Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Blosum62ColourSchemeTest	29	13	1	0.00%	Show methods

Class Blosum62ColourSchemeTest

Class Blosum62ColourSchemeTest	Line # 29	Total Statements 13	Complexity 1	TOTAL Coverage 0.00%
testFindColour() : void   testFindColour() : void	4444	13.013	1.01	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.schemes;
22
23		import static org.testng.Assert.assertEquals;
24
25		import java.awt.Color;
26
27		import org.testng.annotations.Test;
28
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.08
29		public class Blosum62ColourSchemeTest
30		{
31		/**
32		* Test the method that determines colour as:
33		* <ul>
34		* <li>white if there is no consensus</li>
35		* <li>white if 'residue' is a gap</li>
36		* <li>dark blue if residue matches consensus (or joint consensus)</li>
37		* <li>else, total the residue's Blosum score with the consensus
38		* residue(s)</li>
39		* <ul>
40		* <li>if positive, light blue, else white</li>
41		* </ul>
42		* <ul>
43		*/
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
44	0	@Test(groups = "Functional")...
45		public void testFindColour()
46		{
47	0	ColourSchemeI blosum = new Blosum62ColourScheme();
48	0	Color lightBlue = new Color(204, 204, 255);
49	0	Color darkBlue = new Color(154, 154, 255);
50
51		/*
52		* findColour does not use column, sequence or pid score
53		* we assume consensus residue is computed as upper case
54		*/
55	0	assertEquals(blosum.findColour('A', 0, null, "A", 0f), darkBlue);
56	0	assertEquals(blosum.findColour('a', 0, null, "A", 0f), darkBlue);
57
58		/*
59		* L has a Blosum score of
60		* -1 with A
61		* -4 with B
62		* 0 with F
63		* 2 with I
64		* -1 with T
65		* 1 with V
66		* etc
67		*/
68	0	assertEquals(blosum.findColour('L', 0, null, "A", 0f), Color.white); // -1
69	0	assertEquals(blosum.findColour('L', 0, null, "B", 0f), Color.white); // -4
70	0	assertEquals(blosum.findColour('L', 0, null, "F", 0f), Color.white); // 0
71	0	assertEquals(blosum.findColour('L', 0, null, "I", 0f), lightBlue); // 2
72	0	assertEquals(blosum.findColour('L', 0, null, "TV", 0f), Color.white); // 0
73	0	assertEquals(blosum.findColour('L', 0, null, "IV", 0f), lightBlue); // 3
74	0	assertEquals(blosum.findColour('L', 0, null, "IT", 0f), lightBlue); // 1
75	0	assertEquals(blosum.findColour('L', 0, null, "IAT", 0f), Color.white); // 0
76		}
77		}