Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ChimeraXCommandsTest	40	142	23	0.00%	Show methods

Class ChimeraXCommandsTest

Class ChimeraXCommandsTest	Line # 40	Total Statements 142	Complexity 23	TOTAL Coverage 0.00%
setUp() : void   setUp() : void	4444	1.01	1.01	0.0 0.00%
testColourByCharge() : void   testColourByCharge() : void	5050	3.03	1.01	0.0 0.00%
testColourByChain() : void   testColourByChain() : void	5959	2.02	1.01	0.0 0.00%
testFocusView() : void   testFocusView() : void	6666	2.02	1.01	0.0 0.00%
testSetBackgroundColour() : void   testSetBackgroundColour() : void	7373	2.02	1.01	0.0 0.00%
testOpenSession() : void   testOpenSession() : void	8080	2.02	1.01	0.0 0.00%
testColourBySequence() : void   testColourBySequence() : void	8787	13.013	1.01	0.0 0.00%
testSetAttributes() : void   testSetAttributes() : void	111111	34.034	1.01	0.0 0.00%
testSuperposeStructures() : void   testSuperposeStructures() : void	179179	15.015	1.01	0.0 0.00%
testGetAtomSpec() : void   testGetAtomSpec() : void	207207	22.022	1.01	0.0 0.00%
testGetAtomSpec_alphaOnly() : void   testGetAtomSpec_alphaOnly() : void	244244	22.022	1.01	0.0 0.00%
testGetModelStartNo() : void   testGetModelStartNo() : void	281281	1.01	1.01	0.0 0.00%
testGetResidueSpec() : void   testGetResidueSpec() : void	287287	1.01	1.01	0.0 0.00%
testShowBackbone() : void   testShowBackbone() : void	293293	3.03	1.01	0.0 0.00%
testOpenCommandFile() : void   testOpenCommandFile() : void	302302	1.01	1.01	0.0 0.00%
testSaveSession() : void   testSaveSession() : void	309309	1.01	1.01	0.0 0.00%
testGetColourCommand() : void   testGetColourCommand() : void	316316	1.01	1.01	0.0 0.00%
testSetAttribute() : void   testSetAttribute() : void	324324	5.05	1.01	0.0 0.00%
testCloseViewer() : void   testCloseViewer() : void	335335	1.01	1.01	0.0 0.00%
testGetSelectedResidues() : void   testGetSelectedResidues() : void	341341	1.01	1.01	0.0 0.00%
testStartNotifications() : void   testStartNotifications() : void	348348	4.04	1.01	0.0 0.00%
testStopNotifications() : void   testStopNotifications() : void	359359	4.04	1.01	0.0 0.00%
testListResidueAttributes() : void   testListResidueAttributes() : void	370370	1.01	1.01	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.ext.rbvi.chimera;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25
26		import java.awt.Color;
27		import java.util.HashMap;
28		import java.util.LinkedHashMap;
29		import java.util.List;
30		import java.util.Map;
31
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.Test;
34
35		import jalview.structure.AtomSpecModel;
36		import jalview.structure.StructureCommand;
37		import jalview.structure.StructureCommandI;
38		import jalview.structure.StructureCommandsI.AtomSpecType;
39
		0% Uncovered Elements: 165 (165) Complexity: 23 Complexity Density: 0.16
40		public class ChimeraXCommandsTest
41		{
42		private ChimeraXCommands testee;
43
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
44	0	@BeforeClass(alwaysRun = true)...
45		public void setUp()
46		{
47	0	testee = new ChimeraXCommands();
48		}
49
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33 4-
50	0	@Test(groups = { "Functional" })...
51		public void testColourByCharge()
52		{
53	0	List<StructureCommandI> cmd = testee.colourByCharge();
54	0	assertEquals(cmd.size(), 1);
55	0	assertEquals(cmd.get(0).getCommand(),
56		"color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
57		}
58
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
59	0	@Test(groups = { "Functional" })...
60		public void testColourByChain()
61		{
62	0	StructureCommandI cmd = testee.colourByChain();
63	0	assertEquals(cmd.getCommand(), "rainbow chain");
64		}
65
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
66	0	@Test(groups = { "Functional" })...
67		public void testFocusView()
68		{
69	0	StructureCommandI cmd = testee.focusView();
70	0	assertEquals(cmd.getCommand(), "view");
71		}
72
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
73	0	@Test(groups = { "Functional" })...
74		public void testSetBackgroundColour()
75		{
76	0	StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
77	0	assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
78		}
79
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5 4-
80	0	@Test(groups = { "Functional" })...
81		public void testOpenSession()
82		{
83	0	StructureCommandI cmd = testee.openSession("/some/filepath");
84	0	assertEquals(cmd.getCommand(), "open /some/filepath format session");
85		}
86
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
87	0	@Test(groups = { "Functional" })...
