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.StructureCommandI;
38 public class ChimeraXCommandsTest
40 private ChimeraXCommands testee;
42 @BeforeClass(alwaysRun = true)
45 testee = new ChimeraXCommands();
48 @Test(groups = { "Functional" })
49 public void testColourByCharge()
51 List<StructureCommandI> cmd = testee.colourByCharge();
52 assertEquals(cmd.size(), 1);
53 assertEquals(cmd.get(0).getCommand(),
54 "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
57 @Test(groups = { "Functional" })
58 public void testColourByChain()
60 StructureCommandI cmd = testee.colourByChain();
61 assertEquals(cmd.getCommand(), "rainbow chain");
64 @Test(groups = { "Functional" })
65 public void testFocusView()
67 StructureCommandI cmd = testee.focusView();
68 assertEquals(cmd.getCommand(), "view");
71 @Test(groups = { "Functional" })
72 public void testSetBackgroundColour()
74 StructureCommandI cmd = testee.setBackgroundColour(Color.PINK);
75 assertEquals(cmd.getCommand(), "set bgColor #ffafaf");
78 @Test(groups = { "Functional" })
79 public void testOpenSession()
81 StructureCommandI cmd = testee.openSession("/some/filepath");
82 assertEquals(cmd.getCommand(), "open /some/filepath format session");
85 @Test(groups = { "Functional" })
86 public void testColourBySequence()
88 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
89 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
90 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
91 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
92 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
93 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
94 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
95 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
96 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
97 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
100 * Colours should appear in the Chimera command in the order in which
101 * they were added; within colour, by model, by chain, ranges in start order
103 List<StructureCommandI> commands = testee.colourBySequence(map);
104 assertEquals(commands.size(), 1);
105 assertEquals(commands.get(0).getCommand(),
106 "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");
109 @Test(groups = { "Functional" })
110 public void testSetAttributes()
113 * make a map of { featureType, {featureValue, {residue range specification } } }
115 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
116 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
119 * start with just one feature/value...
121 featuresMap.put("chain", featureValues);
122 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
124 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
125 assertEquals(commands.size(), 1);
128 * feature name gets a jv_ namespace prefix
129 * feature value is quoted in case it contains spaces
131 assertEquals(commands.get(0).getCommand(),
132 "setattr #0/A:8-20 res jv_chain 'X' create true");
134 // add same feature value, overlapping range
135 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
136 // same feature value, contiguous range
137 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
138 commands = testee.setAttributes(featuresMap);
139 assertEquals(commands.size(), 1);
140 assertEquals(commands.get(0).getCommand(),
141 "setattr #0/A:3-25 res jv_chain 'X' create true");
143 // same feature value and model, different chain
144 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
145 // same feature value and chain, different model
146 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
147 commands = testee.setAttributes(featuresMap);
148 assertEquals(commands.size(), 1);
149 String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
150 assertEquals(commands.get(0).getCommand(), expected1);
152 // same feature, different value
153 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
154 commands = testee.setAttributes(featuresMap);
155 assertEquals(2, commands.size());
156 // commands are ordered by feature type but not by value
157 // so test for the expected command in either order
158 String cmd1 = commands.get(0).getCommand();
159 String cmd2 = commands.get(1).getCommand();
160 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
161 String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
162 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
165 featureValues.clear();
166 featuresMap.put("side-chain binding!", featureValues);
167 ChimeraCommands.addAtomSpecRange(featureValues,
168 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
169 // feature names are sanitised to change non-alphanumeric to underscore
170 // feature values are sanitised to encode single quote characters
171 commands = testee.setAttributes(featuresMap);
172 assertEquals(commands.size(), 1);
173 String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true";
174 assertTrue(commands.get(0).getCommand().equals(expected3));
177 @Test(groups = { "Functional" })
178 public void testSuperposeStructures()
180 AtomSpecModel ref = new AtomSpecModel();
181 ref.addRange("1", 12, 14, "A");
182 ref.addRange("1", 18, 18, "B");
183 ref.addRange("1", 22, 23, "B");
184 AtomSpecModel toAlign = new AtomSpecModel();
185 toAlign.addRange("2", 15, 17, "B");
186 toAlign.addRange("2", 20, 21, "B");
187 toAlign.addRange("2", 22, 22, "C");
188 List<StructureCommandI> command = testee.superposeStructures(ref,
190 assertEquals(command.size(), 1);
