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  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.ext.rbvi.chimera

File ChimeraCommandsTest.java

 

Code metrics

0
148
26
1
401
312
26
0.18
5.69
26
1

Classes

Class Line # Actions
ChimeraCommandsTest 40 148 26
1.0100%
 

Contributing tests

This file is covered by 25 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 ChimeraCommandsTest
41    {
42    private ChimeraCommands testee;
43   
 
44  1 toggle @BeforeClass(alwaysRun = true)
45    public void setUp()
46    {
47  1 testee = new ChimeraCommands();
48    }
49   
 
50  1 toggle @Test(groups = { "Functional" })
51    public void testColourBySequence()
52    {
53   
54  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
55  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
56  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
57  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
58  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
59  1 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
60  1 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
61  1 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
62  1 ChimeraCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
63  1 ChimeraCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
64   
65    // Colours should appear in the Chimera command in the order in which
66    // they were added; within colour, by model, by chain, ranges in start order
67  1 List<StructureCommandI> commands = testee.colourBySequence(map);
68  1 assertEquals(commands.size(), 1);
69  1 assertEquals(commands.get(0).getCommand(),
70    "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B;color #ffff00 #1:3-5.A,8.A;color #ff0000 #0:3-9.A");
71    }
72   
 
73  1 toggle @Test(groups = { "Functional" })
74    public void testSetAttributes()
75    {
76    /*
77    * make a map of { featureType, {featureValue, {residue range specification } } }
78    */
79  1 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
80  1 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
81   
82    /*
83    * start with just one feature/value...
84    */
85  1 featuresMap.put("chain", featureValues);
86  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
87   
88  1 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
89  1 assertEquals(1, commands.size());
90   
91    /*
92    * feature name gets a jv_ namespace prefix
93    * feature value is quoted in case it contains spaces
94    */
95  1 assertEquals(commands.get(0).getCommand(),
96    "setattr res jv_chain 'X' #0:8-20.A");
97   
98    // add same feature value, overlapping range
99  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
100    // same feature value, contiguous range
101  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
102  1 commands = testee.setAttributes(featuresMap);
103  1 assertEquals(1, commands.size());
104  1 assertEquals(commands.get(0).getCommand(),
105    "setattr res jv_chain 'X' #0:3-25.A");
106   
107    // same feature value and model, different chain
108  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
109    // same feature value and chain, different model
110  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
111  1 commands = testee.setAttributes(featuresMap);
112  1 assertEquals(1, commands.size());
113  1 String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A";
114  1 assertEquals(commands.get(0).getCommand(), expected1);
115   
116    // same feature, different value
117  1 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
118  1 commands = testee.setAttributes(featuresMap);
119  1 assertEquals(2, commands.size());
120    // commands are ordered by feature type but not by value
121    // so test for the expected command in either order
122  1 String cmd1 = commands.get(0).getCommand();
123  1 String cmd2 = commands.get(1).getCommand();
124  1 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
125  1 String expected2 = "setattr res jv_chain 'Y' #0:40-50.A";
126  1 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
127   
128  1 featuresMap.clear();
129  1 featureValues.clear();
130  1 featuresMap.put("side-chain binding!", featureValues);
131  1 ChimeraCommands.addAtomSpecRange(featureValues,
132    "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
133    // feature names are sanitised to change non-alphanumeric to underscore
134    // feature values are sanitised to encode single quote characters
135  1 commands = testee.setAttributes(featuresMap);
136  1 assertEquals(commands.size(), 1);
137  1 String expected3 = "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' #0:7-15.A";
138  1 assertTrue(commands.get(0).getCommand().equals(expected3));
139    }
140   
141    /**
142    * Tests for the method that prefixes and sanitises a feature name so it can
143    * be used as a valid, namespaced attribute name in Chimera or PyMol
144    */
 
145  1 toggle @Test(groups = { "Functional" })
146    public void testMakeAttributeName()
147    {
148  1 assertEquals(testee.makeAttributeName(null), "jv_");
149  1 assertEquals(testee.makeAttributeName(""), "jv_");
150  1 assertEquals(testee.makeAttributeName("helix"), "jv_helix");
151  1 assertEquals(testee.makeAttributeName("Hello World 24"),
152    "jv_Hello_World_24");
153  1 assertEquals(testee.makeAttributeName("!this is-a_very*{odd(name"),
154    "jv__this_is_a_very__odd_name");
155    // name ending in color gets underscore appended
156  1 assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_");
157    }
158   
 
