Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
Blosum62ColourSchemeTest	9	13	1	0	1.0100%	Show methods

Class Blosum62ColourSchemeTest

Class Blosum62ColourSchemeTest	Line # 9	Total Statements 13	Complexity 1	Uncovered Elements 0	TOTAL Coverage 1.0100%
testFindColour() : void   testFindColour() : void	2323	13.013	1.01	0.00	1.0 1.0100%

 

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	Test contribution	Test	Result	Actions
	1.0	jalview.schemes.Blosum62ColourSchemeTest.testFindColourjalview.schemes.Blosum62ColourSchemeTest.testFindColour	1PASS

 

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1		package jalview.schemes;
2
3		import static org.testng.Assert.assertEquals;
4
5		import java.awt.Color;
6
7		import org.testng.annotations.Test;
8
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.08
9		public class Blosum62ColourSchemeTest
10		{
11		/**
12		* Test the method that determines colour as:
13		* <ul>
14		* <li>white if there is no consensus</li>
15		* <li>white if 'residue' is a gap</li>
16		* <li>dark blue if residue matches consensus (or joint consensus)</li>
17		* <li>else, total the residue's Blosum score with the consensus residue(s)</li>
18		* <ul>
19		* <li>if positive, light blue, else white</li>
20		* </ul>
21		* <ul>
22		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
23	1	@Test(groups = "Functional")...
24		public void testFindColour()
25		{
26	1	ColourSchemeI blosum = new Blosum62ColourScheme();
27	1	Color lightBlue = new Color(204, 204, 255);
28	1	Color darkBlue = new Color(154, 154, 255);
29
30		/*
31		* findColour does not use column, sequence or pid score
32		* we assume consensus residue is computed as upper case
33		*/
34	1	assertEquals(blosum.findColour('A', 0, null, "A", 0f), darkBlue);
35	1	assertEquals(blosum.findColour('a', 0, null, "A", 0f), darkBlue);
36
37		/*
38		* L has a Blosum score of
39		* -1 with A
40		* -4 with B
41		* 0 with F
42		* 2 with I
43		* -1 with T
44		* 1 with V
45		* etc
46		*/
47	1	assertEquals(blosum.findColour('L', 0, null, "A", 0f), Color.white); // -1
48	1	assertEquals(blosum.findColour('L', 0, null, "B", 0f), Color.white); // -4
49	1	assertEquals(blosum.findColour('L', 0, null, "F", 0f), Color.white); // 0
50	1	assertEquals(blosum.findColour('L', 0, null, "I", 0f), lightBlue); // 2
51	1	assertEquals(blosum.findColour('L', 0, null, "TV", 0f), Color.white); // 0
52	1	assertEquals(blosum.findColour('L', 0, null, "IV", 0f), lightBlue); // 3
53	1	assertEquals(blosum.findColour('L', 0, null, "IT", 0f), lightBlue); // 1
54	1	assertEquals(blosum.findColour('L', 0, null, "IAT", 0f), Color.white); // 0
55		}
56		}