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.datamodel.Alignment;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
31 import jalview.gui.AlignFrame;
32 import jalview.gui.SequenceRenderer;
33 import jalview.schemes.JalviewColourScheme;
34 import jalview.structure.AtomSpecModel;
35 import jalview.structure.StructureCommandsI;
36 import jalview.structure.StructureMapping;
37 import jalview.structure.StructureSelectionManager;
39 import java.awt.Color;
40 import java.util.HashMap;
41 import java.util.LinkedHashMap;
42 import java.util.List;
45 import org.testng.annotations.Test;
47 public class ChimeraCommandsTest
50 @Test(groups = { "Functional" })
51 public void testBuildColourCommands()
54 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
55 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
56 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
57 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
58 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
59 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
60 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
61 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
62 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
63 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A");
65 // Colours should appear in the Chimera command in the order in which
66 // they were added; within colour, by model, by chain, ranges in start order
67 String command = new ChimeraCommands().buildColourCommands(map).get(0);
70 "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A");
73 @Test(groups = { "Functional" })
74 public void testBuildSetAttributeCommands()
77 * make a map of { featureType, {featureValue, {residue range specification } } }
79 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
80 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
83 * start with just one feature/value...
85 featuresMap.put("chain", featureValues);
86 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
88 ChimeraCommands commandGenerator = new ChimeraCommands();
89 List<String> commands = commandGenerator
90 .buildSetAttributeCommands(featuresMap);
91 assertEquals(1, commands.size());
94 * feature name gets a jv_ namespace prefix
95 * feature value is quoted in case it contains spaces
97 assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:8-20.A");
99 // add same feature value, overlapping range
100 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
101 // same feature value, contiguous range
102 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
103 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
104 assertEquals(1, commands.size());
105 assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
107 // same feature value and model, different chain
108 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
109 // same feature value and chain, different model
110 ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
111 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
112 assertEquals(1, commands.size());
113 assertEquals(commands.get(0),
114 "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
116 // same feature, different value
117 ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
118 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
119 assertEquals(2, commands.size());
120 // commands are ordered by feature type but not by value
121 // so use contains to test for the expected command:
124 "setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
125 assertTrue(commands.contains("setattr res jv_chain 'Y' #0:40-50.A"));
128 featureValues.clear();
129 featuresMap.put("side-chain binding!", featureValues);
130 ChimeraCommands.addAtomSpecRange(featureValues,
131 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
133 // feature names are sanitised to change non-alphanumeric to underscore
134 // feature values are sanitised to encode single quote characters
135 commands = commandGenerator.buildSetAttributeCommands(featuresMap);
138 "setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
142 * Tests for the method that prefixes and sanitises a feature name so it can
143 * be used as a valid, namespaced attribute name in Chimera
145 @Test(groups = { "Functional" })
146 public void testMakeAttributeName()
148 assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
149 assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
150 assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
151 assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
152 "jv_Hello_World_24");
154 ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
155 "jv__this_is_a_very__odd_name");
156 // name ending in color gets underscore appended
157 assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
161 @Test(groups = { "Functional" })
162 public void testColourBySequence_hiddenColumns()
165 * load these sequences, coloured by Strand propensity,
166 * with columns 2-4 hidden
168 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
169 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
170 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
171 AlignFrame af = new AlignFrame(al, 800, 500);
172 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
173 ColumnSelection cs = new ColumnSelection();
177 af.getViewport().setColumnSelection(cs);
178 af.hideSelColumns_actionPerformed(null);
