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  1. Project Clover database Tue Nov 4 2025 11:21:43 GMT
  2. Package jalview.ext.jmol

File JmolCommandsTest.java

 

Code metrics

2
121
18
1
376
283
19
0.16
6.72
18
1.06

Classes

Class Line # Actions
JmolCommandsTest 50 121 19
1.0100%
 

Contributing tests

This file is covered by 21 tests. .

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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.jmol;
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.DataProvider;
34    import org.testng.annotations.Test;
35   
36    import jalview.datamodel.Alignment;
37    import jalview.datamodel.AlignmentI;
38    import jalview.datamodel.ColumnSelection;
39    import jalview.datamodel.Sequence;
40    import jalview.datamodel.SequenceI;
41    import jalview.gui.AlignFrame;
42    import jalview.gui.SequenceRenderer;
43    import jalview.schemes.JalviewColourScheme;
44    import jalview.structure.AtomSpecModel;
45    import jalview.structure.StructureCommandI;
46    import jalview.structure.StructureCommandsI.AtomSpecType;
47    import jalview.structure.StructureMapping;
48    import jalview.structure.StructureSelectionManager;
49   
 
50    public class JmolCommandsTest
51    {
52    private JmolCommands testee;
53   
 
54  1 toggle @BeforeClass(alwaysRun = true)
55    public void setUp()
56    {
57  1 testee = new JmolCommands();
58    }
59   
 
60  1 toggle @Test(groups = { "Functional" })
61    public void testGetColourBySequenceCommands_hiddenColumns()
62    {
63    /*
64    * load these sequences, coloured by Strand propensity,
65    * with columns 2-4 hidden
66    */
67  1 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
68  1 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
69  1 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
70  1 AlignFrame af = new AlignFrame(al, 800, 500);
71  1 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
72  1 ColumnSelection cs = new ColumnSelection();
73  1 cs.addElement(2);
74  1 cs.addElement(3);
75  1 cs.addElement(4);
76  1 af.getViewport().setColumnSelection(cs);
77  1 af.hideSelColumns_actionPerformed(null);
78  1 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
79  1 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
80  1 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
81  1 StructureSelectionManager ssm = new StructureSelectionManager();
82   
83    /*
84    * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
85    */
86  1 HashMap<Integer, int[]> map = new HashMap<>();
87  11 for (int pos = 1; pos <= seq1.getLength(); pos++)
88    {
89  10 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
90    }
91  1 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
92    "A", map, null);
93  1 ssm.addStructureMapping(sm1);
94  1 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
95    "B", map, null);
96  1 ssm.addStructureMapping(sm2);
97   
98  1 String[] commands = testee.colourBySequence(ssm, files, seqs, sr,
99    af.alignPanel);
100  1 assertEquals(commands.length, 2);
101   
102  1 String chainACommand = commands[0];
103    // M colour is #82827d == (130, 130, 125) (see strand.html help page)
104  1 assertTrue(
105    chainACommand.contains("select 21:A/1.1;color[130,130,125]")); // first
106    // one
107    // H colour is #60609f == (96, 96, 159)
108  1 assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
109    // hidden columns are Gray (128, 128, 128)
110  1 assertTrue(chainACommand
111    .contains(";select 23-25:A/1.1;color[128,128,128]"));
112    // S and G are both coloured #4949b6 == (73, 73, 182)
113  1 assertTrue(
114    chainACommand.contains(";select 26-30:A/1.1;color[73,73,182]"));
115   
116  1 String chainBCommand = commands[1];
117    // M colour is #82827d == (130, 130, 125)
118  1 assertTrue(
119    chainBCommand.contains("select 21:B/2.1;color[130,130,125]"));
120    // V colour is #ffff00 == (255, 255, 0)
121  1 assertTrue(chainBCommand.contains(";select 22:B/2.1;color[255,255,0]"));
122    // hidden columns are Gray (128, 128, 128)
123  1 assertTrue(chainBCommand
124    .contains(";select 23-25:B/2.1;color[128,128,128]"));
125    // S and G are both coloured #4949b6 == (73, 73, 182)
126  1 assertTrue(
127    chainBCommand.contains(";select 26-30:B/2.1;color[73,73,182]"));
128    }
129   
 
130  1 toggle @Test(groups = "Functional")
131    public void testGetAtomSpec()
132    {
133  1 AtomSpecModel model = new AtomSpecModel();
134  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
135  1 model.addRange("1", 2, 4, "A");
136  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
137    "2-4:A/1.1");
138  1 model.addRange("1", 8, 8, "A");
139  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
140    "2-4:A/1.1|8:A/1.1");
141  1 model.addRange("1", 5, 7, "B");
142  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
143    "2-4:A/1.1|8:A/1.1|5-7:B/1.1");
144  1 model.addRange("1", 3, 5, "A");
145  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
146    "2-5:A/1.1|8:A/1.1|5-7:B/1.1");
147  1 model.addRange("2", 1, 4, "B");
148  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
149    "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1");
150  1 model.addRange("2", 5, 9, "C");
151  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
152    "2-5:A/1.1|8:A/1.1|5-7:B/1.1|1-4:B/2.1|5-9:C/2.1");
153  1 model.addRange("1", 8, 10, "B");
154  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
155    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
156  1 model.addRange("1", 8, 9, "B");
157  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
158    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|5-9:C/2.1");
159  1 model.addRange("2", 3, 10, "C"); // subsumes 5-9
160  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
161    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1");
162  1 model.addRange("5", 25, 35, " ");
163  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
164    "2-5:A/1.1|8:A/1.1|5-10:B/1.1|1-4:B/2.1|3-10:C/2.1|25-35:/5.1");
165   
166    }
167   
 
