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 jalview.structure.AtomSpecModel;
27 import jalview.structure.StructureCommandI;
28 import jalview.structure.StructureCommandsI;
30 import java.awt.Color;
31 import java.util.HashMap;
32 import java.util.LinkedHashMap;
33 import java.util.List;
36 import org.testng.annotations.Test;
38 public class ChimeraCommandsTest
41 @Test(groups = { "Functional" })
42 public void testColourBySequence()
45 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
46 ChimeraCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
47 ChimeraCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
48 ChimeraCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
49 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
50 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
51 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
52 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
53 ChimeraCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
54 ChimeraCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
56 // Colours should appear in the Chimera command in the order in which
57 // they were added; within colour, by model, by chain, ranges in start order
58 List<StructureCommandI> commands = new ChimeraCommands()
59 .colourBySequence(map);
60 assertEquals(commands.size(), 3);
61 assertEquals(commands.get(0).getCommand(),
62 "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B");
63 assertEquals(commands.get(1).getCommand(),
64 "color #ffff00 #1:3-5.A,8.A");
65 assertEquals(commands.get(2).getCommand(), "color #ff0000 #0:3-9.A");
68 @Test(groups = { "Functional" })
69 public void testSetAttributes()
72 * make a map of { featureType, {featureValue, {residue range specification } } }
74 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
75 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
78 * start with just one feature/value...
80 featuresMap.put("chain", featureValues);
81 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
83 ChimeraCommands commandGenerator = new ChimeraCommands();
84 List<StructureCommandI> commands = commandGenerator
85 .setAttributes(featuresMap);
86 assertEquals(1, commands.size());
89 * feature name gets a jv_ namespace prefix
90 * feature value is quoted in case it contains spaces
92 assertEquals(commands.get(0).getCommand(),
93 "setattr res jv_chain 'X' #0:8-20.A");
95 // add same feature value, overlapping range
96 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
97 // same feature value, contiguous range
98 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
99 commands = commandGenerator.setAttributes(featuresMap);
100 assertEquals(1, commands.size());
101 assertEquals(commands.get(0).getCommand(),
102 "setattr res jv_chain 'X' #0:3-25.A");
104 // same feature value and model, different chain
105 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
106 // same feature value and chain, different model
107 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
108 commands = commandGenerator.setAttributes(featuresMap);
109 assertEquals(1, commands.size());
110 String expected1 = "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A";
111 assertEquals(commands.get(0).getCommand(), expected1);
113 // same feature, different value
114 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
115 commands = commandGenerator.setAttributes(featuresMap);
116 assertEquals(2, commands.size());
117 // commands are ordered by feature type but not by value
118 // so test for the expected command in either order
119 String cmd1 = commands.get(0).getCommand();
120 String cmd2 = commands.get(1).getCommand();
121 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
122 String expected2 = "setattr res jv_chain 'Y' #0:40-50.A";
123 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
126 featureValues.clear();
127 featuresMap.put("side-chain binding!", featureValues);
128 ChimeraCommands.addAtomSpecRange(featureValues,
129 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15,
131 // feature names are sanitised to change non-alphanumeric to underscore
132 // feature values are sanitised to encode single quote characters
133 commands = commandGenerator.setAttributes(featuresMap);
134 assertEquals(commands.size(), 1);
135 String expected3 = "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A";
136 assertTrue(commands.get(0).getCommand().equals(expected3));
140 * Tests for the method that prefixes and sanitises a feature name so it can
141 * be used as a valid, namespaced attribute name in Chimera
143 @Test(groups = { "Functional" })
144 public void testMakeAttributeName()
146 assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
147 assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
148 assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
149 assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
150 "jv_Hello_World_24");
152 ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
153 "jv__this_is_a_very__odd_name");
154 // name ending in color gets underscore appended
155 assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
159 @Test(groups = "Functional")
160 public void testGetAtomSpec()
162 StructureCommandsI testee = new ChimeraCommands();
163 AtomSpecModel model = new AtomSpecModel();
164 assertEquals(testee.getAtomSpec(model, false), "");
165 model.addRange("1", 2, 4, "A");
166 assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
