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;
38 import jalview.structure.StructureCommandsI.AtomSpecType;
40 public class ChimeraXCommandsTest
42 private ChimeraXCommands testee;
44 @BeforeClass(alwaysRun = true)
47 testee = new ChimeraXCommands();
50 @Test(groups = { "Functional" })
51 public void testColourByCharge()
53 List<StructureCommandI> cmd = testee.colourByCharge();
54 assertEquals(cmd.size(), 1);
55 assertEquals(cmd.get(0).getCommand(),
56 "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
59 @Test(groups = { "Functional" })
60 public void testColourByChain()
62 StructureCommandI cmd = testee.colourByChain();
63 assertEquals(cmd.getCommand(), "rainbow chain");
66 @Test(groups = { "Functional" })
67 public void testFocusView()
69 StructureCommandI cmd = testee.focusView();
70 assertEquals(cmd.getCommand(), "view");
73 @Test(groups = { "Functional" })
74 public void testSetBackgroundColour()
76 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
77 assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
80 @Test(groups = { "Functional" })
81 public void testOpenSession()
83 StructureCommandI cmd = testee.openSession("/some/filepath");
84 assertEquals(cmd.getCommand(), "open /some/filepath format session");
87 @Test(groups = { "Functional" })
88 public void testColourBySequence()
90 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
91 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
92 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
93 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
94 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
95 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
96 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
97 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
98 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
99 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
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
105 List<StructureCommandI> commands = testee.colourBySequence(map);
106 assertEquals(commands.size(), 1);
107 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");
111 @Test(groups = { "Functional" })
112 public void testSetAttributes()
115 * make a map of { featureType, {featureValue, {residue range specification } } }
117 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
118 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
121 * start with just one feature/value...
123 featuresMap.put("chain", featureValues);
124 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
126 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
127 assertEquals(commands.size(), 1);
130 * feature name gets a jv_ namespace prefix
131 * feature value is quoted in case it contains spaces
133 assertEquals(commands.get(0).getCommand(),
134 "setattr #0/A:8-20 res jv_chain 'X' create true");
136 // add same feature value, overlapping range
137 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
138 // same feature value, contiguous range
139 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
140 commands = testee.setAttributes(featuresMap);
141 assertEquals(commands.size(), 1);
142 assertEquals(commands.get(0).getCommand(),
143 "setattr #0/A:3-25 res jv_chain 'X' create true");
145 // same feature value and model, different chain
146 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
147 // same feature value and chain, different model
148 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
149 commands = testee.setAttributes(featuresMap);
150 assertEquals(commands.size(), 1);
151 String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
152 assertEquals(commands.get(0).getCommand(), expected1);
154 // same feature, different value
155 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
156 commands = testee.setAttributes(featuresMap);
157 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 String cmd1 = commands.get(0).getCommand();
161 String cmd2 = commands.get(1).getCommand();
162 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
163 String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
164 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
167 featureValues.clear();
168 featuresMap.put("side-chain binding!", featureValues);
169 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 commands = testee.setAttributes(featuresMap);
174 assertEquals(commands.size(), 1);
175 String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true";
176 assertTrue(commands.get(0).getCommand().equals(expected3));
179 @Test(groups = { "Functional" })
180 public void testSuperposeStructures()
182 AtomSpecModel ref = new AtomSpecModel();
183 ref.addRange("1", 12, 14, "A");
184 ref.addRange("1", 18, 18, "B");
185 ref.addRange("1", 22, 23, "B");
186 AtomSpecModel toAlign = new AtomSpecModel();
187 toAlign.addRange("2", 15, 17, "B");
188 toAlign.addRange("2", 20, 21, "B");
189 toAlign.addRange("2", 22, 22, "C");
190 List<StructureCommandI> command = testee.superposeStructures(ref,
191 toAlign, AtomSpecType.ALPHA);
192 assertEquals(command.size(), 1);
193 String cmd = command.get(0).getCommand();
194 String refSpec = "#1/A:12-14/B:18,22-23";
195 String toAlignSpec = "#2/B:15-17,20-21/C:22";
198 * superposition arguments include AlphaCarbon restriction,
199 * ribbon command does not
201 String expected = String.format(
