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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ext.pymol

File PymolCommandsTest.java

 

Code metrics

0
135
19
1
350
272
19
0.14
7.11
19
1

Classes

Class Line # Actions
PymolCommandsTest 40 135 19
1.0100%
 

Contributing tests

This file is covered by 18 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.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   
 
40    public class PymolCommandsTest
41    {
42    private PymolCommands testee;
43   
 
44  1 toggle @BeforeClass(alwaysRun = true)
45    public void setUp()
46    {
47  1 testee = new PymolCommands();
48    }
49   
 
50  1 toggle @Test(groups = { "Functional" })
51    public void testColourBySequence()
52    {
53   
54  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
55  1 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
56  1 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
57  1 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
58  1 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
59  1 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
60  1 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
61  1 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
62  1 PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
63  1 PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
64   
65    // Colours should appear in the Pymol 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(), 3);
69  1 assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
70    "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
71  1 assertEquals(commands.get(
72    1),
73    new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
74  1 assertEquals(commands.get(
75    2),
76    new StructureCommand("color", "0xff0000", "0//A/3-9/"));
77    }
78   
 
79  1 toggle @Test(groups = "Functional")
80    public void testGetAtomSpec()
81    {
82  1 AtomSpecModel model = new AtomSpecModel();
83  1 assertEquals(testee.getAtomSpec(model, false), "");
84  1 model.addRange("1", 2, 4, "A");
85  1 assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
86  1 model.addRange("1", 8, 8, "A");
87  1 assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
88  1 model.addRange("1", 5, 7, "B");
89  1 assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
90  1 model.addRange("1", 3, 5, "A");
91  1 assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
92  1 model.addRange("0", 1, 4, "B");
93  1 assertEquals(testee.getAtomSpec(model, false),
94    "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
95  1 model.addRange("0", 5, 9, "C");
96  1 assertEquals(testee.getAtomSpec(model, false),
97    "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
98  1 model.addRange("1", 8, 10, "B");
99  1 assertEquals(testee.getAtomSpec(model, false),
100    "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
101  1 model.addRange("1", 8, 9, "B");
102  1 assertEquals(testee.getAtomSpec(model, false),
103    "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
104  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
105  1 assertEquals(testee.getAtomSpec(model, false),
106    "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
107  1 model.addRange("5", 25, 35, " ");
108  1 assertEquals(testee.getAtomSpec(model, false),
109    "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
110   
111    }
112   
 
113  1 toggle @Test(groups = { "Functional" })
114    public void testSuperposeStructures()
115    {
116  1 AtomSpecModel ref = new AtomSpecModel();
117  1 ref.addRange("1", 12, 14, "A");
118  1 ref.addRange("1", 18, 18, "B");
119  1 ref.addRange("1", 22, 23, "B");
120  1 AtomSpecModel toAlign = new AtomSpecModel();
121  1 toAlign.addRange("2", 15, 17, "B");
122  1 toAlign.addRange("2", 20, 21, "B");
123  1 toAlign.addRange("2", 22, 22, "C");
124  1 List<StructureCommandI> commands = testee.superposeStructures(ref,
125    toAlign);
126  1 assertEquals(commands.size(), 2);
127  1 String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
128  1 String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
129  1 String refSpec = "1//A/12-14/ 1//B/18+22-23/";
130  1 String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
131   
132    // super command: separate arguments for regions to align
133  1 assertEquals(commands.get(0),
134    new StructureCommand("super", refSpecCA, toAlignSpecCA));
135    // show aligned regions: one argument for combined atom specs
136  1 assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
137    refSpec + " " + toAlignSpec));
138    }
139   
 
140  1 toggle @Test(groups = "Functional")
141    public void testGetAtomSpec_alphaOnly()
142    {
143  1 AtomSpecModel model = new AtomSpecModel();
144  1 assertEquals(testee.getAtomSpec(model, true), "");
145  1 model.addRange("1", 2, 4, "A");
146  1 assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
147  1 model.addRange("1", 8, 8, "A");
148  1 assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
149  1 model.addRange("1", 5, 7, "B");
150  1 assertEquals(testee.getAtomSpec(model, true),
151    "1//A/2-4+8/CA 1//B/5-7/CA");
152  1 model.addRange("1", 3, 5, "A");
153  1 assertEquals(testee.getAtomSpec(model, true),
154    "1//A/2-5+8/CA 1//B/5-7/CA");
155  1 model.addRange("0", 1, 4, "B");
156  1 assertEquals(testee.getAtomSpec(model, true),
157    "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
158  1 model.addRange("0", 5, 9, "C");
159  1 assertEquals(testee.getAtomSpec(model, true),
160    "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
161  1 model.addRange("1", 8, 10, "B");
162  1 assertEquals(testee.getAtomSpec(model, true),
163    "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
164  1 model.addRange("1", 8, 9, "B");
165  1 assertEquals(testee.getAtomSpec(model, true),
166    "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
167  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
168  1 assertEquals(testee.getAtomSpec(model, true),
169    "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
170  1 model.addRange("5", 25, 35, " ");
171  1 assertEquals(testee.getAtomSpec(model, true),
172    "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");
173    }
174   
 
175  1 toggle @Test(groups = "Functional")
176    public void testGetModelStartNo()
177    {
178  1 assertEquals(testee.getModelStartNo(), 0);
179    }
180   
 
181  1 toggle @Test(groups = "Functional")
182    public void testGetResidueSpec()
183    {
184  1 assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
185    }
186   
 
187  1 toggle @Test(groups = "Functional")
188    public void testShowBackbone()
189    {
190  1 List<StructureCommandI> cmds = testee.showBackbone();
191  1 assertEquals(cmds.size(), 2);
192  1 assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
193  1 assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
194    }
195   
 