179 SequenceRenderer sr = new SequenceRenderer(af.getViewport());
180 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
181 String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
182 StructureSelectionManager ssm = new StructureSelectionManager();
185 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
187 HashMap<Integer, int[]> map = new HashMap<>();
188 for (int pos = 1; pos <= seq1.getLength(); pos++)
190 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
192 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
194 ssm.addStructureMapping(sm1);
195 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
197 ssm.addStructureMapping(sm2);
199 String[] commands = new ChimeraCommands()
200 .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
201 assertEquals(1, commands.length);
202 String theCommand = commands[0];
203 // M colour is #82827d (see strand.html help page)
204 assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
205 // H colour is #60609f
206 assertTrue(theCommand.contains("color #60609f #0:22.A"));
207 // V colour is #ffff00
208 assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
209 // hidden columns are Gray (128, 128, 128)
210 assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
211 // S and G are both coloured #4949b6
212 assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
215 @Test(groups = "Functional")
216 public void testGetAtomSpec()
218 StructureCommandsI testee = new ChimeraCommands();
219 AtomSpecModel model = new AtomSpecModel();
220 assertEquals(testee.getAtomSpec(model, false), "");
221 model.addRange(1, 2, 4, "A");
222 assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
223 model.addRange(1, 8, 8, "A");
224 assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
225 model.addRange(1, 5, 7, "B");
226 assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
227 model.addRange(1, 3, 5, "A");
228 assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
229 model.addRange(0, 1, 4, "B");
230 assertEquals(testee.getAtomSpec(model, false),
231 "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
232 model.addRange(0, 5, 9, "C");
233 assertEquals(testee.getAtomSpec(model, false),
234 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
235 model.addRange(1, 8, 10, "B");
236 assertEquals(testee.getAtomSpec(model, false),
237 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
238 model.addRange(1, 8, 9, "B");
239 assertEquals(testee.getAtomSpec(model, false),
240 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
241 model.addRange(0, 3, 10, "C"); // subsumes 5-9
242 assertEquals(testee.getAtomSpec(model, false),
243 "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
244 model.addRange(5, 25, 35, " "); // empty chain code - e.g. from homology
246 assertEquals(testee.getAtomSpec(model, false),
247 "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
251 @Test(groups = "Functional")
252 public void testGetAtomSpec_alphaOnly()
254 StructureCommandsI testee = new ChimeraCommands();
255 AtomSpecModel model = new AtomSpecModel();
256 assertEquals(testee.getAtomSpec(model, true), "");
257 model.addRange(1, 2, 4, "A");
258 assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A@CA|P");
259 model.addRange(1, 8, 8, "A");
260 assertEquals(testee.getAtomSpec(model, true), "#1:2-4.A,8.A@CA|P");
261 model.addRange(1, 5, 7, "B");
262 assertEquals(testee.getAtomSpec(model, true),
263 "#1:2-4.A,8.A,5-7.B@CA|P");
264 model.addRange(1, 3, 5, "A");
265 assertEquals(testee.getAtomSpec(model, true),
266 "#1:2-5.A,8.A,5-7.B@CA|P");
267 model.addRange(0, 1, 4, "B");
268 assertEquals(testee.getAtomSpec(model, true),
269 "#0:1-4.B@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
270 model.addRange(0, 5, 9, "C");
271 assertEquals(testee.getAtomSpec(model, true),
272 "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-7.B@CA|P");
273 model.addRange(1, 8, 10, "B");
274 assertEquals(testee.getAtomSpec(model, true),
275 "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
276 model.addRange(1, 8, 9, "B");
277 assertEquals(testee.getAtomSpec(model, true),
278 "#0:1-4.B,5-9.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
279 model.addRange(0, 3, 10, "C"); // subsumes 5-9
280 assertEquals(testee.getAtomSpec(model, true),
281 "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P");
282 model.addRange(5, 25, 35, " "); // empty chain code
283 assertEquals(testee.getAtomSpec(model, true),
284 "#0:1-4.B,3-10.C@CA|P|#1:2-5.A,8.A,5-10.B@CA|P|#5:25-35.@CA|P");
288 @Test(groups = { "Functional" })
289 public void testSuperposeStructures()
291 StructureCommandsI testee = new ChimeraCommands();
292 AtomSpecModel ref = new AtomSpecModel();
293 ref.addRange(1, 12, 14, "A");
294 ref.addRange(1, 18, 18, "B");
295 ref.addRange(1, 22, 23, "B");
296 AtomSpecModel toAlign = new AtomSpecModel();
297 toAlign.addRange(2, 15, 17, "B");
298 toAlign.addRange(2, 20, 21, "B");
299 toAlign.addRange(2, 22, 22, "C");
300 String command = testee.superposeStructures(ref, toAlign);
301 String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
302 String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
303 String expected = String.format(
304 "match %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
305 refSpec, toAlignSpec, refSpec, toAlignSpec);
306 assertEquals(command, expected);