Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
OverviewResColourFinderTest	43	97	7	56	0.4666666746.7%	Show methods

Class OverviewResColourFinderTest

Class OverviewResColourFinderTest	Line # 43	Total Statements 97	Complexity 7	Uncovered Elements 56	TOTAL Coverage 0.4666666746.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4646	3.03	1.01	0.00	1.0 1.0100%
testGetResidueBoxColour_none() : void   testGetResidueBoxColour_none() : void	5454	8.08	1.01	0.00	1.0 1.0100%
testGetResidueBoxColour_zappo() : void   testGetResidueBoxColour_zappo() : void	7777	15.015	1.01	0.00	1.0 1.0100%
testGetResidueBoxColour_userdef() : void   testGetResidueBoxColour_userdef() : void	123123	17.017	2.02	0.00	1.0 1.0100%
testGetResidueBoxColour_group() : void   testGetResidueBoxColour_group() : void	167167	22.022	1.01	22.022	0.0 0.00%
testGetBoxColour() : void   testGetBoxColour() : void	228228	32.032	1.01	32.032	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.1904762	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdefjalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdef	1PASS
	0.15238096	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappojalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappo	1PASS
	0.08571429	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_nonejalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_none	1PASS

 

Source view

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.bin.Cache;
26		import jalview.datamodel.Alignment;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.Sequence;
29		import jalview.datamodel.SequenceGroup;
30		import jalview.datamodel.SequenceI;
31		import jalview.gui.AlignViewport;
32		import jalview.gui.JvOptionPane;
33		import jalview.schemes.ColourSchemeI;
34		import jalview.schemes.UserColourScheme;
35		import jalview.schemes.ZappoColourScheme;
36
37		import java.awt.Color;
38		import java.util.ArrayList;
39
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.Test;
42
		46.7% Uncovered Elements: 56 (105) Complexity: 7 Complexity Density: 0.07
43		public class OverviewResColourFinderTest
44		{
45
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUpJvOptionPane()
48		{
49	1	JvOptionPane.setInteractiveMode(false);
50	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
52		}
53
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
54	1	@Test(groups = { "Functional" })...
55		public void testGetResidueBoxColour_none()
56		{
57	1	SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
58	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
59	1	final AlignViewport av = new AlignViewport(al);
60	1	ResidueColourFinder rcf = new OverviewResColourFinder();
61
62		// gaps are grey, residues white
63	1	assertEquals(Color.white, rcf.getResidueColour(true,
64		av.getResidueShading(),
65		null, seq, 0, null));
66	1	assertEquals(Color.lightGray, rcf
67		.getResidueColour(true, av.getResidueShading(), null, seq, 2,
68		null));
69
70		// unaffected by showBoxes setting
71	1	assertEquals(Color.white, rcf.getResidueColour(false,
72		av.getResidueShading(), null, seq, 0, null));
73	1	assertEquals(Color.lightGray, rcf.getResidueColour(false,
74		av.getResidueShading(), null, seq, 2, null));
75		}
76
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
77	1	@Test(groups = { "Functional" })...
78		public void testGetResidueBoxColour_zappo()
79		{
80	1	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
81		// gap
82	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
83	1	final AlignViewport av = new AlignViewport(al);
84	1	ResidueColourFinder rcf = new OverviewResColourFinder();
85	1	av.setGlobalColourScheme(new ZappoColourScheme());
86
87		// @see ResidueProperties.zappo
88	1	assertEquals(Color.pink,
89		rcf.getResidueColour(true, av.getResidueShading(),
90		null, seq, 0, null)); // M
91	1	assertEquals(Color.green,
92		rcf.getResidueColour(true, av.getResidueShading(),
93		null, seq, 2, null)); // T
94	1	assertEquals(Color.magenta,
95		rcf.getResidueColour(true, av.getResidueShading(),
96		null, seq, 5, null)); // G
97	1	assertEquals(Color.orange,
98		rcf.getResidueColour(true, av.getResidueShading(),
99		null, seq, 12, null)); // F
100
101		// gap colour not specified so gaps are lightGray
102	1	assertEquals(Color.lightGray, rcf
103		.getResidueColour(true, av.getResidueShading(), null, seq, 3,
104		null));
105
106		// unaffected by showBoxes setting
107	1	assertEquals(Color.pink, rcf.getResidueColour(false,
108		av.getResidueShading(), null, seq, 0, null)); // M
109	1	assertEquals(Color.green, rcf.getResidueColour(false,
110		av.getResidueShading(), null, seq, 2, null)); // T
111	1	assertEquals(Color.magenta, rcf.getResidueColour(false,
112		av.getResidueShading(), null, seq, 5, null)); // G
113	1	assertEquals(Color.orange, rcf.getResidueColour(false,
114		av.getResidueShading(), null, seq, 12, null)); // F
115
116		// gap colour not specified so gaps are lightGray
117	1	assertEquals(Color.lightGray, rcf
118		.getResidueColour(false, av.getResidueShading(), null, seq, 3,
119		null));
120
121		}
122
		100% Uncovered Elements: 0 (19) Complexity: 2 Complexity Density: 0.12 1PASS
123	1	@Test(groups = { "Functional" })...
124		public void testGetResidueBoxColour_userdef()
125		{
126	1	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
127		// gap
128	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
129	1	final AlignViewport av = new AlignViewport(al);
130	1	ResidueColourFinder rcf = new OverviewResColourFinder();
131
132	1	Color[] newColours = new Color[24];
133	25	for (int i = 0; i < 24; i++)
134		{
135	24	newColours[i] = null;
