Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewResColourFinderTest	44	97	7	0.4666666746.7%	Show methods

Class OverviewResColourFinderTest

Class OverviewResColourFinderTest	Line # 44	Total Statements 97	Complexity 7	TOTAL Coverage 0.4666666746.7%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4747	3.03	1.01	1.0 1.0100%
testGetResidueBoxColour_none() : void   testGetResidueBoxColour_none() : void	5555	8.08	1.01	1.0 1.0100%
testGetResidueBoxColour_zappo() : void   testGetResidueBoxColour_zappo() : void	7676	15.015	1.01	1.0 1.0100%
testGetResidueBoxColour_userdef() : void   testGetResidueBoxColour_userdef() : void	116116	17.017	2.02	1.0 1.0100%
testGetResidueBoxColour_group() : void   testGetResidueBoxColour_group() : void	158158	22.022	1.01	0.0 0.00%
testGetBoxColour() : void   testGetBoxColour() : void	220220	32.032	1.01	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

 

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