Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HmmerGlobalBackgroundTest	17	22	1	1.0100%	Show methods

Class HmmerGlobalBackgroundTest

Class HmmerGlobalBackgroundTest	Line # 17	Total Statements 22	Complexity 1	TOTAL Coverage 1.0100%
testFindColour() : void   testFindColour() : void	1919	22.022	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	1.0	jalview.schemes.HmmerGlobalBackgroundTest.testFindColourjalview.schemes.HmmerGlobalBackgroundTest.testFindColour	1PASS

 

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1		package jalview.schemes;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.datamodel.Alignment;
6		import jalview.datamodel.AlignmentI;
7		import jalview.datamodel.SequenceI;
8		import jalview.io.DataSourceType;
9		import jalview.io.HMMFile;
10
11		import java.awt.Color;
12		import java.io.IOException;
13		import java.net.MalformedURLException;
14
15		import org.testng.annotations.Test;
16
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.05
17		public class HmmerGlobalBackgroundTest {
18
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
19	1	@Test(groups = "Functional")...
20		public void testFindColour() throws MalformedURLException, IOException
21		{
22	1	HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
23		DataSourceType.FILE);
24
25	1	SequenceI hmmSeq = file.getSeqsAsArray()[0];
26	1	AlignmentI al = new Alignment(new SequenceI[] { hmmSeq });
27	1	ColourSchemeI scheme = new HmmerGlobalBackground(al);
28
29		/*
30		* 'A' in column 1, node 2, match emission 2.77204
31		* e-2.77204 = 0.0625
32		* background frequency is 0.0826
33		* ratio is 0.757, log is negative, colour is Orange
34		*/
35	1	Color actual = scheme.findColour('A', 1, null, null, 0);
36	1	assertEquals(actual, Color.ORANGE);
37
38		// gap is white
39	1	actual = scheme.findColour('-', 2, null, null, 0);
40	1	assertEquals(actual, Color.WHITE);
41	1	actual = scheme.findColour(' ', 2, null, null, 0);
42	1	assertEquals(actual, Color.WHITE);
43	1	actual = scheme.findColour('.', 2, null, null, 0);
44	1	assertEquals(actual, Color.WHITE);
45
46		/*
47		* 'Y' in column 4, node 5, match emission 4.41426
48		* e-4.41426 = 0.0121
49		* background frequency is 0.0292
50		* ratio is 0.414, log is negative, colour is Orange
51		*/
52	1	actual = scheme.findColour('Y', 4, null, null, 0);
53	1	assertEquals(actual, Color.ORANGE);
54
55		/*
56		* 'M' in column 109, no matching node, colour is reddish
57		*/
58	1	actual = scheme.findColour('M', 109, null, null, 0);
59	1	assertEquals(actual, new Color(230, 0, 0));
60
61		/*
62		* 'I' in column 6, node 7, match emission 1.33015
63		* e-1.33015 = 0.2644
64		* background frequency is 0.0593
65		* ratio is 4.459, log is 1.495
66		* colour is graduated 1.495/4.52 or 84/255 of the way from
67		* white(255, 255, 255) to blue(0, 0, 255)
68		*/
69	1	actual = scheme.findColour('I', 6, null, null, 0);
70	1	assertEquals(actual, new Color(171, 171, 255));
71
72		/*
73		* 'V' in column 14, node 15, match emission 0.44769
74		* e-0.44769 = 0.6391
75		* background frequency is 0.0686
76		* ratio is 9.316, log is 2.232
77		* colour is graduated 2.232/4.52 or 126/255 of the way from
78		* white(255, 255, 255) to blue(0, 0, 255)
79		*/
80	1	actual = scheme.findColour('V', 14, null, null, 0);
81	1	assertEquals(actual, new Color(129, 129, 255));
82
83		/*
84		* invalid symbol is White
85		*/
86	1	actual = scheme.findColour('X', 2, null, null, 0);
87	1	assertEquals(actual, Color.WHITE);
88		}
89
90		}