Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PymolCommandsTest	41	136	19	1.0100%	Show methods

Class PymolCommandsTest

Class PymolCommandsTest	Line # 41	Total Statements 136	Complexity 19	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	4545	1.01	1.01	1.0 1.0100%
testColourBySequence() : void   testColourBySequence() : void	5151	15.015	1.01	1.0 1.0100%
testGetAtomSpec() : void   testGetAtomSpec() : void	7878	22.022	1.01	1.0 1.0100%
testSuperposeStructures() : void   testSuperposeStructures() : void	116116	17.017	1.01	1.0 1.0100%
testGetAtomSpec_alphaOnly() : void   testGetAtomSpec_alphaOnly() : void	143143	22.022	1.01	1.0 1.0100%
testGetModelStartNo() : void   testGetModelStartNo() : void	180180	1.01	1.01	1.0 1.0100%
testGetResidueSpec() : void   testGetResidueSpec() : void	186186	1.01	1.01	1.0 1.0100%
testShowBackbone() : void   testShowBackbone() : void	192192	4.04	1.01	1.0 1.0100%
testColourByCharge() : void   testColourByCharge() : void	201201	6.06	1.01	1.0 1.0100%
testOpenCommandFile() : void   testOpenCommandFile() : void	215215	1.01	1.01	1.0 1.0100%
testSaveSession() : void   testSaveSession() : void	222222	1.01	1.01	1.0 1.0100%
testOpenSession() : void   testOpenSession() : void	229229	1.01	1.01	1.0 1.0100%
testColourByChain() : void   testColourByChain() : void	236236	1.01	1.01	1.0 1.0100%
testColourResidues() : void   testColourResidues() : void	243243	1.01	1.01	1.0 1.0100%
testLoadFile() : void   testLoadFile() : void	250250	1.01	1.01	1.0 1.0100%
testSetBackgroundColour() : void   testSetBackgroundColour() : void	257257	1.01	1.01	1.0 1.0100%
testSetAttribute() : void   testSetAttribute() : void	264264	5.05	1.01	1.0 1.0100%
testSetAttributes() : void   testSetAttributes() : void	276276	34.034	1.01	1.0 1.0100%
testCloseViewer() : void   testCloseViewer() : void	348348	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22580644	jalview.ext.pymol.PymolCommandsTest.testSetAttributesjalview.ext.pymol.PymolCommandsTest.testSetAttributes	1PASS
	0.14838709	jalview.ext.pymol.PymolCommandsTest.testGetAtomSpecjalview.ext.pymol.PymolCommandsTest.testGetAtomSpec	1PASS
	0.14838709	jalview.ext.pymol.PymolCommandsTest.testGetAtomSpec_alphaOnlyjalview.ext.pymol.PymolCommandsTest.testGetAtomSpec_alphaOnly	1PASS
	0.11612903	jalview.ext.pymol.PymolCommandsTest.testSuperposeStructuresjalview.ext.pymol.PymolCommandsTest.testSuperposeStructures	1PASS
	0.103225805	jalview.ext.pymol.PymolCommandsTest.testColourBySequencejalview.ext.pymol.PymolCommandsTest.testColourBySequence	1PASS
	0.045161292	jalview.ext.pymol.PymolCommandsTest.testColourByChargejalview.ext.pymol.PymolCommandsTest.testColourByCharge	1PASS
	0.038709678	jalview.ext.pymol.PymolCommandsTest.testSetAttributejalview.ext.pymol.PymolCommandsTest.testSetAttribute	1PASS
	0.032258064	jalview.ext.pymol.PymolCommandsTest.testShowBackbonejalview.ext.pymol.PymolCommandsTest.testShowBackbone	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testCloseViewerjalview.ext.pymol.PymolCommandsTest.testCloseViewer	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testSaveSessionjalview.ext.pymol.PymolCommandsTest.testSaveSession	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testGetResidueSpecjalview.ext.pymol.PymolCommandsTest.testGetResidueSpec	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testSetBackgroundColourjalview.ext.pymol.PymolCommandsTest.testSetBackgroundColour	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testLoadFilejalview.ext.pymol.PymolCommandsTest.testLoadFile	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testColourResiduesjalview.ext.pymol.PymolCommandsTest.testColourResidues	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testGetModelStartNojalview.ext.pymol.PymolCommandsTest.testGetModelStartNo	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testOpenCommandFilejalview.ext.pymol.PymolCommandsTest.testOpenCommandFile	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testColourByChainjalview.ext.pymol.PymolCommandsTest.testColourByChain	1PASS
	0.012903226	jalview.ext.pymol.PymolCommandsTest.testOpenSessionjalview.ext.pymol.PymolCommandsTest.testOpenSession	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.ext.pymol;
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.ext.rbvi.chimera.ChimeraCommands;
36		import jalview.structure.AtomSpecModel;
37		import jalview.structure.StructureCommand;
38		import jalview.structure.StructureCommandI;
39		import jalview.structure.StructureCommandsI.AtomSpecType;
40
		100% Uncovered Elements: 0 (155) Complexity: 19 Complexity Density: 0.14
41		public class PymolCommandsTest