136		}
137
138	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
139
140		// gap colour not specified so gaps are lightGray
141	1	assertEquals(Color.lightGray, rcf
142		.getResidueColour(true, av.getResidueShading(), null, seq, 3,
143		null));
144
145	1	newColours[23] = Color.pink;
146	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
147
148		// gap colour specified as pink
149	1	assertEquals(Color.pink, rcf.getResidueColour(true,
150		av.getResidueShading(),
151		null, seq, 3, null));
152
153		// unaffected by showBoxes setting
154		// gap colour not specified so gaps are lightGray
155	1	newColours[23] = null;
156	1	assertEquals(Color.lightGray, rcf.getResidueColour(false,
157		av.getResidueShading(), null, seq, 3, null));
158
159	1	newColours[23] = Color.pink;
160	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
161
162		// gap colour specified as pink
163	1	assertEquals(Color.pink, rcf.getResidueColour(false,
164		av.getResidueShading(), null, seq, 3, null));
165		}
166
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05 1PASS
167	0	@Test...
168		public void testGetResidueBoxColour_group()
169		{
170	0	SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
171	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
172
173	0	ColourSchemeI cs = new ZappoColourScheme();
174	0	ArrayList<SequenceI> seqlist = new ArrayList<>();
175	0	seqlist.add(seq);
176	0	SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
177		true, true, 5, 9);
178	0	al.addGroup(sg);
179	0	SequenceGroup[] groups = new SequenceGroup[1];
180	0	groups[0] = sg;
181
182	0	final AlignViewport av = new AlignViewport(al);
183	0	ResidueColourFinder rcf = new OverviewResColourFinder();
184
185		// G in group specified as magenta in Zappo
186	0	assertEquals(Color.magenta, rcf.getResidueColour(false,
187		av.getResidueShading(), groups, seq, 7, null));
188
189		// Residue outside group coloured white
190	0	assertEquals(Color.white, rcf.getResidueColour(false,
191		av.getResidueShading(), groups, seq, 0, null));
192
193		// Gap outside group coloured lightgray
194	0	assertEquals(Color.lightGray, rcf.getResidueColour(false,
195		av.getResidueShading(), groups, seq, 2, null));
196
197		// use legacy colouring
198	0	rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
199
200		// G in group specified as magenta in Zappo
201	0	assertEquals(Color.magenta, rcf.getResidueColour(false,
202		av.getResidueShading(), groups, seq, 7, null));
203
204		// Residue outside group coloured lightgray
205	0	assertEquals(Color.lightGray, rcf.getResidueColour(false,
206		av.getResidueShading(), groups, seq, 0, null));
207
208		// Gap outside group coloured white
209	0	assertEquals(Color.white, rcf.getResidueColour(false,
210		av.getResidueShading(), groups, seq, 2, null));
211
212		// use new colouring
213	0	rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
214
215		// G in group specified as magenta in Zappo
216	0	assertEquals(Color.magenta, rcf.getResidueColour(false,
217		av.getResidueShading(), groups, seq, 7, null));
218
219		// Residue outside group coloured white
220	0	assertEquals(Color.white, rcf.getResidueColour(false,
221		av.getResidueShading(), groups, seq, 0, null));
222
223		// Gap outside group coloured blue
224	0	assertEquals(Color.blue, rcf.getResidueColour(false,
225		av.getResidueShading(), groups, seq, 2, null));
226		}
227
		0% Uncovered Elements: 32 (32) Complexity: 1 Complexity Density: 0.03 1PASS
228	0	@Test...
229		public void testGetBoxColour()
230		{
231	0	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
232		// gap
233	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
234	0	final AlignViewport av = new AlignViewport(al);
235
236		// non-legacy colouring
237	0	ResidueColourFinder rcf = new OverviewResColourFinder();
238	0	ResidueShaderI shader = new ResidueShader();
239
240		// residues white
241	0	Color c = rcf.getBoxColour(shader, seq, 0);
242	0	assertEquals(Color.white, c);
243
244		// gaps gap colour
245	0	c = rcf.getBoxColour(shader, seq, 3);
246	0	assertEquals(
247		jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
248		c);
249
250		// legacy colouring set explicitly via constructor
251	0	rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
252	0	shader = new ResidueShader();
253
254		// residues light gray
255	0	c = rcf.getBoxColour(shader, seq, 0);
256	0	assertEquals(Color.lightGray, c);
257
258		// gaps white
259	0	c = rcf.getBoxColour(shader, seq, 3);
260	0	assertEquals(Color.white, c);
261
262		// legacy colouring off
263	0	rcf = new OverviewResColourFinder();
264	0	shader = new ResidueShader();
265
266		// residues white
267	0	c = rcf.getBoxColour(shader, seq, 0);
268	0	assertEquals(Color.white, c);
269
270		// gaps gap colour
271	0	c = rcf.getBoxColour(shader, seq, 3);
272	0	assertEquals(
273		jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
274		c);
275
276		// non legacy colouring with colour scheme
277	0	rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
278	0	shader = new ResidueShader(new ZappoColourScheme());
279
280		// M residue pink
281	0	c = rcf.getBoxColour(shader, seq, 0);
282	0	assertEquals(Color.pink, c);
283
284		// gaps blue
285	0	c = rcf.getBoxColour(shader, seq, 3);
286	0	assertEquals(Color.blue, c);
287
288		// legacy colouring with colour scheme
289	0	rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
290
291		// M residue pink
292	0	c = rcf.getBoxColour(shader, seq, 0);
293	0	assertEquals(Color.pink, c);
294
295		// gaps white
296	0	c = rcf.getBoxColour(shader, seq, 3);
297	0	assertEquals(Color.white, c);
298		}
299		}