85		public void testGetStateTransitionProbabilities()
86		{
87		// * in model file treated as negative infinity
88	1	double stp = hmm.getStateTransitionProbability(475,
89		HiddenMarkovModel.MATCHTODELETE);
90	1	assertEquals(stp, Double.NEGATIVE_INFINITY);
91
92		// file value is 5.01631, saved as e^-5.01631
93	1	stp = hmm.getStateTransitionProbability(8,
94		HiddenMarkovModel.MATCHTOINSERT);
95	1	assertEquals(stp, Math.pow(Math.E, -5.01631), 0.0001D);
96
97	1	stp = hmm.getStateTransitionProbability(36,
98		HiddenMarkovModel.MATCHTODELETE);
99	1	assertEquals(stp, Math.pow(Math.E, -5.73865), 0.0001D);
100
101	1	stp = hmm.getStateTransitionProbability(22,
102		HiddenMarkovModel.INSERTTOMATCH);
103	1	assertEquals(stp, Math.pow(Math.E, -0.61958), 0.0001D);
104
105	1	stp = hmm.getStateTransitionProbability(80,
106		HiddenMarkovModel.INSERTTOINSERT);
107	1	assertEquals(stp, Math.pow(Math.E, -0.77255), 0.0001D);
108
109	1	stp = hmm.getStateTransitionProbability(475,
110		HiddenMarkovModel.DELETETOMATCH);
111	1	assertEquals(stp, 1D, 0.0001D);
112
113	1	stp = hmm.getStateTransitionProbability(218,
114		HiddenMarkovModel.DELETETODELETE);
115	1	assertEquals(stp, Math.pow(Math.E, -0.95510), 0.0001D);
116		}
117
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
118	1	@Test(groups = "Functional")...
119		public void testGetConsensusSequence()
120		{
121	1	SequenceI seq = hmm.getConsensusSequence();
122	1	String subStr = seq.getSequenceAsString().substring(0, 10);
123	1	assertEquals(subStr, "yelleklGsG");
124	1	subStr = seq.getSequenceAsString().substring(150, 161);
125	1	assertEquals(subStr, "-dllk------");
126
127		// test to see if consensus sequence maps to alignment correctly
128		// see HMMAlignmentTest.sto for corresponding alignment file
129	1	SequenceI seq2 = alignmentHmm.getConsensusSequence();
130	1	assertEquals(seq2.getCharAt(0), '-');
131	1	assertEquals(seq2.getCharAt(7), '-');
132	1	assertEquals(seq2.getCharAt(8), 's');
133
134		}
135
136		/**
137		* A rather pointless test that reproduces the code implemented and asserts
138		* the result is the same...
139		*/
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
140	1	@Test(groups = "Functional")...
141		public void testGetInformationContent()
142		{
143		/*
144		* information measure is sum over all symbols of
145		* emissionProb * log(emissionProb / background) / log(2)
146		*/
147	1	Map<Character, Float> uniprotFreqs = ResidueProperties.backgroundFrequencies
148		.get("amino");
149	1	int col = 4;
150	1	float expected = 0f;
151	1	for (char aa : hmm.getSymbols().toCharArray())
152		{
153	20	double mep = hmm.getMatchEmissionProbability(col, aa);
154	20	float background = uniprotFreqs.get(aa);
155	20	expected += mep * Math.log(mep / background);
156		}
157	1	expected /= Math.log(2D);
158
159	1	float actual = hmm.getInformationContent(col);
160	1	assertEquals(actual, expected, 0.0001d);
161		}
162		}