159  1 toggle @Test(groups = "Functional")
160    public void testGetAtomSpec()
161    {
162  1 AtomSpecModel model = new AtomSpecModel();
163  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
164  1 model.addRange("1", 2, 4, "A");
165  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
166    "#1:2-4.A");
167  1 model.addRange("1", 8, 8, "A");
168  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
169    "#1:2-4.A,8.A");
170  1 model.addRange("1", 5, 7, "B");
171  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
172    "#1:2-4.A,8.A,5-7.B");
173  1 model.addRange("1", 3, 5, "A");
174  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
175    "#1:2-5.A,8.A,5-7.B");
176  1 model.addRange("0", 1, 4, "B");
177  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
178    "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
179  1 model.addRange("0", 5, 9, "C");
180  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
181    "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
182  1 model.addRange("1", 8, 10, "B");
183  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
184    "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
185  1 model.addRange("1", 8, 9, "B");
186  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
187    "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
188  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
189  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
190    "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
191  1 model.addRange("5", 25, 35, " ");
192  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
193    "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
194   
195    }
196   
 
197  1 toggle @Test(groups = { "Functional" })
198    public void testSuperposeStructures()
199    {
200  1 AtomSpecModel ref = new AtomSpecModel();
201  1 ref.addRange("1", 12, 14, "A");
202  1 ref.addRange("1", 18, 18, "B");
203  1 ref.addRange("1", 22, 23, "B");
204  1 AtomSpecModel toAlign = new AtomSpecModel();
205  1 toAlign.addRange("2", 15, 17, "B");
206  1 toAlign.addRange("2", 20, 21, "B");
207  1 toAlign.addRange("2", 22, 22, "C");
208  1 List<StructureCommandI> command = testee.superposeStructures(ref,
209    toAlign, AtomSpecType.ALPHA);
210    // qualifier to restrict match to CA and no altlocs
211  1 String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
212  1 String refSpec = "#1:12-14.A,18.B,22-23.B";
213  1 String toAlignSpec = "#2:15-17.B,20-21.B,22.C";
214  1 String expected = String.format("match %s%s %s%s; ribbon %s|%s; focus",
215    toAlignSpec, carbonAlphas, refSpec, carbonAlphas, toAlignSpec,
216    refSpec);
217  1 assertEquals(command.get(0).getCommand(), expected);
218    }
219   
 
220  1 toggle @Test(groups = "Functional")
221    public void testGetAtomSpec_alphaOnly()
222    {
223  1 AtomSpecModel model = new AtomSpecModel();
224  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
225  1 model.addRange("1", 2, 4, "A");
226  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
227    "#1:2-4.A@CA&~@.B-Z&~@.2-9");
228  1 model.addRange("1", 8, 8, "A");
229  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
230    "#1:2-4.A,8.A@CA&~@.B-Z&~@.2-9");
231  1 model.addRange("1", 5, 7, "B");
232  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
233    "#1:2-4.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
234  1 model.addRange("1", 3, 5, "A");
235  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
236    "#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
237  1 model.addRange("0", 1, 4, "B");
238  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
239    "#0:1-4.B@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
240  1 model.addRange("0", 5, 9, "C");
241  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
242    "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA&~@.B-Z&~@.2-9");
243  1 model.addRange("1", 8, 10, "B");
244  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
245    "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
246  1 model.addRange("1", 8, 9, "B");
247  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
248    "#0:1-4.B,5-9.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
249  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
250  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
251    "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9");
252  1 model.addRange("5", 25, 35, " "); // empty chain code
253  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
254    "#0:1-4.B,3-10.C@CA&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA&~@.B-Z&~@.2-9|#5:25-35.@CA&~@.B-Z&~@.2-9");
255   
256    }
257   
 
258  1 toggle @Test(groups = "Functional")
259    public void testGetModelStartNo()
260    {
261  1 assertEquals(testee.getModelStartNo(), 0);
262    }
263   
 
264  1 toggle @Test(groups = "Functional")
265    public void testGetResidueSpec()
266    {
267  1 assertEquals(testee.getResidueSpec("ALA"), "::ALA");
268    }
269   
 
270  1 toggle @Test(groups = "Functional")
271    public void testShowBackbone()
272    {
273  1 List<StructureCommandI> cmds = testee.showBackbone();
274  1 assertEquals(cmds.size(), 1);
275  1 assertEquals(cmds.get(0).getCommand(),
276    "~display all;~ribbon;chain @CA|P");
277    }
278   
 
