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  1. Project Clover database Mon Oct 6 2025 17:39:40 BST
  2. Package jalview.ext.rbvi.chimera

File ChimeraXCommandsTest.java

 

Code metrics

0
142
23
1
376
292
23
0.16
6.17
23
1

Classes

Class Line # Actions
ChimeraXCommandsTest 40 142 23
1.0100%
 

Contributing tests

This file is covered by 22 tests. .

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.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   
 
40    public class ChimeraXCommandsTest
41    {
42    private ChimeraXCommands testee;
43   
 
44  1 toggle @BeforeClass(alwaysRun = true)
45    public void setUp()
46    {
47  1 testee = new ChimeraXCommands();
48    }
49   
 
50  1 toggle @Test(groups = { "Functional" })
51    public void testColourByCharge()
52    {
53  1 List<StructureCommandI> cmd = testee.colourByCharge();
54  1 assertEquals(cmd.size(), 1);
55  1 assertEquals(cmd.get(0).getCommand(),
56    "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
57    }
58   
 
59  1 toggle @Test(groups = { "Functional" })
60    public void testColourByChain()
61    {
62  1 StructureCommandI cmd = testee.colourByChain();
63  1 assertEquals(cmd.getCommand(), "rainbow chain");
64    }
65   
 
66  1 toggle @Test(groups = { "Functional" })
67    public void testFocusView()
68    {
69  1 StructureCommandI cmd = testee.focusView();
70  1 assertEquals(cmd.getCommand(), "view");
71    }
72   
 
73  1 toggle @Test(groups = { "Functional" })
74    public void testSetBackgroundColour()
75    {
76  1 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
77  1 assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
78    }
79   
 
80  1 toggle @Test(groups = { "Functional" })
81    public void testOpenSession()
82    {
83  1 StructureCommandI cmd = testee.openSession("/some/filepath");
84  1 assertEquals(cmd.getCommand(), "open /some/filepath format session");
85    }
86   
 
87  1 toggle @Test(groups = { "Functional" })
88    public void testColourBySequence()
89    {
90  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
91  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
92  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
93  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
94  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
95  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
96  1 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
97  1 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
98  1 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
99  1 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  1 List<StructureCommandI> commands = testee.colourBySequence(map);
106  1 assertEquals(commands.size(), 1);
107  1 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   
 
111  1 toggle @Test(groups = { "Functional" })
112    public void testSetAttributes()
113    {
114    /*
115    * make a map of { featureType, {featureValue, {residue range specification } } }
116    */
117  1 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
118  1 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
119   
120    /*
121    * start with just one feature/value...
122    */
123  1 featuresMap.put("chain", featureValues);
124  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
125   
126  1 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
127  1 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  1 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  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
138    // same feature value, contiguous range
139  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
140  1 commands = testee.setAttributes(featuresMap);
141  1 assertEquals(commands.size(), 1);
142  1 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  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
147    // same feature value and chain, different model
148  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
149  1 commands = testee.setAttributes(featuresMap);
150  1 assertEquals(commands.size(), 1);
151  1 String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
152  1 assertEquals(commands.get(0).getCommand(), expected1);
153   
154    // same feature, different value
155  1 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
156  1 commands = testee.setAttributes(featuresMap);
157  1 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  1 String cmd1 = commands.get(0).getCommand();
161  1 String cmd2 = commands.get(1).getCommand();
162  1 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
163  1 String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
164  1 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
165   
166  1 featuresMap.clear();
167  1 featureValues.clear();
168  1 featuresMap.put("side-chain binding!", featureValues);
169  1 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  1 commands = testee.setAttributes(featuresMap);
174  1 assertEquals(commands.size(), 1);
175  1 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  1 assertTrue(commands.get(0).getCommand().equals(expected3));
177    }
178   
 
179  1 toggle @Test(groups = { "Functional" })
180    public void testSuperposeStructures()
181    {
182  1 AtomSpecModel ref = new AtomSpecModel();
183  1 ref.addRange("1", 12, 14, "A");
184  1 ref.addRange("1", 18, 18, "B");
185  1 ref.addRange("1", 22, 23, "B");
186  1 AtomSpecModel toAlign = new AtomSpecModel();
187  1 toAlign.addRange("2", 15, 17, "B");
188  1 toAlign.addRange("2", 20, 21, "B");
189  1 toAlign.addRange("2", 22, 22, "C");
190  1 List<StructureCommandI> command = testee.superposeStructures(ref,
191    toAlign, AtomSpecType.ALPHA);
192  1 assertEquals(command.size(), 1);
193  1 String cmd = command.get(0).getCommand();
194  1 String refSpec = "#1/A:12-14/B:18,22-23";
195  1 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  1 String expected = String.format(
202    "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
203    refSpec, toAlignSpec, refSpec);
204  1 assertEquals(cmd, expected);
205    }
206   
 