168  1 toggle @Test(groups = { "Functional" })
169    public void testColourBySequence()
170    {
171  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
172  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
173  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
174  1 JmolCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
175  1 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
176  1 JmolCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
177  1 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
178  1 JmolCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
179  1 JmolCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
180  1 JmolCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
181   
182    // Colours should appear in the Jmol command in the order in which
183    // they were added; within colour, by model, by chain, ranges in start order
184  1 List<StructureCommandI> commands = testee.colourBySequence(map);
185  1 assertEquals(commands.size(), 1);
186  1 String expected1 = "select 2-5:A/1.1|9-23:A/1.1|7:B/1.1|1:A/2.1|4-7:B/2.1;color[0,0,255]";
187  1 String expected2 = "select 3-5:A/2.1|8:A/2.1;color[255,255,0]";
188  1 String expected3 = "select 3-9:A/1.1;color[255,0,0]";
189  1 assertEquals(commands.get(0).getCommand(),
190    expected1 + ";" + expected2 + ";" + expected3);
191    }
192   
 
193  1 toggle @Test(groups = { "Functional" })
194    public void testSuperposeStructures()
195    {
196  1 AtomSpecModel ref = new AtomSpecModel();
197  1 ref.addRange("1", 12, 14, "A");
198  1 ref.addRange("1", 18, 18, "B");
199  1 ref.addRange("1", 22, 23, "B");
200  1 AtomSpecModel toAlign = new AtomSpecModel();
201  1 toAlign.addRange("2", 15, 17, "B");
202  1 toAlign.addRange("2", 20, 21, "B");
203  1 toAlign.addRange("2", 22, 22, "C");
204  1 List<StructureCommandI> command = testee.superposeStructures(ref,
205    toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc
206    // or protein
207  1 assertEquals(command.size(), 1);
208  1 String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
209  1 String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
210  1 String expected = String.format(
211    "compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS {%s}{%s} ROTATE TRANSLATE ;select %s|%s;cartoons",
212    toAlignSpec, refSpec, toAlignSpec, refSpec);
213  1 assertEquals(command.get(0).getCommand(), expected);
214    }
215   
 
216  1 toggle @Test(groups = "Functional")
217    public void testGetModelStartNo()
218    {
219  1 assertEquals(testee.getModelStartNo(), 1);
220    }
221   
 
222  1 toggle @Test(groups = "Functional")
223    public void testColourByChain()
224    {
225  1 StructureCommandI cmd = testee.colourByChain();
226  1 assertEquals(cmd.getCommand(), "select *;color chain");
227    }
228   
 
229  1 toggle @Test(groups = "Functional")
230    public void testColourByCharge()
231    {
232  1 List<StructureCommandI> cmds = testee.colourByCharge();
233  1 assertEquals(cmds.size(), 1);
234  1 assertEquals(cmds.get(0).getCommand(),
235    "select *;color white;select ASP,GLU;color red;"
236    + "select LYS,ARG;color blue;select CYS;color yellow");
237    }
238   
 
239  1 toggle @Test(groups = "Functional")
240    public void testSetBackgroundColour()
241    {
242  1 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
243  1 assertEquals(cmd.getCommand(), "background [255,175,175]");
244    }
245   
 
246  1 toggle @Test(groups = "Functional")
247    public void testFocusView()
248    {
249  1 StructureCommandI cmd = testee.focusView();
250  1 assertEquals(cmd.getCommand(), "zoom 0");
251    }
252   
 
253  1 toggle @Test(groups = "Functional")
254    public void testSaveSession()
255    {
256  1 StructureCommandI cmd = testee.saveSession("/some/filepath");
257  1 assertEquals(cmd.getCommand(), "write STATE \"/some/filepath\"");
258  1 cmd = testee.saveSession("\\some\\filepath");
259  1 assertEquals(cmd.getCommand(), "write STATE \"\\\\some\\\\filepath\"");
260    }
261   
 
262  1 toggle @Test(groups = "Functional")
263    public void testShowBackbone()
264    {
265  1 List<StructureCommandI> cmds = testee.showBackbone();
266  1 assertEquals(cmds.size(), 1);
267  1 assertEquals(cmds.get(0).getCommand(),
268    "select *; cartoons off; backbone");
269    }
270   
 
