Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HmmerLocalBackgroundTest	18	18	1	1.0100%	Show methods

Class HmmerLocalBackgroundTest

Class HmmerLocalBackgroundTest	Line # 18	Total Statements 18	Complexity 1	TOTAL Coverage 1.0100%
testFindColour() : void   testFindColour() : void	2020	18.018	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	1.0	jalview.schemes.HmmerLocalBackgroundTest.testFindColourjalview.schemes.HmmerLocalBackgroundTest.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.AnnotatedCollectionI;
7		import jalview.datamodel.Sequence;
8		import jalview.datamodel.SequenceI;
9		import jalview.io.DataSourceType;
10		import jalview.io.HMMFile;
11
12		import java.awt.Color;
13		import java.io.IOException;
14		import java.net.MalformedURLException;
15
16		import org.testng.annotations.Test;
17
		100% Uncovered Elements: 0 (19) Complexity: 1 Complexity Density: 0.06
18		public class HmmerLocalBackgroundTest {
19
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
20	1	@Test(groups = "Functional")...
21		public void testFindColour() throws MalformedURLException, IOException
22		{
23	1	HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
24		DataSourceType.FILE);
25
26		/*
27		* alignment with 20 residues and background frequencies:
28		* A/a, S 3/20 = 0.15
29		* M, K 4/20 = 0.2
30		* V 2/20 = 0.1
31		* Q, R, L 1/20 = 0.05
32		* log(totalCount) = log(20) = 2.996
33		*/
34	1	SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
35	1	SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
36	1	SequenceI hmmSeq = file.getSeqsAsArray()[0];
37	1	AnnotatedCollectionI ac = new Alignment(
38		new SequenceI[]
39		{ hmmSeq, seq1, seq2 });
40	1	ColourSchemeI scheme = new HmmerLocalBackground(ac);
41
42		/*
43		* 'A' in column 1, node 2, match emission 2.77204
44		* e-2.77204 = 0.0625
45		* background frequency is 0.15
46		* ratio is < 1, log is negative, colour is Orange
47		*/
48	1	Color actual = scheme.findColour('A', 1, null, null, 0);
49	1	assertEquals(actual, Color.ORANGE);
50
51		// gap is white
52	1	actual = scheme.findColour('-', 2, null, null, 0);
53	1	assertEquals(actual, Color.WHITE);
54	1	actual = scheme.findColour(' ', 2, null, null, 0);
55	1	assertEquals(actual, Color.WHITE);
56	1	actual = scheme.findColour('.', 2, null, null, 0);
57	1	assertEquals(actual, Color.WHITE);
58
59		/*
60		* 'L' in column 3, node 4, match emission 1.98342
61		* e-1.98342 = 0.1376
62		* background frequency is 0.05
63		* ratio is 2.752, log is 1.012
64		* colour is graduated 1.012/2.996 or 86/255 of the way from
65		* white(255, 255, 255) to blue(0, 0, 255)
66		*/
67	1	actual = scheme.findColour('L', 3, null, null, 0);
68	1	assertEquals(actual, new Color(169, 169, 255));
69
70		/*
71		* invalid symbol is White
72		*/
73	1	actual = scheme.findColour('X', 2, null, null, 0);
74	1	assertEquals(actual, Color.WHITE);
75		}
76
77		}