2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ext.rbvi.chimera;
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertTrue;
26 import java.awt.Color;
27 import java.util.HashMap;
28 import java.util.LinkedHashMap;
29 import java.util.List;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.Test;
35 import jalview.structure.AtomSpecModel;
36 import jalview.structure.StructureCommand;
37 import jalview.structure.StructureCommandI;
39 public class ChimeraXCommandsTest
41 private ChimeraXCommands testee;
43 @BeforeClass(alwaysRun = true)
46 testee = new ChimeraXCommands();
49 @Test(groups = { "Functional" })
50 public void testColourByCharge()
52 List<StructureCommandI> cmd = testee.colourByCharge();
53 assertEquals(cmd.size(), 1);
54 assertEquals(cmd.get(0).getCommand(),
55 "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
58 @Test(groups = { "Functional" })
59 public void testColourByChain()
61 StructureCommandI cmd = testee.colourByChain();
62 assertEquals(cmd.getCommand(), "rainbow chain");
65 @Test(groups = { "Functional" })
66 public void testFocusView()
68 StructureCommandI cmd = testee.focusView();
69 assertEquals(cmd.getCommand(), "view");
72 @Test(groups = { "Functional" })
73 public void testSetBackgroundColour()
75 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
76 assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
79 @Test(groups = { "Functional" })
80 public void testOpenSession()
82 StructureCommandI cmd = testee.openSession("/some/filepath");
83 assertEquals(cmd.getCommand(), "open /some/filepath format session");
86 @Test(groups = { "Functional" })
87 public void testColourBySequence()
89 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
90 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
91 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
92 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
93 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
94 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
95 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
96 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
97 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
98 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
101 * Colours should appear in the Chimera command in the order in which
102 * they were added; within colour, by model, by chain, ranges in start order
104 List<StructureCommandI> commands = testee.colourBySequence(map);
105 assertEquals(commands.size(), 1);
106 assertEquals(commands.get(0).getCommand(),
107 "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");
110 @Test(groups = { "Functional" })
111 public void testSetAttributes()
114 * make a map of { featureType, {featureValue, {residue range specification } } }
116 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
117 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
120 * start with just one feature/value...
122 featuresMap.put("chain", featureValues);
123 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
125 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
126 assertEquals(commands.size(), 1);
129 * feature name gets a jv_ namespace prefix
130 * feature value is quoted in case it contains spaces
132 assertEquals(commands.get(0).getCommand(),
133 "setattr #0/A:8-20 res jv_chain 'X' create true");
135 // add same feature value, overlapping range
136 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
137 // same feature value, contiguous range
138 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
139 commands = testee.setAttributes(featuresMap);
140 assertEquals(commands.size(), 1);
141 assertEquals(commands.get(0).getCommand(),
142 "setattr #0/A:3-25 res jv_chain 'X' create true");
144 // same feature value and model, different chain
145 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
146 // same feature value and chain, different model
147 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
148 commands = testee.setAttributes(featuresMap);
149 assertEquals(commands.size(), 1);
150 String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
151 assertEquals(commands.get(0).getCommand(), expected1);
153 // same feature, different value
154 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
155 commands = testee.setAttributes(featuresMap);
156 assertEquals(2, commands.size());
157 // commands are ordered by feature type but not by value
158 // so test for the expected command in either order
159 String cmd1 = commands.get(0).getCommand();
160 String cmd2 = commands.get(1).getCommand();
161 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
162 String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
163 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
166 featureValues.clear();
167 featuresMap.put("side-chain binding!", featureValues);
168 ChimeraCommands.addAtomSpecRange(featureValues,
169 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
170 // feature names are sanitised to change non-alphanumeric to underscore
171 // feature values are sanitised to encode single quote characters
172 commands = testee.setAttributes(featuresMap);
173 assertEquals(commands.size(), 1);
174 String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true";
175 assertTrue(commands.get(0).getCommand().equals(expected3));
178 @Test(groups = { "Functional" })
179 public void testSuperposeStructures()
181 AtomSpecModel ref = new AtomSpecModel();
182 ref.addRange("1", 12, 14, "A");
183 ref.addRange("1", 18, 18, "B");
184 ref.addRange("1", 22, 23, "B");
185 AtomSpecModel toAlign = new AtomSpecModel();
186 toAlign.addRange("2", 15, 17, "B");
187 toAlign.addRange("2", 20, 21, "B");
188 toAlign.addRange("2", 22, 22, "C");
189 List<StructureCommandI> command = testee.superposeStructures(ref,
191 assertEquals(command.size(), 1);
192 String cmd = command.get(0).getCommand();