88		public void testColourBySequence()
89		{
90	0	Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
91	0	ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
92	0	ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
93	0	ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
94	0	ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
95	0	ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
96	0	ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
97	0	ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
98	0	ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
99	0	ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
100
101		/*
102		* Colours should appear in the Chimera command in the order in which
103		* they were added; within colour, by model, by chain, ranges in start order
104		*/
105	0	List<StructureCommandI> commands = testee.colourBySequence(map);
106	0	assertEquals(commands.size(), 1);
107	0	assertEquals(commands.get(0).getCommand(),
108		"color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff;color #2/A:3-5,8 #ffff00;color #1/A:3-9 #ff0000");
109		}
110
		0% Uncovered Elements: 34 (34) Complexity: 1 Complexity Density: 0.03 4-
111	0	@Test(groups = { "Functional" })...
112		public void testSetAttributes()
113		{
114		/*
115		* make a map of { featureType, {featureValue, {residue range specification } } }
116		*/
117	0	Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
118	0	Map<Object, AtomSpecModel> featureValues = new HashMap<>();
119
120		/*
121		* start with just one feature/value...
122		*/
123	0	featuresMap.put("chain", featureValues);
124	0	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
125
126	0	List<StructureCommandI> commands = testee.setAttributes(featuresMap);
127	0	assertEquals(commands.size(), 1);
128
129		/*
130		* feature name gets a jv_ namespace prefix
131		* feature value is quoted in case it contains spaces
132		*/
133	0	assertEquals(commands.get(0).getCommand(),
134		"setattr #0/A:8-20 res jv_chain 'X' create true");
135
136		// add same feature value, overlapping range
137	0	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
138		// same feature value, contiguous range
139	0	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
140	0	commands = testee.setAttributes(featuresMap);
141	0	assertEquals(commands.size(), 1);
142	0	assertEquals(commands.get(0).getCommand(),
143		"setattr #0/A:3-25 res jv_chain 'X' create true");
144
145		// same feature value and model, different chain
146	0	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
147		// same feature value and chain, different model
148	0	ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
149	0	commands = testee.setAttributes(featuresMap);
150	0	assertEquals(commands.size(), 1);
151	0	String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
152	0	assertEquals(commands.get(0).getCommand(), expected1);
153
154		// same feature, different value
155	0	ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
156	0	commands = testee.setAttributes(featuresMap);
157	0	assertEquals(2, commands.size());
158		// commands are ordered by feature type but not by value
159		// so test for the expected command in either order
160	0	String cmd1 = commands.get(0).getCommand();
161	0	String cmd2 = commands.get(1).getCommand();
162	0	assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
163	0	String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
164	0	assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
165
166	0	featuresMap.clear();
167	0	featureValues.clear();
168	0	featuresMap.put("side-chain binding!", featureValues);
169	0	ChimeraCommands.addAtomSpecRange(featureValues,
170		"<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
171		// feature names are sanitised to change non-alphanumeric to underscore
172		// feature values are sanitised to encode single quote characters
173	0	commands = testee.setAttributes(featuresMap);
174	0	assertEquals(commands.size(), 1);
175	0	String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' create true";
176	0	assertTrue(commands.get(0).getCommand().equals(expected3));
177		}
178
		0% Uncovered Elements: 15 (15) Complexity: 1 Complexity Density: 0.07 4-
179	0	@Test(groups = { "Functional" })...
180		public void testSuperposeStructures()
181		{
182	0	AtomSpecModel ref = new AtomSpecModel();
183	0	ref.addRange("1", 12, 14, "A");
184	0	ref.addRange("1", 18, 18, "B");
185	0	ref.addRange("1", 22, 23, "B");
186	0	AtomSpecModel toAlign = new AtomSpecModel();
187	0	toAlign.addRange("2", 15, 17, "B");
188	0	toAlign.addRange("2", 20, 21, "B");
189	0	toAlign.addRange("2", 22, 22, "C");
190	0	List<StructureCommandI> command = testee.superposeStructures(ref,
191		toAlign, AtomSpecType.ALPHA);
192	0	assertEquals(command.size(), 1);
193	0	String cmd = command.get(0).getCommand();
194	0	String refSpec = "#1/A:12-14/B:18,22-23";
195	0	String toAlignSpec = "#2/B:15-17,20-21/C:22";
196
197		/*
198		* superposition arguments include AlphaCarbon restriction,
199		* ribbon command does not
200		*/
201	0	String expected = String.format(
202		"align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
203		refSpec, toAlignSpec, refSpec);
204	0	assertEquals(cmd, expected);
205		}
206
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05 4-
207	0	@Test(groups = "Functional")...
208		public void testGetAtomSpec()
209		{
210	0	AtomSpecModel model = new AtomSpecModel();
211	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
212	0	model.addRange("1", 2, 4, "A");
213	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
214		"#1/A:2-4");
215	0	model.addRange("1", 8, 8, "A");
216	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
217		"#1/A:2-4,8");
218	0	model.addRange("1", 5, 7, "B");
219	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
220		"#1/A:2-4,8/B:5-7");
221	0	model.addRange("1", 3, 5, "A");
222	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
223		"#1/A:2-5,8/B:5-7");
224	0	model.addRange("0", 1, 4, "B");
225	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
226		"#0/B:1-4|#1/A:2-5,8/B:5-7");
227	0	model.addRange("0", 5, 9, "C");
228	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
229		"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
230	0	model.addRange("1", 8, 10, "B");
231	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
232		"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
233	0	model.addRange("1", 8, 9, "B");
234	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
235		"#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
236	0	model.addRange("0", 3, 10, "C"); // subsumes 5-9
237	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
238		"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
239	0	model.addRange("5", 25, 35, " ");
240	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
241		"#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
242		}
243
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05 4-
244	0	@Test(groups = "Functional")...
