Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HMMProbabilityDistributionAnalyserTest	23	51	6	0.00%	Show methods

Class HMMProbabilityDistributionAnalyserTest

Class HMMProbabilityDistributionAnalyserTest	Line # 23	Total Statements 51	Complexity 6	TOTAL Coverage 0.00%
testMoveToFile() : void   testMoveToFile() : void	2727	8.08	1.01	0.0 0.00%
testCountValidResidues() : void   testCountValidResidues() : void	4444	16.016	2.02	0.0 0.00%
testReadBinned() : void   testReadBinned() : void	7373	6.06	1.01	0.0 0.00%
testReadRaw() : void   testReadRaw() : void	8484	7.07	1.01	0.0 0.00%
testProcessData() : void   testProcessData() : void	9898	14.014	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.util;
2
3		import jalview.datamodel.HMMNode;
4		import jalview.datamodel.HiddenMarkovModel;
5		import jalview.datamodel.Sequence;
6		import jalview.datamodel.SequenceI;
7
8		import static org.testng.Assert.assertEquals;
9		import static org.testng.Assert.assertNull;
10
11		import java.io.BufferedReader;
12		import java.io.FileReader;
13		import java.io.IOException;
14		import java.util.ArrayList;
15		import java.util.List;
16		import java.util.Map;
17		import java.util.Vector;
18
19		import org.testng.annotations.Test;
20
21		import junit.extensions.PA;
22
		0% Uncovered Elements: 58 (58) Complexity: 6 Complexity Density: 0.12
23		public class HMMProbabilityDistributionAnalyserTest {
24
25		HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
26
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12 4-
27	0	@Test...
28		public void testMoveToFile() throws IOException
29		{
30
31	0	BufferedReader br = new BufferedReader(new FileReader(
32		"test/jalview/util/test_Fams_for_probability_analysis"));
33	0	analyser.moveLocationBy(1, br);
34
35	0	String line = br.readLine();
36	0	assertEquals(line, "# STOCKHOLM 1.0");
37	0	line = br.readLine();
38	0	assertEquals(line, "seq1 ATW");
39	0	line = br.readLine();
40	0	assertEquals(line, "seq2 ATI");
41
42		}
43
		0% Uncovered Elements: 18 (18) Complexity: 2 Complexity Density: 0.12 4-
44	0	@Test...
45		public void testCountValidResidues()
46		{
47	0	analyser.sequences = new Vector<>();
48	0	analyser.hmm = new HiddenMarkovModel();
49	0	analyser.hmm.setProperty("LENG", "8");
50
51	0	List<HMMNode> nodes = new ArrayList<>();
52	0	nodes.add(new HMMNode());
53	0	for (int i = 1; i < 9; i++)
54		{
55	0	HMMNode node = new HMMNode();
56	0	node.setResidueNumber(i - 1);
57	0	nodes.add(node);
58
59		}
60	0	PA.setValue(analyser.hmm, "nodes", nodes);
61
62	0	SequenceI[] sequence = new Sequence[] {
63		new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
64		new Sequence("seq3", "--.ATccGc") };
65	0	analyser.sequences.add(sequence[0]);
66	0	analyser.sequences.add(sequence[1]);
67	0	analyser.sequences.add(sequence[2]);
68
69	0	int count = analyser.countValidResidues();
70	0	assertEquals(count, 16);
71		}
72
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17 4-
73	0	@Test(priority = 0)...
74		public void testReadBinned() throws IOException
75		{
76	0	analyser.readBinned("test/jalview/util/");
77	0	Map<String, Double> map = analyser.binned;
78	0	assertEquals((double) map.get("1.8"), 4.53);
79	0	assertEquals((double) map.get("3.4"), 2.65);
80	0	assertEquals((double) map.get("6.4"), 10.8);
81	0	assertEquals((double) map.get("0"), 5.4);
82		}
83
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14 4-
84	0	@Test...
85		public void testReadRaw() throws IOException
86		{
87	0	analyser.readRaw("test/jalview/util/");
88	0	List<ArrayList<Double>> list = analyser.raw;
89
90	0	assertEquals((double) list.get(0).get(0), 1.43);
91	0	assertNull(list.get(0).get(2));
92	0	assertEquals((double) list.get(1).get(1), 1.2);
93	0	assertEquals((double) list.get(2).get(0), 5.6);
94	0	assertEquals((double) list.get(2).get(2), 6.8);
95
96		}
97
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 4-
98	0	@Test(priority = 1)...
99		public void testProcessData() throws IOException
100		{
101	0	analyser.keepRaw = true;
102	0	BufferedReader brFam = new BufferedReader(new FileReader(
103		"test/jalview/util/test_Fams_for_probability_analysis"));
104	0	BufferedReader brHMM = new BufferedReader(new FileReader(
105		"test/jalview/util/test_HMMs_for_probability_analysis"));
106	0	analyser.readStockholm(brFam);
107	0	analyser.readHMM(brHMM);
108	0	analyser.processData(6);
109	0	Map<String, Double> map = analyser.binned;
110	0	List<ArrayList<Double>> list = analyser.raw;
111	0	assertEquals((double) map.get("1.8"), 4.863d, 0.001d);
112	0	assertEquals((double) map.get("3.4"), 2.65);
113	0	assertEquals((double) map.get("0"), 5.4);
114	0	assertEquals((double) map.get("6.4"), 10.8);
115	0	assertEquals((double) map.get("1.4"), 0.166667, 0.00001d);
116	0	assertEquals((double) map.get("4.4"), 0.5);
117
118		}
119		}