167 model.addRange("1", 8, 8, "A");
168 assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
169 model.addRange("1", 5, 7, "B");
170 assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
171 model.addRange("1", 3, 5, "A");
172 assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
173 model.addRange("0", 1, 4, "B");
174 assertEquals(testee.getAtomSpec(model, false),
175 "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
176 model.addRange("0", 5, 9, "C");
177 assertEquals(testee.getAtomSpec(model, false),
178 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
179 model.addRange("1", 8, 10, "B");
180 assertEquals(testee.getAtomSpec(model, false),
181 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
182 model.addRange("1", 8, 9, "B");
183 assertEquals(testee.getAtomSpec(model, false),
184 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
185 model.addRange("0", 3, 10, "C"); // subsumes 5-9
186 assertEquals(testee.getAtomSpec(model, false),
187 "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
188 model.addRange("5", 25, 35, " ");
189 assertEquals(testee.getAtomSpec(model, false),
190 "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
194 @Test(groups = { "Functional" })
195 public void testSuperposeStructures()
197 StructureCommandsI testee = new ChimeraCommands();
198 AtomSpecModel ref = new AtomSpecModel();
199 ref.addRange("1", 12, 14, "A");
200 ref.addRange("1", 18, 18, "B");
201 ref.addRange("1", 22, 23, "B");
202 AtomSpecModel toAlign = new AtomSpecModel();
203 toAlign.addRange("2", 15, 17, "B");
204 toAlign.addRange("2", 20, 21, "B");
205 toAlign.addRange("2", 22, 22, "C");
206 List<StructureCommandI> command = testee.superposeStructures(ref,
208 String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
209 String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
210 String expected = String.format(
211 "match %s %s; ribbon %s|%s; focus",
212 refSpec, toAlignSpec, refSpec, toAlignSpec);
213 assertEquals(command.get(0).getCommand(), expected);
216 @Test(groups = "Functional")
217 public void testGetAtomSpec_alphaOnly()
219 StructureCommandsI testee = new ChimeraCommands();
220 AtomSpecModel model = new AtomSpecModel();
221 assertEquals(testee.getAtomSpec(model, true), "");
222 model.addRange("1", 2, 4, "A");
223 assertEquals(testee.getAtomSpec(model, true),
224 "#1:2-4.A@CA|P&~@.B-Z&~@.2-9");
225 model.addRange("1", 8, 8, "A");
226 assertEquals(testee.getAtomSpec(model, true),
227 "#1:2-4.A,8.A@CA|P&~@.B-Z&~@.2-9");
228 model.addRange("1", 5, 7, "B");
229 assertEquals(testee.getAtomSpec(model, true),
230 "#1:2-4.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
231 model.addRange("1", 3, 5, "A");
232 assertEquals(testee.getAtomSpec(model, true),
233 "#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
234 model.addRange("0", 1, 4, "B");
235 assertEquals(testee.getAtomSpec(model, true),
236 "#0:1-4.B@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
237 model.addRange("0", 5, 9, "C");
238 assertEquals(testee.getAtomSpec(model, true),
239 "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
240 model.addRange("1", 8, 10, "B");
241 assertEquals(testee.getAtomSpec(model, true),
242 "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
243 model.addRange("1", 8, 9, "B");
244 assertEquals(testee.getAtomSpec(model, true),
245 "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
246 model.addRange("0", 3, 10, "C"); // subsumes 5-9
247 assertEquals(testee.getAtomSpec(model, true),
248 "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
249 model.addRange("5", 25, 35, " "); // empty chain code
250 assertEquals(testee.getAtomSpec(model, true),
251 "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9|#5:25-35.@CA|P&~@.B-Z&~@.2-9");
255 @Test(groups = "Functional")
256 public void testGetModelStartNo()
258 StructureCommandsI testee = new ChimeraCommands();
259 assertEquals(testee.getModelStartNo(), 0);
262 @Test(groups = "Functional")
263 public void testGetResidueSpec()
265 ChimeraCommands testee = new ChimeraCommands();
266 assertEquals(testee.getResidueSpec("ALA"), "::ALA");
269 @Test(groups = "Functional")
270 public void testShowBackbone()
272 ChimeraCommands testee = new ChimeraCommands();
273 List<StructureCommandI> cmds = testee.showBackbone();
274 assertEquals(cmds.size(), 1);
275 assertEquals(cmds.get(0).getCommand(), "~display all;chain @CA|P");
278 @Test(groups = "Functional")
279 public void testOpenCommandFile()
281 ChimeraCommands testee = new ChimeraCommands();
282 assertEquals(testee.openCommandFile("nowhere").getCommand(),
286 @Test(groups = "Functional")
287 public void testSaveSession()
289 ChimeraCommands testee = new ChimeraCommands();
290 assertEquals(testee.saveSession("somewhere").getCommand(),
294 @Test(groups = "Functional")
295 public void testGetColourCommand()
297 ChimeraCommands testee = new ChimeraCommands();
298 assertEquals(testee.getColourCommand("something", Color.MAGENTA)
300 "color #ff00ff something");
303 @Test(groups = "Functional")
304 public void testSetAttribute()
306 ChimeraCommands testee = new ChimeraCommands();
307 AtomSpecModel model = new AtomSpecModel();
308 model.addRange("1", 89, 92, "A");
309 model.addRange("2", 12, 20, "B");
310 model.addRange("2", 8, 9, "B");
311 assertEquals(testee.setAttribute("phi", "27.3", model).getCommand(),
312 "setattr res phi '27.3' #1:89-92.A|#2:8-9.B,12-20.B");