Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ClustalxColourSchemeTest	14	28	2	0	1.0100%	Show methods

Class ClustalxColourSchemeTest

Class ClustalxColourSchemeTest	Line # 14	Total Statements 28	Complexity 2	Uncovered Elements 0	TOTAL Coverage 1.0100%
testFindColour() : void   testFindColour() : void	3030	16.016	1.01	0.00	1.0 1.0100%
testFindColour_ignoreGaps() : void   testFindColour_ignoreGaps() : void	9595	12.012	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.56666666	jalview.schemes.ClustalxColourSchemeTest.testFindColourjalview.schemes.ClustalxColourSchemeTest.testFindColour	1PASS
	0.43333334	jalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGaps	1PASS

 

Source view

1		package jalview.schemes;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.datamodel.AlignmentI;
6		import jalview.gui.AlignFrame;
7		import jalview.io.DataSourceType;
8		import jalview.io.FileLoader;
9
10		import java.awt.Color;
11
12		import org.testng.annotations.Test;
13
		100% Uncovered Elements: 0 (30) Complexity: 2 Complexity Density: 0.07
14		public class ClustalxColourSchemeTest
15		{
16		// @formatter:off
17		private static final String FASTA =
18		">seq1\nAAANNNRQ\n" +
19		">seq2\nAAANNNRQ\n" +
20		">seq3\nAAANNNRQ\n" +
21		">seq4\nAAANNNRQ\n" +
22		">seq5\nAAANYYKQ\n" +
23		">seq6\nAAANYYKQ\n" +
24		">seq7\nAVKWYYKQ\n" +
25		">seq8\nKKKWYYQQ\n" +
26		">seq9\nKKKWWYQQ\n" +
27		">seq0\nKKKWWWQW\n";
28		// @formatter:on
29
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
30	1	@Test(groups = "Functional")...
31		public void testFindColour()
32		{
33	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
34		DataSourceType.PASTE);
35	1	AlignmentI al = af.getViewport().getAlignment();
36	1	ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
37
38		/*
39		* column 1 is 70% A which is above Clustalx threshold of 60%
40		*/
41	1	Color clustalBlue = new Color(0.5f, 0.7f, 0.9f);
42	1	assertEquals(cs.findColour('A', 0, al.getSequenceAt(0)), clustalBlue);
43
44		/*
45		* column 2 is 70% A or V which is above Clustalx threshold for group
46		*/
47	1	assertEquals(cs.findColour('A', 0, al.getSequenceAt(1)), clustalBlue);
48
49		/*
50		* column 3 is 60% A which is not above Clustalx threshold
51		* the Ks in the other rows are not in the same Clustalx group
52		*/
53	1	assertEquals(cs.findColour('A', 2, al.getSequenceAt(1)), Color.white);
54
55		/*
56		* column 4 is 60% N which is above Clustalx threshold of 50%
57		*/
58	1	Color clustalGreen = new Color(0.1f, 0.8f, 0.1f);
59	1	assertEquals(cs.findColour('N', 3, al.getSequenceAt(1)), clustalGreen);
60
61		/*
62		* column 5 is 40% N and 40% Y which fails to pass the threshold of
63		* 50% N or 85% either
64		*/
65	1	assertEquals(cs.findColour('N', 4, al.getSequenceAt(1)), Color.white);
66
67		/*
68		* column 6 is 40% N and 50% Y which fails to pass the threshold of
69		* 85% for either
70		*/
71	1	assertEquals(cs.findColour('N', 5, al.getSequenceAt(1)), Color.white);
72
73		/*
74		* column 7 is 40% R and 30% K which combine to make > 60%
75		*/
76	1	Color clustalRed = new Color(0.9f, 0.2f, 0.1f);
77	1	assertEquals(cs.findColour('R', 6, al.getSequenceAt(1)), clustalRed);
78	1	assertEquals(cs.findColour('K', 6, al.getSequenceAt(7)), clustalRed);
79
80		/*
81		* column 8 is >85% Q which qualifies K and R to be red
82		*/
83	1	assertEquals(cs.findColour('R', 7, al.getSequenceAt(1)), clustalRed);
84	1	assertEquals(cs.findColour('K', 7, al.getSequenceAt(1)), clustalRed);
85
86		// TODO more test cases; check if help documentation matches implementation
87		}
88
89		// @formatter:on
90
91		/**
92		* Test for colour calculation when the consensus percentage ignores gapped
93		* sequences
94		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
95	1	@Test(groups = "Functional")...
96		public void testFindColour_ignoreGaps()
97		{
98		/*
99		* CCC
100		* CCC
101		* -CC
102		* first column is 66% C (blue) including gaps
103		* or 100% C ignoring gaps
104		*/
105	1	String fasta = ">seq1\nCCC\n>seq2\nccc\n>seq3\n-CC\n";
106	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
107		DataSourceType.PASTE);
108	1	AlignmentI al = af.getViewport().getAlignment();
109	1	ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
110
111		/*
112		* column 1 is 66% C which is above Clustalx threshold of 60%
113		*/
114	1	Color clustalBlue = ClustalxColourScheme.ClustalColour.BLUE.colour;
115	1	assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
116
117		/*
118		* set directly to ignore gaps
119		*/
120	1	cs.setIncludeGaps(false);
121	1	Color clustalPink = ClustalxColourScheme.ClustalColour.PINK.colour;
122	1	assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
123
124		/*
125		* set ignore gaps on the viewport...
126		*/
127	1	cs.setIncludeGaps(true);
128	1	assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
129	1	af.getViewport().setIgnoreGapsConsensus(true, af.alignPanel);
130		// next test fails: colour scheme does not read ignore gaps flag from
131		// viewport
132		// assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
133		}
134		}