245		public void testGetAtomSpec_alphaOnly()
246		{
247	0	AtomSpecModel model = new AtomSpecModel();
248	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
249	0	model.addRange("1", 2, 4, "A");
250	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
251		"#1/A:2-4@CA");
252	0	model.addRange("1", 8, 8, "A");
253	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
254		"#1/A:2-4,8@CA");
255	0	model.addRange("1", 5, 7, "B");
256	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
257		"#1/A:2-4,8/B:5-7@CA");
258	0	model.addRange("1", 3, 5, "A");
259	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
260		"#1/A:2-5,8/B:5-7@CA");
261	0	model.addRange("0", 1, 4, "B");
262	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
263		"#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
264	0	model.addRange("0", 5, 9, "C");
265	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
266		"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
267	0	model.addRange("1", 8, 10, "B");
268	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
269		"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
270	0	model.addRange("1", 8, 9, "B");
271	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
272		"#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
273	0	model.addRange("0", 3, 10, "C"); // subsumes 5-9
274	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
275		"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
276	0	model.addRange("5", 25, 35, " "); // empty chain code
277	0	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
278		"#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
279		}
280
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
281	0	@Test(groups = "Functional")...
282		public void testGetModelStartNo()
283		{
284	0	assertEquals(testee.getModelStartNo(), 1);
285		}
286
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
287	0	@Test(groups = "Functional")...
288		public void testGetResidueSpec()
289		{
290	0	assertEquals(testee.getResidueSpec("ALA"), ":ALA");
291		}
292
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33 4-
293	0	@Test(groups = "Functional")...
294		public void testShowBackbone()
295		{
296	0	List<StructureCommandI> showBackbone = testee.showBackbone();
297	0	assertEquals(showBackbone.size(), 1);
298	0	assertEquals(showBackbone.get(0).getCommand(),
299		"~display all;~ribbon;show @CA|P atoms");
300		}
301
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
302	0	@Test(groups = "Functional")...
303		public void testOpenCommandFile()
304		{
305	0	assertEquals(testee.openCommandFile("nowhere").getCommand(),
306		"open nowhere");
307		}
308
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
309	0	@Test(groups = "Functional")...
310		public void testSaveSession()
311		{
312	0	assertEquals(testee.saveSession("somewhere").getCommand(),
313		"save somewhere format session");
314		}
315
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
316	0	@Test(groups = "Functional")...
317		public void testGetColourCommand()
318		{
319	0	assertEquals(
320		testee.colourResidues("something", Color.MAGENTA).getCommand(),
321		"color something #ff00ff");
322		}
323
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2 4-
324	0	@Test(groups = "Functional")...
325		public void testSetAttribute()
326		{
327	0	AtomSpecModel model = new AtomSpecModel();
328	0	model.addRange("1", 89, 92, "A");
329	0	model.addRange("2", 12, 20, "B");
330	0	model.addRange("2", 8, 9, "B");
331	0	assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(),
332		"setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
333		}
334
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
335	0	@Test(groups = "Functional")...
336		public void testCloseViewer()
337		{
338	0	assertEquals(testee.closeViewer(), new StructureCommand("exit"));
339		}
340
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
341	0	@Test(groups = "Functional")...
342		public void testGetSelectedResidues()
343		{
344	0	assertEquals(testee.getSelectedResidues(),
345		new StructureCommand("info selection level residue"));
346		}
347
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
348	0	@Test(groups = "Functional")...
349		public void testStartNotifications()
350		{
351	0	List<StructureCommandI> cmds = testee.startNotifications("to here");
352	0	assertEquals(cmds.size(), 2);
353	0	assertEquals(cmds.get(0), new StructureCommand(
354		"info notify start models jalview prefix ModelChanged url to here"));
355	0	assertEquals(cmds.get(1), new StructureCommand(
356		"info notify start selection jalview prefix SelectionChanged url to here"));
357		}
358
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 4-
359	0	@Test(groups = "Functional")...
360		public void testStopNotifications()
361		{
362	0	List<StructureCommandI> cmds = testee.stopNotifications();
363	0	assertEquals(cmds.size(), 2);
364	0	assertEquals(cmds.get(0),
365		new StructureCommand("info notify stop models jalview"));
366	0	assertEquals(cmds.get(1),
367		new StructureCommand("info notify stop selection jalview"));
368		}
369
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
370	0	@Test(groups = "Functional")...
371		public void testListResidueAttributes()
372		{
373	0	assertEquals(testee.listResidueAttributes(),
374		new StructureCommand("info resattr"));
375		}
376		}