202 "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
203 refSpec, toAlignSpec, refSpec);
204 assertEquals(cmd, expected);
207 @Test(groups = "Functional")
208 public void testGetAtomSpec()
210 AtomSpecModel model = new AtomSpecModel();
211 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
212 model.addRange("1", 2, 4, "A");
213 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
215 model.addRange("1", 8, 8, "A");
216 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
218 model.addRange("1", 5, 7, "B");
219 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
221 model.addRange("1", 3, 5, "A");
222 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
224 model.addRange("0", 1, 4, "B");
225 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
226 "#0/B:1-4|#1/A:2-5,8/B:5-7");
227 model.addRange("0", 5, 9, "C");
228 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
229 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
230 model.addRange("1", 8, 10, "B");
231 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
232 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
233 model.addRange("1", 8, 9, "B");
234 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
235 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
236 model.addRange("0", 3, 10, "C"); // subsumes 5-9
237 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
238 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
239 model.addRange("5", 25, 35, " ");
240 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");
244 @Test(groups = "Functional")
245 public void testGetAtomSpec_alphaOnly()
247 AtomSpecModel model = new AtomSpecModel();
248 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
249 model.addRange("1", 2, 4, "A");
250 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
252 model.addRange("1", 8, 8, "A");
253 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
255 model.addRange("1", 5, 7, "B");
256 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
257 "#1/A:2-4,8/B:5-7@CA");
258 model.addRange("1", 3, 5, "A");
259 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
260 "#1/A:2-5,8/B:5-7@CA");
261 model.addRange("0", 1, 4, "B");
262 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
263 "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
264 model.addRange("0", 5, 9, "C");
265 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 model.addRange("1", 8, 10, "B");
268 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 model.addRange("1", 8, 9, "B");
271 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 model.addRange("0", 3, 10, "C"); // subsumes 5-9
274 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 model.addRange("5", 25, 35, " "); // empty chain code
277 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");
281 @Test(groups = "Functional")
282 public void testGetModelStartNo()
284 assertEquals(testee.getModelStartNo(), 1);
287 @Test(groups = "Functional")
288 public void testGetResidueSpec()
290 assertEquals(testee.getResidueSpec("ALA"), ":ALA");
293 @Test(groups = "Functional")
294 public void testShowBackbone()
296 List<StructureCommandI> showBackbone = testee.showBackbone();
297 assertEquals(showBackbone.size(), 1);
298 assertEquals(showBackbone.get(0).getCommand(),
299 "~display all;~ribbon;show @CA|P atoms");
302 @Test(groups = "Functional")
303 public void testOpenCommandFile()
305 assertEquals(testee.openCommandFile("nowhere").getCommand(),
309 @Test(groups = "Functional")
310 public void testSaveSession()
312 assertEquals(testee.saveSession("somewhere").getCommand(),
313 "save somewhere format session");
316 @Test(groups = "Functional")
317 public void testGetColourCommand()
320 testee.colourResidues("something", Color.MAGENTA).getCommand(),
321 "color something #ff00ff");
324 @Test(groups = "Functional")
325 public void testSetAttribute()
327 AtomSpecModel model = new AtomSpecModel();
328 model.addRange("1", 89, 92, "A");
329 model.addRange("2", 12, 20, "B");
330 model.addRange("2", 8, 9, "B");
331 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");
335 @Test(groups = "Functional")
336 public void testCloseViewer()
338 assertEquals(testee.closeViewer(), new StructureCommand("exit"));
341 @Test(groups = "Functional")
342 public void testGetSelectedResidues()
344 assertEquals(testee.getSelectedResidues(),
345 new StructureCommand("info selection level residue"));
348 @Test(groups = "Functional")
349 public void testStartNotifications()
351 List<StructureCommandI> cmds = testee.startNotifications("to here");
352 assertEquals(cmds.size(), 2);
353 assertEquals(cmds.get(0), new StructureCommand(
354 "info notify start models jalview prefix ModelChanged url to here"));
355 assertEquals(cmds.get(1), new StructureCommand(
356 "info notify start selection jalview prefix SelectionChanged url to here"));
359 @Test(groups = "Functional")
360 public void testStopNotifications()
362 List<StructureCommandI> cmds = testee.stopNotifications();
363 assertEquals(cmds.size(), 2);
364 assertEquals(cmds.get(0),
365 new StructureCommand("info notify stop models jalview"));
366 assertEquals(cmds.get(1),
367 new StructureCommand("info notify stop selection jalview"));
370 @Test(groups = "Functional")
371 public void testListResidueAttributes()
373 assertEquals(testee.listResidueAttributes(),
374 new StructureCommand("info resattr"));