Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PIDColourSchemeTest	15	28	4	4	0.87587.5%	Show methods

Class PIDColourSchemeTest

Class PIDColourSchemeTest	Line # 15	Total Statements 28	Complexity 4	Uncovered Elements 4	TOTAL Coverage 0.87587.5%
testFindColour() : void   testFindColour() : void	3838	13.013	1.01	0.00	1.0 1.0100%
testFindColour_ignoreGaps() : void   testFindColour_ignoreGaps() : void	6767	15.015	3.03	4.04	0.7647059 0.764705976.5%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.4375	jalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGaps	1PASS
	0.4375	jalview.schemes.PIDColourSchemeTest.testFindColourjalview.schemes.PIDColourSchemeTest.testFindColour	1PASS

 

Source view

1		package jalview.schemes;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.datamodel.SequenceI;
6		import jalview.gui.AlignFrame;
7		import jalview.gui.AlignViewport;
8		import jalview.io.DataSourceType;
9		import jalview.io.FileLoader;
10
11		import java.awt.Color;
12
13		import org.testng.annotations.Test;
14
		87.5% Uncovered Elements: 4 (32) Complexity: 4 Complexity Density: 0.14
15		public class PIDColourSchemeTest
16		{
17		static final Color white = Color.white;
18
19		static final Color over40 = new Color(204, 204, 255);
20
21		static final Color over60 = new Color(153, 153, 255);
22
23		static final Color over80 = new Color(100, 100, 255);
24
25		/**
26		* Test findColour for cases:
27		* <ul>
28		* <li>gap: white</li>
29		* <li>no match to consensus: white</li>
30		* <li>match consensus with pid > 80%: 100,100,255</li>
31		* <li>match consensus with pid > 60%: 153, 153, 255</li>
32		* <li>match consensus with pid > 40%: 204, 204, 255</li>
33		* <li>match consensus with pid <= 40%: white</li>
34		* <li>joint consensus matching</li>
35		* <li>case insensitive matching</li>
36		* <ul>
37		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
38	1	@Test(groups = "Functional")...
39		public void testFindColour()
40		{
41	1	ColourSchemeI scheme = new PIDColourScheme();
42
43		/*
44		* doesn't use column or sequence
45		* we assume consensus residue is computed as upper case
46		*/
47	1	assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
48	1	assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
49	1	assertEquals(scheme.findColour('A', 0, null, "A", 40.1f), over40);
50	1	assertEquals(scheme.findColour('A', 0, null, "A", 60f), over40);
51	1	assertEquals(scheme.findColour('A', 0, null, "A", 60.1f), over60);
52	1	assertEquals(scheme.findColour('A', 0, null, "A", 80f), over60);
53	1	assertEquals(scheme.findColour('A', 0, null, "A", 80.1f), over80);
54	1	assertEquals(scheme.findColour('A', 0, null, "A", 100f), over80);
55	1	assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
56
57	1	assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
58	1	assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
59	1	assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
60		}
61
62		/**
63		* Test that changing the 'ignore gaps in consensus' in the viewport (an
64		* option on the annotation label popup menu) results in a change to the
65		* colouring
66		*/
		76.5% Uncovered Elements: 4 (17) Complexity: 3 Complexity Density: 0.2 1PASS
67	1	@Test(groups = "Functional")...
68		public void testFindColour_ignoreGaps()
69		{
70		/*
71		* AAAAA
72		* AAAAA
73		* -CCCC
74		* FFFFF
75		*
76		* first column consensus is A
77		* first column PID is 50%, or 67% ignoring gaps
78		*/
79	1	String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
80
81		/*
82		* load data and wait for consensus to be computed
83		*/
84	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
85		DataSourceType.PASTE);
86	1	AlignViewport viewport = af.getViewport();
87	1	viewport.setIgnoreGapsConsensus(false, af.alignPanel);
88	1	while (viewport.getConsensusSeq() == null)
89		{
90	0	synchronized (this)
91		{
92	0	try
93		{
94	0	wait(50);
95		} catch (InterruptedException e)
96		{
97		}
98		}
99		}
100	1	af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
101
102	1	SequenceI seq = viewport.getAlignment().getSequenceAt(0);
103
104		/*
105		* including gaps, A should be coloured for 50% consensus
106		*/
107	1	Color c = viewport
108		.getResidueShading().findColour('A', 0, seq);
109	1	assertEquals(c, over40);
110
111		/*
112		* now choose to ignore gaps; colour should be for 67%
113		*/
114	1	viewport.setIgnoreGapsConsensus(true, af.alignPanel);
115	1	c = viewport
116		.getResidueShading().findColour('A', 0, seq);
117	1	assertEquals(c, over60);
118		}
119		}