271  1 toggle @Test(groups = "Functional")
272    public void testLoadFile()
273    {
274  1 StructureCommandI cmd = testee.loadFile("/some/filepath");
275  1 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
276   
277    // single backslash gets escaped to double
278  1 cmd = testee.loadFile("\\some\\filepath");
279  1 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
280   
281    // double backslash gets escaped to file:\\\\
282  1 cmd = testee.loadFile("\\\\some\\filepath");
283  1 assertEquals(cmd.getCommand(),
284    "load FILES \"file:\\\\\\\\some\\\\filepath\"");
285   
286    // double forward slash is escaped to file:////
287  1 cmd = testee.loadFile("//some/filepath");
288  1 assertEquals(cmd.getCommand(), "load FILES \"file://some/filepath\"");
289   
290    }
291   
 
292  4 toggle @Test(
293    groups = "Functional",
294    dataProvider = "testFilePathEquivalence",
295    singleThreaded = true)
296    public void testFilePathEquivalence(String jalviewpath, String jmolpath)
297    {
298  4 assertEquals(JmolCommands.escapeQuotedFilename(jalviewpath), jmolpath,
299    "for " + jalviewpath);
300    // simple unescape
301  4 assertTrue(JmolCommands.filePathMatch(jmolpath.replace("\\\\", "\\"),
302    jalviewpath));
303    }
304   
305    /**
306    * Windows path transformations for Jmol 14.31.53 NOLOG4J positive examples
307    * for escapeQuotedFilename - results of escaping should, after a simple
308    * unescape (remove escape backslashes) also work for filePathMatch
309    *
310    * @return
311    */
312   
 
313  1 toggle @DataProvider(name = "testFilePathEquivalence")
314    public Object[][] fileEquivalences()
315    {
316  1 return new String[][] {
317    new String[]
318    { "/some/filepath", "/some/filepath" },
319    new String[]
320    { "\\some\\filepath", "\\\\some\\\\filepath" },
321    new String[]
322    { "\\\\some\\filepath", "file:\\\\\\\\some\\\\filepath" },
323    new String[]
324    { "//some/filepath", "file://some/filepath" } };
325    }
326   
 
327  7 toggle @Test(
328    groups = "Functional",
329    dataProvider = "testForwardBackslashFilePathEquivalence")
330    public void filePathMatchTest(String jmolPath, String jalviewPath)
331    {
332  7 assertTrue(JmolCommands.filePathMatch(jmolPath, jalviewPath));
333    }
334   
335    /**
336    * Windows path transformations for Jmol 14.31.53 NOLOG4J positive examples
337    * for JmolCommands.filePathMatch - handles windows network drive
338    * transformations
339    *
340    * @return
341    */
 
342  1 toggle @DataProvider(name = "testForwardBackslashFilePathEquivalence")
343    public Object[][] forwardBackslashFilePathEquivalence()
344    {
345  1 return new String[][] {
346    new String[]
347    { "file:\\\\some\\filepath", "\\\\some\\filepath" },
348    new String[]
349    { "file://some/filepath", "\\\\some\\filepath" },
350    new String[]
351    { "file:////some//filepath", "\\\\some\\filepath" },
352    new String[]
353    { "file:\\\\\\\\estorage.dundee.ac.uk\\\\cluster-gjb_lab\\\\jprocter\\\\public_html\\\\1QIP.cif",
354    "//estorage.dundee.ac.uk/cluster-gjb_lab/jprocter/public_html/1QIP.cif" },
355    new String[]
356    { "file:\\\\\\\\estorage.dundee.ac.uk\\\\cluster-gjb_lab\\\\jprocter\\\\public_html\\\\1QIP.cif",
357    "\\\\estorage.dundee.ac.uk\\cluster-gjb_lab\\jprocter\\public_html\\1QIP.cif" },
358    new String[]
359    { "file://estorage.dundee.ac.uk/cluster-gjb_lab/jprocter/public_html/1QIP.cif",
360    "\\\\estorage.dundee.ac.uk\\cluster-gjb_lab\\jprocter\\public_html\\1QIP.cif" },
361    new String[]
362    { "file:////estorage.dundee.ac.uk//cluster-gjb_lab//jprocter//public_html//1QIP.cif",
363    "\\\\estorage.dundee.ac.uk\\cluster-gjb_lab\\jprocter\\public_html\\1QIP.cif" } };
364    }
365   
 
366  1 toggle @Test(groups = "Functional")
367    public void testOpenSession()
368    {
369  1 StructureCommandI cmd = testee.openSession("/some/filepath");
370  1 assertEquals(cmd.getCommand(), "load FILES \"/some/filepath\"");
371   
372    // single backslash gets escaped to double
373  1 cmd = testee.openSession("\\some\\filepath");
374  1 assertEquals(cmd.getCommand(), "load FILES \"\\\\some\\\\filepath\"");
375    }
376    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 4 2025 11:32:25 GMT using coverage data from Tue Nov 4 2025 11:32:11 GMT.
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