Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewResColourFinderTest	45	95	7	0.4757281547.6%	Show methods

Class OverviewResColourFinderTest

Class OverviewResColourFinderTest	Line # 45	Total Statements 95	Complexity 7	TOTAL Coverage 0.4757281547.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4848	3.03	1.01	1.0 1.0100%
testGetResidueBoxColour_none() : void   testGetResidueBoxColour_none() : void	5656	8.08	1.01	1.0 1.0100%
testGetResidueBoxColour_zappo() : void   testGetResidueBoxColour_zappo() : void	7979	15.015	1.01	1.0 1.0100%
testGetResidueBoxColour_userdef() : void   testGetResidueBoxColour_userdef() : void	125125	17.017	2.02	1.0 1.0100%
testGetResidueBoxColour_group() : void   testGetResidueBoxColour_group() : void	169169	22.022	1.01	0.0 0.00%
testGetBoxColour() : void   testGetBoxColour() : void	231231	30.030	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.19417475	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdefjalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdef	1PASS
	0.1553398	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappojalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappo	1PASS
	0.08737864	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_nonejalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_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 java.awt.Color;
26		import java.util.ArrayList;
27
28		import org.testng.annotations.BeforeClass;
29		import org.testng.annotations.Test;
30
31		import jalview.api.AlignViewportI;
32		import jalview.bin.Cache;
33		import jalview.datamodel.Alignment;
34		import jalview.datamodel.AlignmentI;
35		import jalview.datamodel.Sequence;
36		import jalview.datamodel.SequenceGroup;
37		import jalview.datamodel.SequenceI;
38		import jalview.gui.AlignViewport;
39		import jalview.gui.JvOptionPane;
40		import jalview.gui.OverviewCanvas;
41		import jalview.schemes.ColourSchemeI;
42		import jalview.schemes.UserColourScheme;
43		import jalview.schemes.ZappoColourScheme;
44
		47.6% Uncovered Elements: 54 (103) Complexity: 7 Complexity Density: 0.07
45		public class OverviewResColourFinderTest
46		{
47
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
48	1	@BeforeClass(alwaysRun = true)...
49		public void setUpJvOptionPane()
50		{
51	1	JvOptionPane.setInteractiveMode(false);
52	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
53	1	Cache.loadProperties("test/jalview/io/testProps.jvprops");
54		}
55
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
56	1	@Test(groups = { "Functional" })...
57		public void testGetResidueBoxColour_none()
58		{
59	1	SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
60	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
61	1	final AlignViewportI av = new AlignViewport(al);
62	1	ResidueColourFinder rcf = new OverviewResColourFinder();
63
64		// gaps are grey, residues white
65	1	assertEquals(Color.white, rcf.getResidueColour(true,
66		av.getResidueShading(),
67		null, seq, 0, null));
68	1	assertEquals(Color.lightGray, rcf
69		.getResidueColour(true, av.getResidueShading(), null, seq, 2,
70		null));
71
72		// unaffected by showBoxes setting
73	1	assertEquals(Color.white, rcf.getResidueColour(false,
74		av.getResidueShading(), null, seq, 0, null));
75	1	assertEquals(Color.lightGray, rcf.getResidueColour(false,
76		av.getResidueShading(), null, seq, 2, null));
77		}
78
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
79	1	@Test(groups = { "Functional" })...
80		public void testGetResidueBoxColour_zappo()
81		{
82	1	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
83		// gap
84	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
85	1	final AlignViewportI av = new AlignViewport(al);
86	1	ResidueColourFinder rcf = new OverviewResColourFinder();
87	1	av.setGlobalColourScheme(new ZappoColourScheme());
88
89		// @see ResidueProperties.zappo
90	1	assertEquals(Color.pink,
91		rcf.getResidueColour(true, av.getResidueShading(),
92		null, seq, 0, null)); // M
93	1	assertEquals(Color.green,
94		rcf.getResidueColour(true, av.getResidueShading(),
95		null, seq, 2, null)); // T
96	1	assertEquals(Color.magenta,
97		rcf.getResidueColour(true, av.getResidueShading(),
98		null, seq, 5, null)); // G
99	1	assertEquals(Color.orange,
100		rcf.getResidueColour(true, av.getResidueShading(),
101		null, seq, 12, null)); // F
102
103		// gap colour not specified so gaps are lightGray
104	1	assertEquals(Color.lightGray, rcf
105		.getResidueColour(true, av.getResidueShading(), null, seq, 3,
106		null));
107
108		// unaffected by showBoxes setting
109	1	assertEquals(Color.pink, rcf.getResidueColour(false,
110		av.getResidueShading(), null, seq, 0, null)); // M
111	1	assertEquals(Color.green, rcf.getResidueColour(false,
112		av.getResidueShading(), null, seq, 2, null)); // T
113	1	assertEquals(Color.magenta, rcf.getResidueColour(false,
114		av.getResidueShading(), null, seq, 5, null)); // G
115	1	assertEquals(Color.orange, rcf.getResidueColour(false,
116		av.getResidueShading(), null, seq, 12, null)); // F
117
118		// gap colour not specified so gaps are lightGray
119	1	assertEquals(Color.lightGray, rcf
120		.getResidueColour(false, av.getResidueShading(), null, seq, 3,
121		null));
122
123		}
124
		100% Uncovered Elements: 0 (19) Complexity: 2 Complexity Density: 0.12 1PASS
125	1	@Test(groups = { "Functional" })...
