Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ResidueColourFinderTest	39	40	5	0	1.0100%	Show methods

Class ResidueColourFinderTest

Class ResidueColourFinderTest	Line # 39	Total Statements 40	Complexity 5	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	0.00	1.0 1.0100%
testGetResidueColour_zappo() : void   testGetResidueColour_zappo() : void	4949	13.013	1.01	0.00	1.0 1.0100%
testGetResidueColour_none() : void   testGetResidueColour_none() : void	8484	8.08	1.01	0.00	1.0 1.0100%
testGetResidueColour_userdef() : void   testGetResidueColour_userdef() : void	106106	17.017	2.02	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.4347826	jalview.renderer.ResidueColourFinderTest.testGetResidueColour_userdefjalview.renderer.ResidueColourFinderTest.testGetResidueColour_userdef	1PASS
	0.3043478	jalview.renderer.ResidueColourFinderTest.testGetResidueColour_zappojalview.renderer.ResidueColourFinderTest.testGetResidueColour_zappo	1PASS
	0.19565217	jalview.renderer.ResidueColourFinderTest.testGetResidueColour_nonejalview.renderer.ResidueColourFinderTest.testGetResidueColour_none	1PASS

 

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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.renderer;
22
23		import static org.testng.AssertJUnit.assertEquals;
24
25		import jalview.datamodel.Alignment;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.Sequence;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.AlignViewport;
30		import jalview.gui.JvOptionPane;
31		import jalview.schemes.UserColourScheme;
32		import jalview.schemes.ZappoColourScheme;
33
34		import java.awt.Color;
35
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.Test;
38
		100% Uncovered Elements: 0 (46) Complexity: 5 Complexity Density: 0.12
39		public class ResidueColourFinderTest
40		{
41
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
42	1	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	1	JvOptionPane.setInteractiveMode(false);
46	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
49	1	@Test(groups = { "Functional" })...
50		public void testGetResidueColour_zappo()
51		{
52	1	SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
53	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
54	1	final AlignViewport av = new AlignViewport(al);
55	1	ResidueColourFinder rcf = new ResidueColourFinder();
56	1	av.setGlobalColourScheme(new ZappoColourScheme());
57
58		// @see ResidueProperties.zappo
59	1	assertEquals(Color.pink,
60		rcf.getResidueColour(true, av.getResidueShading(), null, seq, 0,
61		null)); // M
62	1	assertEquals(Color.green,
63		rcf.getResidueColour(true, av.getResidueShading(), null, seq, 2,
64		null)); // T
65	1	assertEquals(Color.magenta,
66		rcf.getResidueColour(true, av.getResidueShading(), null, seq, 5,
67		null)); // G
68	1	assertEquals(Color.orange,
69		rcf.getResidueColour(true, av.getResidueShading(), null, seq,
70		12,
71		null)); // F
72
73		// everything is white if showBoxes is false
74	1	assertEquals(Color.white, rcf.getResidueColour(false,
75		av.getResidueShading(), null, seq, 0, null)); // M
76	1	assertEquals(Color.white, rcf.getResidueColour(false,
77		av.getResidueShading(), null, seq, 2, null)); // T
78	1	assertEquals(Color.white, rcf.getResidueColour(false,
79		av.getResidueShading(), null, seq, 5, null)); // G
80	1	assertEquals(Color.white, rcf.getResidueColour(false,
81		av.getResidueShading(), null, seq, 12, null)); // F
82		}
83
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
84	1	@Test(groups = { "Functional" })...
85		public void testGetResidueColour_none()
86		{
87	1	SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
88	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
89	1	final AlignViewport av = new AlignViewport(al);
90	1	ResidueColourFinder rcf = new ResidueColourFinder();
91
92	1	assertEquals(Color.white,
93		rcf.getResidueColour(true, av.getResidueShading(),
94		null, seq, 0, null));
95	1	assertEquals(Color.white,
96		rcf.getResidueColour(true, av.getResidueShading(),
97		null, seq, 2, null));
98
99		// no change if showBoxes is false
100	1	assertEquals(Color.white, rcf.getResidueColour(false,
101		av.getResidueShading(), null, seq, 0, null));
102	1	assertEquals(Color.white, rcf.getResidueColour(false,
103		av.getResidueShading(), null, seq, 2, null));
104		}
105
		100% Uncovered Elements: 0 (19) Complexity: 2 Complexity Density: 0.12 1PASS
106	1	@Test(groups = { "Functional" })...
107		public void testGetResidueColour_userdef()
108		{
109	1	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
110		// gap
111	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
112	1	final AlignViewport av = new AlignViewport(al);
113	1	ResidueColourFinder rcf = new ResidueColourFinder();
114
115	1	Color[] newColours = new Color[24];
116	25	for (int i = 0; i < 24; i++)
117		{
118	24	newColours[i] = null;
119		}
120
121	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
122
123		// gap colour not specified so gap colour is null
124		// this is consistent with previous behaviour, but may not be correct?
125	1	assertEquals(null, rcf.getResidueColour(true, av.getResidueShading(),
126		null, seq, 3, null));
127
128	1	newColours[23] = Color.pink;
129	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
130
131		// gap colour specified as pink
132	1	assertEquals(Color.pink, rcf.getResidueColour(true,
133		av.getResidueShading(),
134		null, seq, 3, null));
135
136		// everything is white if showBoxes is false
137	1	newColours[23] = null;
138	1	assertEquals(Color.white, rcf.getResidueColour(false,
139		av.getResidueShading(),
140		null, seq, 3, null));
141
142	1	newColours[23] = Color.pink;
143	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
144
145		// gap colour specified as pink
146	1	assertEquals(Color.white, rcf.getResidueColour(false,
147		av.getResidueShading(), null, seq, 3, null));
148		}
149
150		// TODO more tests for getResidueColour covering groups, feature rendering...
151		}