207  1 toggle @Test(groups = "Functional")
208    public void testGetAtomSpec()
209    {
210  1 AtomSpecModel model = new AtomSpecModel();
211  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
212  1 model.addRange("1", 2, 4, "A");
213  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
214    "#1/A:2-4");
215  1 model.addRange("1", 8, 8, "A");
216  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
217    "#1/A:2-4,8");
218  1 model.addRange("1", 5, 7, "B");
219  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
220    "#1/A:2-4,8/B:5-7");
221  1 model.addRange("1", 3, 5, "A");
222  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
223    "#1/A:2-5,8/B:5-7");
224  1 model.addRange("0", 1, 4, "B");
225  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
226    "#0/B:1-4|#1/A:2-5,8/B:5-7");
227  1 model.addRange("0", 5, 9, "C");
228  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
229    "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
230  1 model.addRange("1", 8, 10, "B");
231  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
232    "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
233  1 model.addRange("1", 8, 9, "B");
234  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
235    "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
236  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
237  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
238    "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
239  1 model.addRange("5", 25, 35, " ");
240  1 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   
 
244  1 toggle @Test(groups = "Functional")
245    public void testGetAtomSpec_alphaOnly()
246    {
247  1 AtomSpecModel model = new AtomSpecModel();
248  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
249  1 model.addRange("1", 2, 4, "A");
250  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
251    "#1/A:2-4@CA");
252  1 model.addRange("1", 8, 8, "A");
253  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
254    "#1/A:2-4,8@CA");
255  1 model.addRange("1", 5, 7, "B");
256  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
257    "#1/A:2-4,8/B:5-7@CA");
258  1 model.addRange("1", 3, 5, "A");
259  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
260    "#1/A:2-5,8/B:5-7@CA");
261  1 model.addRange("0", 1, 4, "B");
262  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
263    "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
264  1 model.addRange("0", 5, 9, "C");
265  1 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  1 model.addRange("1", 8, 10, "B");
268  1 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  1 model.addRange("1", 8, 9, "B");
271  1 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  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
274  1 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  1 model.addRange("5", 25, 35, " "); // empty chain code
277  1 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   
 
281  1 toggle @Test(groups = "Functional")
282    public void testGetModelStartNo()
283    {
284  1 assertEquals(testee.getModelStartNo(), 1);
285    }
286   
 
287  1 toggle @Test(groups = "Functional")
288    public void testGetResidueSpec()
289    {
290  1 assertEquals(testee.getResidueSpec("ALA"), ":ALA");
291    }
292   
 
293  1 toggle @Test(groups = "Functional")
294    public void testShowBackbone()
295    {
296  1 List<StructureCommandI> showBackbone = testee.showBackbone();
297  1 assertEquals(showBackbone.size(), 1);
298  1 assertEquals(showBackbone.get(0).getCommand(),
299    "~display all;~ribbon;show @CA|P atoms");
300    }
301   
 
302  1 toggle @Test(groups = "Functional")
303    public void testOpenCommandFile()
304    {
305  1 assertEquals(testee.openCommandFile("nowhere").getCommand(),
306    "open nowhere");
307    }
308   
 
309  1 toggle @Test(groups = "Functional")
310    public void testSaveSession()
311    {
312  1 assertEquals(testee.saveSession("somewhere").getCommand(),
313    "save somewhere format session");
314    }
315   
 
316  1 toggle @Test(groups = "Functional")
317    public void testGetColourCommand()
318    {
319  1 assertEquals(
320    testee.colourResidues("something", Color.MAGENTA).getCommand(),
321    "color something #ff00ff");
322    }
323   
 
324  1 toggle @Test(groups = "Functional")
325    public void testSetAttribute()
326    {
327  1 AtomSpecModel model = new AtomSpecModel();
328  1 model.addRange("1", 89, 92, "A");
329  1 model.addRange("2", 12, 20, "B");
330  1 model.addRange("2", 8, 9, "B");
331  1 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   
 
335  1 toggle @Test(groups = "Functional")
336    public void testCloseViewer()
337    {
338  1 assertEquals(testee.closeViewer(), new StructureCommand("exit"));
339    }
340   
 
341  1 toggle @Test(groups = "Functional")
342    public void testGetSelectedResidues()
343    {
344  1 assertEquals(testee.getSelectedResidues(),
345    new StructureCommand("info selection level residue"));
346    }
347   
 
348  1 toggle @Test(groups = "Functional")
349    public void testStartNotifications()
350    {
351  1 List<StructureCommandI> cmds = testee.startNotifications("to here");
352  1 assertEquals(cmds.size(), 2);
353  1 assertEquals(cmds.get(0), new StructureCommand(
354    "info notify start models jalview prefix ModelChanged url to here"));
355  1 assertEquals(cmds.get(1), new StructureCommand(
356    "info notify start selection jalview prefix SelectionChanged url to here"));
357    }
358   
 
359  1 toggle @Test(groups = "Functional")
360    public void testStopNotifications()
361    {
362  1 List<StructureCommandI> cmds = testee.stopNotifications();
363  1 assertEquals(cmds.size(), 2);
364  1 assertEquals(cmds.get(0),
365    new StructureCommand("info notify stop models jalview"));
366  1 assertEquals(cmds.get(1),
367    new StructureCommand("info notify stop selection jalview"));
368    }
369   
 
370  1 toggle @Test(groups = "Functional")
371    public void testListResidueAttributes()
372    {
373  1 assertEquals(testee.listResidueAttributes(),
374    new StructureCommand("info resattr"));
375    }
376    }
  • Report generated by OpenClover v 4.4.1 on Mon Oct 6 2025 17:49:54 BST using coverage data from Mon Oct 6 2025 17:49:41 BST.
  • OpenClover is free and open-source software.