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.api.AlignmentViewPanel;
27 import jalview.api.FeatureRenderer;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.AlignFrame;
35 import jalview.gui.JvOptionPane;
36 import jalview.gui.SequenceRenderer;
37 import jalview.schemes.ColourSchemeI;
38 import jalview.schemes.JalviewColourScheme;
39 import jalview.structure.AtomSpec;
40 import jalview.structure.StructureMapping;
41 import jalview.structure.StructureSelectionManager;
42 import jalview.structures.models.AAStructureBindingModel;
44 import java.awt.Color;
45 import java.util.HashMap;
46 import java.util.LinkedHashMap;
47 import java.util.List;
50 import org.testng.annotations.BeforeClass;
51 import org.testng.annotations.Test;
53 import junit.extensions.PA;
55 public class ChimeraCommandsTest
57 private SequenceRenderer sr;
59 private String[] files;
61 private AAStructureBindingModel mockBinding = new AAStructureBindingModel(
65 public void releaseReferences(Object svl)
70 public void highlightAtoms(List<AtomSpec> atoms)
75 public void setJalviewColourScheme(ColourSchemeI cs)
80 public String superposeStructures(AlignmentI[] alignments,
81 int[] structureIndices, HiddenColumns[] hiddenCols)
87 public void setBackgroundColour(Color col)
92 protected String[] getColourBySequenceCommands(String[] files,
93 AlignmentViewPanel avp)
99 public jalview.api.SequenceRenderer getSequenceRenderer(
100 AlignmentViewPanel alignment)
106 protected void colourBySequence(String[] colourBySequenceCommands)
111 public void colourByChain()
116 public void colourByCharge()
121 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
127 public String[] getStructureFiles()
133 public String getModelSpec(int model)
135 return "#" + String.valueOf(model);
139 @BeforeClass(alwaysRun = true)
140 public void setUpJvOptionPane()
142 JvOptionPane.setInteractiveMode(false);
143 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
146 @Test(groups = { "Functional" })
147 public void testBuildColourCommands()
149 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
150 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
151 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
152 ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
153 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
154 ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
155 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
156 ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
157 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
158 ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 6, 9, "A");
160 // Colours should appear in the Chimera command in the order in which
161 // they were added; within colour, by model, by chain, ranges in start order
162 // all prefixed with #808080 to colour hidden regions (if shown) gray
163 String command = ChimeraCommands.buildColourCommands(map, mockBinding)
167 "color #808080; 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");
170 @Test(groups = { "Functional" })
171 public void testBuildSetAttributeCommands()
174 * make a map of { featureType, {featureValue, {residue range specification } } }
176 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
177 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
180 * start with just one feature/value...
182 featuresMap.put("chain", featureValues);
183 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
185 List<String> commands = ChimeraCommands
186 .buildSetAttributeCommands(featuresMap, mockBinding);
187 assertEquals(1, commands.size());
190 * feature name gets a jv_ namespace prefix
191 * feature value is quoted in case it contains spaces
193 assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
195 // add same feature value, overlapping range
196 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
197 // same feature value, contiguous range
198 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
199 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
201 assertEquals(1, commands.size());
202 assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
204 // same feature value and model, different chain
205 ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
206 // same feature value and chain, different model
207 ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
208 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
210 assertEquals(1, commands.size());
211 assertEquals(commands.get(0),
212 "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
214 // same feature, different value
215 ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
216 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
218 assertEquals(2, commands.size());
219 // commands are ordered by feature type but not by value
220 // so use contains to test for the expected command:
222 .contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
223 assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A"));
226 featureValues.clear();
227 featuresMap.put("side-chain binding!", featureValues);
228 ChimeraCommands.addAtomSpecRange(featureValues,
229 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
231 // feature names are sanitised to change non-alphanumeric to underscore
232 // feature values are sanitised to encode single quote characters
233 commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
236 .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
240 * Tests for the method that prefixes and sanitises a feature name so it can
241 * be used as a valid, namespaced attribute name in Chimera
243 @Test(groups = { "Functional" })
244 public void testMakeAttributeName()
246 assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
247 assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
248 assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
249 assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
250 "jv_Hello_World_24");
252 ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
253 "jv__this_is_a_very__odd_name");
254 // name ending in color gets underscore appended
255 assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
259 @Test(groups = { "Functional" })
260 public void testGetColourBySequenceCommands_hiddenColumns()
263 * load these sequences, coloured by Strand propensity,
264 * with columns 2-4 hidden
266 SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
267 SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
268 AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
269 AlignFrame af = new AlignFrame(al, 800, 500);
270 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
271 ColumnSelection cs = new ColumnSelection();
275 af.getViewport().setColumnSelection(cs);
276 af.hideSelColumns_actionPerformed(null);
277 sr = new SequenceRenderer(af.getViewport());
278 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
279 files = new String[] { "seq1.pdb", "seq2.pdb" };
280 StructureSelectionManager ssm = new StructureSelectionManager();
283 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
285 HashMap<Integer, int[]> map = new HashMap<>();
286 for (int pos = 1; pos <= seq1.getLength(); pos++)
288 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
290 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
292 ssm.addStructureMapping(sm1);
293 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
295 ssm.addStructureMapping(sm2);
298 * put data into the mock binding object
300 PA.setValue(mockBinding, "ssm", ssm);
301 PA.setValue(mockBinding, "sequence", seqs);
303 Map<Object, AtomSpecModel> colourMap = StructureCommands.buildColoursMap(mockBinding, af.alignPanel);
304 String[] commands = ChimeraCommands
305 .getColourBySequenceCommand(colourMap, mockBinding);
306 assertEquals(1, commands.length);
307 String theCommand = commands[0];
308 // M colour is #82827d (see strand.html help page)
309 assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
310 // H colour is #60609f
311 assertTrue(theCommand.contains("color #60609f #0:22.A"));
312 // V colour is #ffff00
313 assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
314 // hidden columns are Gray (128, 128, 128)
315 assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
316 // S and G are both coloured #4949b6
317 assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
320 @Test(groups = "Functional")
321 public void testGetAtomSpec()
323 AtomSpecModel model = new AtomSpecModel();
324 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding), "");
326 model.addRange(1, 2, 4, "A");
327 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
330 model.addRange(1, 8, 8, "A");
331 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
334 model.addRange(1, 5, 7, "B");
335 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
336 "#1:2-4.A,8.A,5-7.B");
338 model.addRange(1, 3, 5, "A");
339 // 3-5 combines with 2-4 to make 2-5:
340 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
341 "#1:2-5.A,8.A,5-7.B");
343 model.addRange(0, 1, 4, "B");
344 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
345 "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
347 model.addRange(0, 5, 9, "C");
348 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
349 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
351 model.addRange(1, 8, 10, "B");
352 // 8-10 extends 5-7 to make 5-10
353 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
354 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
356 model.addRange(1, 8, 9, "B");
357 // subsumed range makes no difference
358 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
359 "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
361 model.addRange(0, 3, 10, "C");
362 // subsumes 5-9 so replaces it
363 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
364 "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
366 // empty chain code - e.g. from homology modelling
367 model.addRange(5, 25, 35, " ");
368 assertEquals(ChimeraCommands.getAtomSpec(model, mockBinding),
369 "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");