196  1 toggle @Test(groups = "Functional")
197    public void testColourByCharge()
198    {
199  1 List<StructureCommandI> cmds = testee.colourByCharge();
200  1 assertEquals(cmds.size(), 4);
201  1 assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
202  1 assertEquals(cmds.get(1),
203    new StructureCommand("color", "red", "resn ASP resn GLU"));
204  1 assertEquals(cmds.get(2),
205    new StructureCommand("color", "blue", "resn LYS resn ARG"));
206  1 assertEquals(cmds.get(3),
207    new StructureCommand("color", "yellow", "resn CYS"));
208    }
209   
 
210  1 toggle @Test(groups = "Functional")
211    public void testOpenCommandFile()
212    {
213  1 assertEquals(testee.openCommandFile("commands.pml"),
214    new StructureCommand("run", "commands.pml"));
215    }
216   
 
217  1 toggle @Test(groups = "Functional")
218    public void testSaveSession()
219    {
220  1 assertEquals(testee.saveSession("somewhere.pse"),
221    new StructureCommand("save", "somewhere.pse"));
222    }
223   
 
224  1 toggle @Test(groups = "Functional")
225    public void testOpenSession()
226    {
227  1 assertEquals(testee.openSession("/some/path"),
228    new StructureCommand("load", "/some/path", "", "0", "pse"));
229    }
230   
 
231  1 toggle @Test(groups = "Functional")
232    public void testColourByChain()
233    {
234  1 assertEquals(testee.colourByChain(),
235    new StructureCommand("spectrum", "chain"));
236    }
237   
 
238  1 toggle @Test(groups = "Functional")
239    public void testColourResidues()
240    {
241  1 assertEquals(testee.colourResidues("something",
242    Color.MAGENTA),
243    new StructureCommand("color", "0xff00ff", "something"));
244    }
245   
 
246  1 toggle @Test(groups = "Functional")
247    public void testLoadFile()
248    {
249  1 assertEquals(testee.loadFile("/some/path"),
250    new StructureCommand("load", "/some/path"));
251    }
252   
 
253  1 toggle @Test(groups = "Functional")
254    public void testSetBackgroundColour()
255    {
256  1 assertEquals(testee.setBackgroundColour(
257    Color.PINK),
258    new StructureCommand("bg_color", "0xffafaf"));
259    }
260   
 
261  1 toggle @Test(groups = "Functional")
262    public void testSetAttribute()
263    {
264  1 AtomSpecModel model = new AtomSpecModel();
265  1 model.addRange("1", 89, 92, "A");
266  1 model.addRange("2", 12, 20, "B");
267  1 model.addRange("2", 8, 9, "B");
268  1 assertEquals(testee.setAttribute("jv_kd", "27.3", model),
269    new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
270    "p.jv_kd='27.3'"));
271    }
272   
 
273  1 toggle @Test(groups = { "Functional" })
274    public void testSetAttributes()
275    {
276    /*
277    * make a map of { featureType, {featureValue, {residue range specification } } }
278    */
279  1 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
280  1 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
281   
282    /*
283    * start with just one feature/value...
284    */
285  1 featuresMap.put("chain", featureValues);
286  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
287   
288  1 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
289  1 assertEquals(commands.size(), 1);
290   
291    /*
292    * feature name gets a jv_ namespace prefix
293    */
294  1 assertEquals(commands.get(0), new StructureCommand("iterate",
295    "0//A/8-20/", "p.jv_chain='X'"));
296   
297    // add same feature value, overlapping range
298  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
299    // same feature value, contiguous range
300  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
301  1 commands = testee.setAttributes(featuresMap);
302  1 assertEquals(commands.size(), 1);
303  1 assertEquals(commands.get(0), new StructureCommand("iterate",
304    "0//A/3-25/", "p.jv_chain='X'"));
305   
306    // same feature value and model, different chain
307  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
308    // same feature value and chain, different model
309  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
310  1 commands = testee.setAttributes(featuresMap);
311  1 assertEquals(commands.size(), 1);
312  1 StructureCommand expected1 = new StructureCommand("iterate",
313    "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
314  1 assertEquals(commands.get(0), expected1);
315   
316    // same feature, different value
317  1 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
318  1 commands = testee.setAttributes(featuresMap);
319  1 assertEquals(2, commands.size());
320    // commands are ordered by feature type but not by value
321    // so test for the expected command in either order
322  1 StructureCommandI cmd1 = commands.get(0);
323  1 StructureCommandI cmd2 = commands.get(1);
324  1 StructureCommand expected2 = new StructureCommand("iterate",
325    "0//A/40-50/", "p.jv_chain='Y'");
326  1 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
327    // String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
328  1 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
329   
330  1 featuresMap.clear();
331  1 featureValues.clear();
332  1 featuresMap.put("side-chain binding!", featureValues);
333  1 ChimeraCommands.addAtomSpecRange(featureValues,
334    "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
335    // feature names are sanitised to change non-alphanumeric to underscore
336    // feature values are sanitised to encode single quote characters
337  1 commands = testee.setAttributes(featuresMap);
338  1 assertEquals(commands.size(), 1);
339  1 StructureCommandI expected3 = new StructureCommand("iterate",
340    "0//A/7-15/",
341    "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!'");
342  1 assertEquals(commands.get(0), expected3);
343    }
344   
 
345  1 toggle @Test(groups = "Functional")
346    public void testCloseViewer()
347    {
348  1 assertEquals(testee.closeViewer(), new StructureCommand("quit"));
349    }
350    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.