42		{
43		private PymolCommands testee;
44
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
45	1	@BeforeClass(alwaysRun = true)...
46		public void setUp()
47		{
48	1	testee = new PymolCommands();
49		}
50
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
51	1	@Test(groups = { "Functional" })...
52		public void testColourBySequence()
53		{
54
55	1	Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
56	1	PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
57	1	PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
58	1	PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
59	1	PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
60	1	PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
61	1	PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
62	1	PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
63	1	PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
64	1	PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
65
66		// Colours should appear in the Pymol command in the order in which
67		// they were added; within colour, by model, by chain, ranges in start order
68	1	List<StructureCommandI> commands = testee.colourBySequence(map);
69	1	assertEquals(commands.size(), 3);
70	1	assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
71		"0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
72	1	assertEquals(commands.get(1),
73		new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
74	1	assertEquals(commands.get(2),
75		new StructureCommand("color", "0xff0000", "0//A/3-9/"));
76		}
77
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
78	1	@Test(groups = "Functional")...
79		public void testGetAtomSpec()
80		{
81	1	AtomSpecModel model = new AtomSpecModel();
82	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
83	1	model.addRange("1", 2, 4, "A");
84	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
85		"1//A/2-4/");
86	1	model.addRange("1", 8, 8, "A");
87	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
88		"1//A/2-4+8/");
89	1	model.addRange("1", 5, 7, "B");
90	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
91		"1//A/2-4+8/ 1//B/5-7/");
92	1	model.addRange("1", 3, 5, "A");
93	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
94		"1//A/2-5+8/ 1//B/5-7/");
95	1	model.addRange("0", 1, 4, "B");
96	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
97		"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
98	1	model.addRange("0", 5, 9, "C");
99	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
100		"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
101	1	model.addRange("1", 8, 10, "B");
102	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
103		"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
104	1	model.addRange("1", 8, 9, "B");
105	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
106		"0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
107	1	model.addRange("0", 3, 10, "C"); // subsumes 5-9
108	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
109		"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
110	1	model.addRange("5", 25, 35, " ");
111	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
112		"0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
113
114		}
115
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
116	1	@Test(groups = { "Functional" })...
117		public void testSuperposeStructures()
118		{
119	1	AtomSpecModel ref = new AtomSpecModel();
120	1	ref.addRange("1", 12, 14, "A");
121	1	ref.addRange("1", 18, 18, "B");
122	1	ref.addRange("1", 22, 23, "B");
123	1	AtomSpecModel toAlign = new AtomSpecModel();
124	1	toAlign.addRange("2", 15, 17, "B");
125	1	toAlign.addRange("2", 20, 21, "B");
126	1	toAlign.addRange("2", 22, 22, "C");
127	1	List<StructureCommandI> commands = testee.superposeStructures(ref,
128		toAlign, AtomSpecType.ALPHA);
129	1	assertEquals(commands.size(), 4);
130	1	String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
131	1	String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
132	1	String refSpec = "1//A/12-14/ 1//B/18+22-23/";
133	1	String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
134	1	String altLoc = " and (altloc '' or altloc 'a'))";
135		// super command: separate arguments for regions to align
136	1	assertEquals(commands.get(1), new StructureCommand("pair_fit",
137		toAlignSpecCA + altLoc, refSpecCA + altLoc));
138		// show aligned regions: one argument for combined atom specs
139	1	assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
140		refSpec + " " + toAlignSpec));
141		}
142
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
143	1	@Test(groups = "Functional")...