191 String cmd = command.get(0).getCommand();
192 String refSpec = "#1/A:12-14/B:18,22-23";
193 String toAlignSpec = "#2/B:15-17,20-21/C:22";
196 * superposition arguments include AlphaCarbon restriction,
197 * ribbon command does not
199 String expected = String.format(
200 "align %s@CA toAtoms %s@CA; ribbon %s|%s; view", toAlignSpec,
201 refSpec, toAlignSpec, refSpec);
202 assertEquals(cmd, expected);
205 @Test(groups = "Functional")
206 public void testGetAtomSpec()
208 AtomSpecModel model = new AtomSpecModel();
209 assertEquals(testee.getAtomSpec(model, false), "");
210 model.addRange("1", 2, 4, "A");
211 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
212 model.addRange("1", 8, 8, "A");
213 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
214 model.addRange("1", 5, 7, "B");
215 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
216 model.addRange("1", 3, 5, "A");
217 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
218 model.addRange("0", 1, 4, "B");
219 assertEquals(testee.getAtomSpec(model, false),
220 "#0/B:1-4|#1/A:2-5,8/B:5-7");
221 model.addRange("0", 5, 9, "C");
222 assertEquals(testee.getAtomSpec(model, false),
223 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
224 model.addRange("1", 8, 10, "B");
225 assertEquals(testee.getAtomSpec(model, false),
226 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
227 model.addRange("1", 8, 9, "B");
228 assertEquals(testee.getAtomSpec(model, false),
229 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
230 model.addRange("0", 3, 10, "C"); // subsumes 5-9
231 assertEquals(testee.getAtomSpec(model, false),
232 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
233 model.addRange("5", 25, 35, " ");
234 assertEquals(testee.getAtomSpec(model, false),
235 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
238 @Test(groups = "Functional")
239 public void testGetAtomSpec_alphaOnly()
241 AtomSpecModel model = new AtomSpecModel();
242 assertEquals(testee.getAtomSpec(model, true), "");
243 model.addRange("1", 2, 4, "A");
244 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
245 model.addRange("1", 8, 8, "A");
246 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
247 model.addRange("1", 5, 7, "B");
248 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
249 model.addRange("1", 3, 5, "A");
250 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
251 model.addRange("0", 1, 4, "B");
252 assertEquals(testee.getAtomSpec(model, true),
253 "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
254 model.addRange("0", 5, 9, "C");
255 assertEquals(testee.getAtomSpec(model, true),
256 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
257 model.addRange("1", 8, 10, "B");
258 assertEquals(testee.getAtomSpec(model, true),
259 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
260 model.addRange("1", 8, 9, "B");
261 assertEquals(testee.getAtomSpec(model, true),
262 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
263 model.addRange("0", 3, 10, "C"); // subsumes 5-9
264 assertEquals(testee.getAtomSpec(model, true),
265 "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
266 model.addRange("5", 25, 35, " "); // empty chain code
267 assertEquals(testee.getAtomSpec(model, true),
268 "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
271 @Test(groups = "Functional")
272 public void testGetResidueSpec()
274 assertEquals(testee.getResidueSpec("ALA"), ":ALA");
277 @Test(groups = "Functional")
278 public void testShowBackbone()
280 List<StructureCommandI> showBackbone = testee.showBackbone();
281 assertEquals(showBackbone.size(), 1);
282 assertEquals(showBackbone.get(0).getCommand(),
283 "~display all;~ribbon;show @CA|P atoms");
286 @Test(groups = "Functional")
287 public void testOpenCommandFile()
289 assertEquals(testee.openCommandFile("nowhere").getCommand(),
293 @Test(groups = "Functional")
294 public void testSaveSession()
296 assertEquals(testee.saveSession("somewhere").getCommand(),
297 "save somewhere format session");
300 @Test(groups = "Functional")
301 public void testGetColourCommand()
303 assertEquals(testee.colourResidues("something", Color.MAGENTA)
305 "color something #ff00ff");
308 @Test(groups = "Functional")
309 public void testSetAttribute()
311 AtomSpecModel model = new AtomSpecModel();
312 model.addRange("1", 89, 92, "A");
313 model.addRange("2", 12, 20, "B");
314 model.addRange("2", 8, 9, "B");
315 assertEquals(testee.setAttribute("jv_kd", "27.3", model)
317 "setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
320 @Test(groups = "Functional")
321 public void testHideAll()
323 StructureCommandI cmd = testee.hideAll();
324 assertEquals(cmd.getCommand(), "~display all; ~ribbon");
327 @Test(groups = "Functional")
328 public void testHideChain()
330 StructureCommandI cmd = testee.hideChain("1.1", "B");
331 assertEquals(cmd.getCommand(), "~ribbon #1.1/B");
334 @Test(groups = "Functional")
335 public void testShowStructures()
338 * with nothing excluded
340 StructureCommandI cmd = testee.showStructures(null);
341 assertEquals(cmd.getCommand(), "ribbon");
344 * restricted to specified positions
346 AtomSpecModel restrictTo = new AtomSpecModel();
347 restrictTo.addRange("1.1", 12, 20, "A");
348 restrictTo.addRange("1.1", 30, 35, "A");
349 restrictTo.addRange("2.1", 11, 30, "B");
350 cmd = testee.showStructures(restrictTo);
351 assertEquals(cmd.getCommand(),
352 "ribbon #1.1/A:12-20,30-35|#2.1/B:11-30");