193 String refSpec = "#1/A:12-14/B:18,22-23";
194 String toAlignSpec = "#2/B:15-17,20-21/C:22";
197 * superposition arguments include AlphaCarbon restriction,
198 * ribbon command does not
200 String expected = String.format(
201 "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
202 refSpec, toAlignSpec, refSpec);
203 assertEquals(cmd, expected);
206 @Test(groups = "Functional")
207 public void testGetAtomSpec()
209 AtomSpecModel model = new AtomSpecModel();
210 assertEquals(testee.getAtomSpec(model, false), "");
211 model.addRange("1", 2, 4, "A");
212 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
213 model.addRange("1", 8, 8, "A");
214 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
215 model.addRange("1", 5, 7, "B");
216 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
217 model.addRange("1", 3, 5, "A");
218 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
219 model.addRange("0", 1, 4, "B");
220 assertEquals(testee.getAtomSpec(model, false),
221 "#0/B:1-4|#1/A:2-5,8/B:5-7");
222 model.addRange("0", 5, 9, "C");
223 assertEquals(testee.getAtomSpec(model, false),
224 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
225 model.addRange("1", 8, 10, "B");
226 assertEquals(testee.getAtomSpec(model, false),
227 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
228 model.addRange("1", 8, 9, "B");
229 assertEquals(testee.getAtomSpec(model, false),
230 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
231 model.addRange("0", 3, 10, "C"); // subsumes 5-9
232 assertEquals(testee.getAtomSpec(model, false),
233 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
234 model.addRange("5", 25, 35, " ");
235 assertEquals(testee.getAtomSpec(model, false),
236 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
239 @Test(groups = "Functional")
240 public void testGetAtomSpec_alphaOnly()
242 AtomSpecModel model = new AtomSpecModel();
243 assertEquals(testee.getAtomSpec(model, true), "");
244 model.addRange("1", 2, 4, "A");
245 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
246 model.addRange("1", 8, 8, "A");
247 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
248 model.addRange("1", 5, 7, "B");
249 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
250 model.addRange("1", 3, 5, "A");
251 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
252 model.addRange("0", 1, 4, "B");
253 assertEquals(testee.getAtomSpec(model, true),
254 "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
255 model.addRange("0", 5, 9, "C");
256 assertEquals(testee.getAtomSpec(model, true),
257 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
258 model.addRange("1", 8, 10, "B");
259 assertEquals(testee.getAtomSpec(model, true),
260 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
261 model.addRange("1", 8, 9, "B");
262 assertEquals(testee.getAtomSpec(model, true),
263 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
264 model.addRange("0", 3, 10, "C"); // subsumes 5-9
265 assertEquals(testee.getAtomSpec(model, true),
266 "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
267 model.addRange("5", 25, 35, " "); // empty chain code
268 assertEquals(testee.getAtomSpec(model, true),
269 "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
272 @Test(groups = "Functional")
273 public void testGetModelStartNo()
275 assertEquals(testee.getModelStartNo(), 1);
278 @Test(groups = "Functional")
279 public void testGetResidueSpec()
281 assertEquals(testee.getResidueSpec("ALA"), ":ALA");
284 @Test(groups = "Functional")
285 public void testShowBackbone()
287 List<StructureCommandI> showBackbone = testee.showBackbone();
288 assertEquals(showBackbone.size(), 1);
289 assertEquals(showBackbone.get(0).getCommand(),
290 "~display all;~ribbon;show @CA|P atoms");
293 @Test(groups = "Functional")
294 public void testOpenCommandFile()
296 assertEquals(testee.openCommandFile("nowhere").getCommand(),
300 @Test(groups = "Functional")
301 public void testSaveSession()
303 assertEquals(testee.saveSession("somewhere").getCommand(),
304 "save somewhere format session");
307 @Test(groups = "Functional")
308 public void testGetColourCommand()
310 assertEquals(testee.colourResidues("something", Color.MAGENTA)
312 "color something #ff00ff");
315 @Test(groups = "Functional")
316 public void testSetAttribute()
318 AtomSpecModel model = new AtomSpecModel();
319 model.addRange("1", 89, 92, "A");
320 model.addRange("2", 12, 20, "B");
321 model.addRange("2", 8, 9, "B");
322 assertEquals(testee.setAttribute("jv_kd", "27.3", model)
324 "setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
327 @Test(groups = "Functional")
328 public void testCloseViewer()
330 assertEquals(testee.closeViewer(), new StructureCommand("exit"));
333 @Test(groups = "Functional")
334 public void testGetSelectedResidues()
336 assertEquals(testee.getSelectedResidues(),
337 new StructureCommand("info selection level residue"));
340 @Test(groups = "Functional")
341 public void testStartNotifications()
343 List<StructureCommandI> cmds = testee.startNotifications("to here");
344 assertEquals(cmds.size(), 2);
345 assertEquals(cmds.get(0), new StructureCommand("info notify start models jalview prefix ModelChanged url to here"));
346 assertEquals(cmds.get(1), new StructureCommand("info notify start selection jalview prefix SelectionChanged url to here"));
349 @Test(groups = "Functional")
350 public void testStopNotifications()
352 List<StructureCommandI> cmds = testee.stopNotifications();
353 assertEquals(cmds.size(), 2);
354 assertEquals(cmds.get(0), new StructureCommand("info notify stop models jalview"));
355 assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview"));
358 @Test(groups = "Functional")
359 public void testListResidueAttributes()
361 assertEquals(testee.listResidueAttributes(),
362 new StructureCommand("info resattr"));