126		public void testGetResidueBoxColour_userdef()
127		{
128	1	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
129		// gap
130	1	AlignmentI al = new Alignment(new SequenceI[] { seq });
131	1	final AlignViewportI av = new AlignViewport(al);
132	1	ResidueColourFinder rcf = new OverviewResColourFinder();
133
134	1	Color[] newColours = new Color[24];
135	25	for (int i = 0; i < 24; i++)
136		{
137	24	newColours[i] = null;
138		}
139
140	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
141
142		// gap colour not specified so gaps are lightGray
143	1	assertEquals(Color.lightGray, rcf
144		.getResidueColour(true, av.getResidueShading(), null, seq, 3,
145		null));
146
147	1	newColours[23] = Color.pink;
148	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
149
150		// gap colour specified as pink
151	1	assertEquals(Color.pink, rcf.getResidueColour(true,
152		av.getResidueShading(),
153		null, seq, 3, null));
154
155		// unaffected by showBoxes setting
156		// gap colour not specified so gaps are lightGray
157	1	newColours[23] = null;
158	1	assertEquals(Color.lightGray, rcf.getResidueColour(false,
159		av.getResidueShading(), null, seq, 3, null));
160
161	1	newColours[23] = Color.pink;
162	1	av.setGlobalColourScheme(new UserColourScheme(newColours));
163
164		// gap colour specified as pink
165	1	assertEquals(Color.pink, rcf.getResidueColour(false,
166		av.getResidueShading(), null, seq, 3, null));
167		}
168
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05 1PASS
169	0	@Test...
170		public void testGetResidueBoxColour_group()
171		{
172	0	SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
173	0	AlignmentI al = new Alignment(new SequenceI[] { seq });
174
175	0	ColourSchemeI cs = new ZappoColourScheme();
176	0	ArrayList<SequenceI> seqlist = new ArrayList<>();
177	0	seqlist.add(seq);
178	0	SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
179		true, true, 5, 9);
180	0	al.addGroup(sg);
181	0	SequenceGroup[] groups = new SequenceGroup[1];
182	0	groups[0] = sg;
183
184	0	final AlignViewportI av = new AlignViewport(al);
185	0	ResidueColourFinder rcf = new OverviewResColourFinder();
186
187		// G in group specified as magenta in Zappo
188	0	assertEquals(Color.magenta, rcf.getResidueColour(false,
189		av.getResidueShading(), groups, seq, 7, null));
190
191		// Residue outside group coloured white
192	0	assertEquals(Color.white, rcf.getResidueColour(false,
193		av.getResidueShading(), groups, seq, 0, null));
194
195		// Gap outside group coloured lightgray
196	0	assertEquals(Color.lightGray, rcf.getResidueColour(false,
197		av.getResidueShading(), groups, seq, 2, null));
198
199		// use legacy colouring
200	0	rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
201		Color.red);
202
203		// G in group specified as magenta in Zappo
204	0	assertEquals(Color.magenta, rcf.getResidueColour(false,
205		av.getResidueShading(), groups, seq, 7, null));
206
207		// Residue outside group coloured lightgray
208	0	assertEquals(Color.lightGray, rcf.getResidueColour(false,
209		av.getResidueShading(), groups, seq, 0, null));
210
211		// Gap outside group coloured white
212	0	assertEquals(Color.white, rcf.getResidueColour(false,
213		av.getResidueShading(), groups, seq, 2, null));
214
215		// use new colouring
216	0	rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
217
218		// G in group specified as magenta in Zappo
219	0	assertEquals(Color.magenta, rcf.getResidueColour(false,
220		av.getResidueShading(), groups, seq, 7, null));
221
222		// Residue outside group coloured white
223	0	assertEquals(Color.white, rcf.getResidueColour(false,
224		av.getResidueShading(), groups, seq, 0, null));
225
226		// Gap outside group coloured blue
227	0	assertEquals(Color.blue, rcf.getResidueColour(false,
228		av.getResidueShading(), groups, seq, 2, null));
229		}
230
		0% Uncovered Elements: 30 (30) Complexity: 1 Complexity Density: 0.03 1PASS
231	0	@Test...
232		public void testGetBoxColour()
233		{
234	0	SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
235		// gap
236
237		// non-legacy colouring
238	0	ResidueColourFinder rcf = new OverviewResColourFinder();
239	0	ResidueShaderI shader = new ResidueShader();
240
241		// residues white
242	0	Color c = rcf.getBoxColour(shader, seq, 0);
243	0	assertEquals(Color.white, c);
244
245		// gaps gap colour
246	0	c = rcf.getBoxColour(shader, seq, 3);
247	0	assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
248
249		// legacy colouring set explicitly via constructor
250	0	rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
251		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(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
273
274		// non legacy colouring with colour scheme
275	0	rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
276	0	shader = new ResidueShader(new ZappoColourScheme());
277
278		// M residue pink
279	0	c = rcf.getBoxColour(shader, seq, 0);
280	0	assertEquals(Color.pink, c);
281
282		// gaps blue
283	0	c = rcf.getBoxColour(shader, seq, 3);
284	0	assertEquals(Color.blue, c);
285
286		// legacy colouring with colour scheme
287	0	rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
288		Color.red);
289
290		// M residue pink
291	0	c = rcf.getBoxColour(shader, seq, 0);
292	0	assertEquals(Color.pink, c);
293
294		// gaps white
295	0	c = rcf.getBoxColour(shader, seq, 3);
296	0	assertEquals(Color.white, c);
297		}
298		}