279  1 toggle @Test(groups = "Functional")
280    public void testOpenCommandFile()
281    {
282  1 assertEquals(testee.openCommandFile("nowhere").getCommand(),
283    "open cmd:nowhere");
284    }
285   
 
286  1 toggle @Test(groups = "Functional")
287    public void testSaveSession()
288    {
289  1 assertEquals(testee.saveSession("somewhere").getCommand(),
290    "save somewhere");
291    }
292   
 
293  1 toggle @Test(groups = "Functional")
294    public void testColourByChain()
295    {
296  1 assertEquals(testee.colourByChain().getCommand(), "rainbow chain");
297    }
298   
 
299  1 toggle @Test(groups = { "Functional" })
300    public void testSetBackgroundColour()
301    {
302  1 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
303  1 assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
304    }
305   
 
306  1 toggle @Test(groups = { "Functional" })
307    public void testLoadFile()
308    {
309  1 StructureCommandI cmd = testee.loadFile("/some/filepath");
310  1 assertEquals(cmd.getCommand(), "open /some/filepath");
311    }
312   
 
313  1 toggle @Test(groups = { "Functional" })
314    public void testOpenSession()
315    {
316  1 StructureCommandI cmd = testee.openSession("/some/filepath");
317  1 assertEquals(cmd.getCommand(), "open chimera:/some/filepath");
318    }
319   
 
320  1 toggle @Test(groups = "Functional")
321    public void testColourByCharge()
322    {
323  1 List<StructureCommandI> cmds = testee.colourByCharge();
324  1 assertEquals(cmds.size(), 1);
325  1 assertEquals(cmds.get(0).getCommand(),
326    "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
327    }
328   
 
329  1 toggle @Test(groups = "Functional")
330    public void testGetColourCommand()
331    {
332  1 assertEquals(
333    testee.colourResidues("something", Color.MAGENTA).getCommand(),
334    "color #ff00ff something");
335    }
336   
 
337  1 toggle @Test(groups = "Functional")
338    public void testFocusView()
339    {
340  1 assertEquals(testee.focusView().getCommand(), "focus");
341    }
342   
 
343  1 toggle @Test(groups = "Functional")
344    public void testSetAttribute()
345    {
346  1 AtomSpecModel model = new AtomSpecModel();
347  1 model.addRange("1", 89, 92, "A");
348  1 model.addRange("2", 12, 20, "B");
349  1 model.addRange("2", 8, 9, "B");
350  1 assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(),
351    "setattr res jv_kd '27.3' #1:89-92.A|#2:8-9.B,12-20.B");
352    }
353   
 
354  1 toggle @Test(groups = "Functional")
355    public void testCloseViewer()
356    {
357  1 assertEquals(testee.closeViewer(), new StructureCommand("stop really"));
358    }
359   
 
360  1 toggle @Test(groups = "Functional")
361    public void testGetSelectedResidues()
362    {
363  1 assertEquals(testee.getSelectedResidues(),
364    new StructureCommand("list selection level residue"));
365    }
366   
 
367  1 toggle @Test(groups = "Functional")
368    public void testListResidueAttributes()
369    {
370  1 assertEquals(testee.listResidueAttributes(),
371    new StructureCommand("list resattr"));
372    }
373   
 
374  1 toggle @Test(groups = "Functional")
375    public void testGetResidueAttributes()
376    {
377  1 assertEquals(testee.getResidueAttributes("binding site"),
378    new StructureCommand("list residues attr 'binding site'"));
379    }
380   
 
381  1 toggle @Test(groups = "Functional")
382    public void testStartNotifications()
383    {
384  1 List<StructureCommandI> cmds = testee.startNotifications("to here");
385  1 assertEquals(cmds.size(), 2);
386  1 assertEquals(cmds.get(0),
387    new StructureCommand("listen start models url to here"));
388  1 assertEquals(cmds.get(1), new StructureCommand(
389    "listen start select prefix SelectionChanged url to here"));
390    }
391   
 
392  1 toggle @Test(groups = "Functional")
393    public void testStopNotifications()
394    {
395  1 List<StructureCommandI> cmds = testee.stopNotifications();
396  1 assertEquals(cmds.size(), 2);
397  1 assertEquals(cmds.get(0), new StructureCommand("listen stop models"));
398  1 assertEquals(cmds.get(1),
399    new StructureCommand("listen stop selection"));
400    }
401    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.