Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueColourFinderTest	39	40	5	0.00%	Show methods

Class ResidueColourFinderTest

Class ResidueColourFinderTest	Line # 39	Total Statements 40	Complexity 5	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	0.0 0.00%
testGetResidueColour_zappo() : void   testGetResidueColour_zappo() : void	4949	13.013	1.01	0.0 0.00%
testGetResidueColour_none() : void   testGetResidueColour_none() : void	7979	8.08	1.01	0.0 0.00%
testGetResidueColour_userdef() : void   testGetResidueColour_userdef() : void	9999	17.017	2.02	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.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
		0% Uncovered Elements: 46 (46) Complexity: 5 Complexity Density: 0.12
39		public class ResidueColourFinderTest
40		{
41
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
42	0	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	0	JvOptionPane.setInteractiveMode(false);
46	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
49	0	@Test(groups = { "Functional" })...
50		public void testGetResidueColour_zappo()
51		{
52	0	SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
53	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
54	0	final AlignViewport av = new AlignViewport(al);
55	0	ResidueColourFinder rcf = new ResidueColourFinder();
56	0	av.setGlobalColourScheme(new ZappoColourScheme());
57
58		// @see ResidueProperties.zappo
59	0	assertEquals(Color.pink, rcf.getResidueColour(true,
60		av.getResidueShading(), null, seq, 0, null)); // M
61	0	assertEquals(Color.green, rcf.getResidueColour(true,
62		av.getResidueShading(), null, seq, 2, null)); // T
63	0	assertEquals(Color.magenta, rcf.getResidueColour(true,
64		av.getResidueShading(), null, seq, 5, null)); // G
65	0	assertEquals(Color.orange, rcf.getResidueColour(true,
66		av.getResidueShading(), null, seq, 12, null)); // F
67
68		// everything is white if showBoxes is false
69	0	assertEquals(Color.white, rcf.getResidueColour(false,
70		av.getResidueShading(), null, seq, 0, null)); // M
71	0	assertEquals(Color.white, rcf.getResidueColour(false,
72		av.getResidueShading(), null, seq, 2, null)); // T
73	0	assertEquals(Color.white, rcf.getResidueColour(false,
74		av.getResidueShading(), null, seq, 5, null)); // G
75	0	assertEquals(Color.white, rcf.getResidueColour(false,
76		av.getResidueShading(), null, seq, 12, null)); // F
77		}
78
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12 4-
79	0	@Test(groups = { "Functional" })...
80		public void testGetResidueColour_none()
81		{
82	0	SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
83	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
84	0	final AlignViewport av = new AlignViewport(al);
85	0	ResidueColourFinder rcf = new ResidueColourFinder();
86
87	0	assertEquals(Color.white, rcf.getResidueColour(true,
88		av.getResidueShading(), null, seq, 0, null));
89	0	assertEquals(Color.white, rcf.getResidueColour(true,
90		av.getResidueShading(), null, seq, 2, null));
91
92		// no change if showBoxes is false
93	0	assertEquals(Color.white, rcf.getResidueColour(false,
94		av.getResidueShading(), null, seq, 0, null));
95	0	assertEquals(Color.white, rcf.getResidueColour(false,
96		av.getResidueShading(), null, seq, 2, null));
97		}
98
		0% Uncovered Elements: 19 (19) Complexity: 2 Complexity Density: 0.12 4-
99	0	@Test(groups = { "Functional" })...
100		public void testGetResidueColour_userdef()
101		{
102	0	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
103		// gap
104	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
105	0	final AlignViewport av = new AlignViewport(al);
106	0	ResidueColourFinder rcf = new ResidueColourFinder();
107
108	0	Color[] newColours = new Color[24];
109	0	for (int i = 0; i < 24; i++)
110		{
111	0	newColours[i] = null;
112		}
113
114	0	av.setGlobalColourScheme(new UserColourScheme(newColours));
115
116		// gap colour not specified so gap colour is null
117		// this is consistent with previous behaviour, but may not be correct?
118	0	assertEquals(null, rcf.getResidueColour(true, av.getResidueShading(),
119		null, seq, 3, null));
120
121	0	newColours[23] = Color.pink;
122	0	av.setGlobalColourScheme(new UserColourScheme(newColours));
123
124		// gap colour specified as pink
125	0	assertEquals(Color.pink, rcf.getResidueColour(true,
126		av.getResidueShading(), null, seq, 3, null));
127
128		// everything is white if showBoxes is false
129	0	newColours[23] = null;
130	0	assertEquals(Color.white, rcf.getResidueColour(false,
131		av.getResidueShading(), null, seq, 3, null));
132
133	0	newColours[23] = Color.pink;
134	0	av.setGlobalColourScheme(new UserColourScheme(newColours));
135
136		// gap colour specified as pink
137	0	assertEquals(Color.white, rcf.getResidueColour(false,
138		av.getResidueShading(), null, seq, 3, null));
139		}
140
141		// TODO more tests for getResidueColour covering groups, feature rendering...
142		}