144		public void testGetAtomSpec_alphaOnly()
145		{
146	1	AtomSpecModel model = new AtomSpecModel();
147	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
148	1	model.addRange("1", 2, 4, "A");
149	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
150		"1//A/2-4/CA");
151	1	model.addRange("1", 8, 8, "A");
152	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
153		"1//A/2-4+8/CA");
154	1	model.addRange("1", 5, 7, "B");
155	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
156		"1//A/2-4+8/CA 1//B/5-7/CA");
157	1	model.addRange("1", 3, 5, "A");
158	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
159		"1//A/2-5+8/CA 1//B/5-7/CA");
160	1	model.addRange("0", 1, 4, "B");
161	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
162		"0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
163	1	model.addRange("0", 5, 9, "C");
164	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
165		"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
166	1	model.addRange("1", 8, 10, "B");
167	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
168		"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
169	1	model.addRange("1", 8, 9, "B");
170	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
171		"0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
172	1	model.addRange("0", 3, 10, "C"); // subsumes 5-9
173	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
174		"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
175	1	model.addRange("5", 25, 35, " ");
176	1	assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
177		"0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
178		}
179
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
180	1	@Test(groups = "Functional")...
181		public void testGetModelStartNo()
182		{
183	1	assertEquals(testee.getModelStartNo(), 0);
184		}
185
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
186	1	@Test(groups = "Functional")...
187		public void testGetResidueSpec()
188		{
189	1	assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
190		}
191
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
192	1	@Test(groups = "Functional")...
193		public void testShowBackbone()
194		{
195	1	List<StructureCommandI> cmds = testee.showBackbone();
196	1	assertEquals(cmds.size(), 2);
197	1	assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
198	1	assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
199		}
200
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
201	1	@Test(groups = "Functional")...
202		public void testColourByCharge()
203		{
204	1	List<StructureCommandI> cmds = testee.colourByCharge();
205	1	assertEquals(cmds.size(), 4);
206	1	assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
207	1	assertEquals(cmds.get(1),
208		new StructureCommand("color", "red", "resn ASP resn GLU"));
209	1	assertEquals(cmds.get(2),
210		new StructureCommand("color", "blue", "resn LYS resn ARG"));
211	1	assertEquals(cmds.get(3),
212		new StructureCommand("color", "yellow", "resn CYS"));
213		}
214
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
215	1	@Test(groups = "Functional")...
216		public void testOpenCommandFile()
217		{
218	1	assertEquals(testee.openCommandFile("commands.pml"),
219		new StructureCommand("run", "commands.pml"));
220		}
221
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
222	1	@Test(groups = "Functional")...
223		public void testSaveSession()
224		{
225	1	assertEquals(testee.saveSession("somewhere.pse"),
226		new StructureCommand("save", "somewhere.pse"));
227		}
228
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
229	1	@Test(groups = "Functional")...
230		public void testOpenSession()
231		{
232	1	assertEquals(testee.openSession("/some/path"),
233		new StructureCommand("load", "/some/path", "", "0", "pse"));
234		}
235
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
236	1	@Test(groups = "Functional")...
237		public void testColourByChain()
238		{
239	1	assertEquals(testee.colourByChain(),
240		new StructureCommand("spectrum", "chain"));
241		}
242
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
243	1	@Test(groups = "Functional")...
244		public void testColourResidues()
245		{
246	1	assertEquals(testee.colourResidues("something", Color.MAGENTA),
247		new StructureCommand("color", "0xff00ff", "something"));
248		}
249
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
250	1	@Test(groups = "Functional")...
251		public void testLoadFile()
252		{
253	1	assertEquals(testee.loadFile("/some/path"),
254		new StructureCommand("load", "/some/path"));
255		}
256
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
257	1	@Test(groups = "Functional")...
258		public void testSetBackgroundColour()
259		{
260	1	assertEquals(testee.setBackgroundColour(Color.PINK),
261		new StructureCommand("bg_color", "0xffafaf"));
262		}
263
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
264	1	@Test(groups = "Functional")...
265		public void testSetAttribute()
266		{
267	1	AtomSpecModel model = new AtomSpecModel();
268	1	model.addRange("1", 89, 92, "A");
269	1	model.addRange("2", 12, 20, "B");
270	1	model.addRange("2", 8, 9, "B");
271	1	assertEquals(testee.setAttribute("jv_kd", "27.3", model),
272		new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
273		"p.jv_kd='27.3'"));
274		}
275
		100% Uncovered Elements: 0 (34) Complexity: 1 Complexity Density: 0.03 1PASS
276	1	@Test(groups = { "Functional" })...
277		public void testSetAttributes()
278		{
279		/*
280		* make a map of { featureType, {featureValue, {residue range specification } } }
281		*/
282	1	Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
283	1	Map<Object, AtomSpecModel> featureValues = new HashMap<>();
284
285		/*
286		* start with just one feature/value...
287		*/
288	1	featuresMap.put("chain", featureValues);
289	1	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
290
291	1	List<StructureCommandI> commands = testee.setAttributes(featuresMap);
292	1	assertEquals(commands.size(), 1);
293
294		/*
295		* feature name gets a jv_ namespace prefix
296		*/
297	1	assertEquals(commands.get(0), new StructureCommand("iterate",
298		"0//A/8-20/", "p.jv_chain='X'"));
299
300		// add same feature value, overlapping range
301	1	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
302		// same feature value, contiguous range
303	1	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
304	1	commands = testee.setAttributes(featuresMap);
305	1	assertEquals(commands.size(), 1);
306	1	assertEquals(commands.get(0), new StructureCommand("iterate",
307		"0//A/3-25/", "p.jv_chain='X'"));
308
309		// same feature value and model, different chain
310	1	ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
311		// same feature value and chain, different model
312	1	ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
313	1	commands = testee.setAttributes(featuresMap);
314	1	assertEquals(commands.size(), 1);
315	1	StructureCommand expected1 = new StructureCommand("iterate",
316		"0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
317	1	assertEquals(commands.get(0), expected1);
318
319		// same feature, different value
320	1	ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
321	1	commands = testee.setAttributes(featuresMap);
322	1	assertEquals(2, commands.size());
323		// commands are ordered by feature type but not by value
324		// so test for the expected command in either order
325	1	StructureCommandI cmd1 = commands.get(0);
326	1	StructureCommandI cmd2 = commands.get(1);
327	1	StructureCommand expected2 = new StructureCommand("iterate",
328		"0//A/40-50/", "p.jv_chain='Y'");
329	1	assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
330		// String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
331	1	assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
332
333	1	featuresMap.clear();
334	1	featureValues.clear();
335	1	featuresMap.put("side-chain binding!", featureValues);
336	1	ChimeraCommands.addAtomSpecRange(featureValues,
337		"<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
338		// feature names are sanitised to change non-alphanumeric to underscore
339		// feature values are sanitised to encode single quote characters
340	1	commands = testee.setAttributes(featuresMap);
341	1	assertEquals(commands.size(), 1);
342	1	StructureCommandI expected3 = new StructureCommand("iterate",
343		"0//A/7-15/",
344		"p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!'");
345	1	assertEquals(commands.get(0), expected3);
346		}
347
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1 1PASS
348	1	@Test(groups = "Functional")...
349		public void testCloseViewer()
350		{
351	1	assertEquals(testee.closeViewer(), new StructureCommand("quit"));
352		}
353		}