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.structures.models;
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertFalse;
25 import static org.testng.Assert.assertNotNull;
26 import static org.testng.AssertJUnit.assertTrue;
28 import java.awt.Color;
29 import java.io.IOException;
30 import java.util.Arrays;
31 import java.util.BitSet;
32 import java.util.HashMap;
33 import java.util.List;
36 import org.testng.annotations.BeforeClass;
37 import org.testng.annotations.BeforeMethod;
38 import org.testng.annotations.Test;
40 import jalview.api.AlignmentViewPanel;
41 import jalview.api.SequenceRenderer;
42 import jalview.datamodel.Alignment;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.PDBEntry.Type;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceI;
49 import jalview.ext.rbvi.chimera.ChimeraCommands;
50 import jalview.gui.AlignFrame;
51 import jalview.gui.JvOptionPane;
52 import jalview.gui.StructureViewer.ViewerType;
53 import jalview.io.DataSourceType;
54 import jalview.io.FileFormats;
55 import jalview.io.FileLoader;
56 import jalview.schemes.JalviewColourScheme;
57 import jalview.structure.AtomSpec;
58 import jalview.structure.AtomSpecModel;
59 import jalview.structure.StructureCommandI;
60 import jalview.structure.StructureMapping;
61 import jalview.structure.StructureSelectionManager;
62 import junit.extensions.PA;
65 * Unit tests for non-abstract methods of abstract base class
70 public class AAStructureBindingModelTest
73 @BeforeClass(alwaysRun = true)
74 public void setUpJvOptionPane()
76 JvOptionPane.setInteractiveMode(false);
77 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
81 * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
83 private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
84 + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
85 + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
86 + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
87 + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
88 // artificial jump in residue numbering to prove it is correctly
90 + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
91 + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
92 + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
93 + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
94 + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
95 + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
97 private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
98 + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
99 + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
100 + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
101 + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
102 + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
104 private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
105 + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
106 + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
107 + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
108 + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
109 + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
112 * Multichain PDB with identical sequences imported - Binding should correctly
113 * recover chain mappings for each derived sequence
115 private static final String PDB_4_MC = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
116 + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
117 + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
118 + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
119 + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
120 + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n"
121 + "ATOM 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n"
122 + "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n"
123 + "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n"
124 + "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n"
125 + "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n";
127 // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
129 @Test(groups = { "Functional" })
130 public void testImportPDBPreservesChainMappings() throws IOException
132 AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
133 PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance()
134 .forName(jalview.io.FileFormat.PDB.toString()));
135 // ideally, we would match on the actual data for the 'File' handle for
137 // see JAL-623 - pasting is still not correctly handled...
138 PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "Paste");
139 AAStructureBindingModel binder = newBindingModel(
143 { importedAl.getSequencesArray() },
144 new StructureSelectionManager(), null);
146 String[][] chains = binder.getChains();
147 assertFalse(chains == null || chains[0] == null,
148 "No chains discovered by binding");
149 assertEquals(chains[0].length, 2);
150 assertEquals(chains[0][0], "A");
151 assertEquals(chains[0][1], "B");
154 AAStructureBindingModel testee;
156 AlignmentI al = null;
159 * Set up test conditions with three aligned sequences,
161 @BeforeMethod(alwaysRun = true)
164 SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
165 SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
166 SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
167 SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
168 al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
172 * give pdb files the name generated by Jalview for PASTE source
174 PDBEntry[] pdbFiles = new PDBEntry[3];
175 pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
176 pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
177 pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
178 SequenceI[][] seqs = new SequenceI[3][];
179 seqs[0] = new SequenceI[] { seq1a, seq1b };
180 seqs[1] = new SequenceI[] { seq2 };
181 seqs[2] = new SequenceI[] { seq3 };
182 StructureSelectionManager ssm = new StructureSelectionManager();
184 ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
185 DataSourceType.PASTE, null);
186 ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
187 DataSourceType.PASTE, null);
188 ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
189 DataSourceType.PASTE, null);
191 testee = newBindingModel(pdbFiles, seqs, ssm, null);
195 * A helper method to construct the test target object
202 protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
203 SequenceI[][] seqs, StructureSelectionManager ssm,
204 AlignmentViewPanel avp)
206 AAStructureBindingModel model = new AAStructureBindingModel(ssm,
207 pdbFiles, seqs, null)
210 public String[] getStructureFiles()
212 String[] files = new String[getPdbCount()];
213 for (int i = 0; i < this.getPdbCount(); i++)
215 files[i] = getPdbEntry(i).getFile();
221 public void updateColours(Object source)
226 public void releaseReferences(Object svl)
231 public void highlightAtoms(List<AtomSpec> atoms)
236 public void setBackgroundColour(Color col)
241 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
243 return avp == null ? null
244 : new jalview.gui.SequenceRenderer(avp.getAlignViewport());
248 protected List<String> executeCommand(StructureCommandI command,
255 * for this test, let structure model ids be 0, 1, ...
256 * corresponding to first, second etc pdbfile
259 protected String getModelIdForFile(String pdbfile)
261 for (int i = 0; i < this.getPdbCount(); i++)
263 if (pdbfile.equals(this.getPdbEntry(i).getFile()))
265 return String.valueOf(i);
272 protected ViewerType getViewerType()
277 PA.setValue(model, "commandGenerator", new ChimeraCommands());
282 * Verify that the method determines that columns 2, 5 and 6 of the alignment
283 * are alignable in structure
285 @Test(groups = { "Functional" })
286 public void testFindSuperposableResidues()
289 * create a data bean to hold data per structure file
291 AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee
292 .getStructureFiles().length];
293 for (int i = 0; i < structs.length; i++)
295 structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
299 * initialise BitSet of 'superposable columns' to true (would be false for
302 BitSet matched = new BitSet();
303 for (int i = 0; i < al.getWidth(); i++)
308 int refStructure = testee.findSuperposableResidues(al, matched,
311 assertEquals(refStructure, 0);
314 * only ungapped, structure-mapped columns are superposable
316 assertFalse(matched.get(0)); // gap in first sequence
317 assertTrue(matched.get(1));
318 assertFalse(matched.get(2)); // gap in third sequence
319 assertFalse(matched.get(3)); // gap in fourth sequence
320 assertTrue(matched.get(4));
321 assertTrue(matched.get(5)); // gap in second sequence
323 assertEquals(structs[0].pdbId, "1YCS");
324 assertEquals(structs[1].pdbId, "3A6S");
325 assertEquals(structs[2].pdbId, "1OOT");
326 assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B
327 assertEquals(structs[1].chain, "B");
328 assertEquals(structs[2].chain, "A");
329 // the 0's for unsuperposable positions propagate down the columns:
330 assertEquals(Arrays.toString(structs[0].pdbResNo),
331 "[0, 97, 98, 99, 100, 102]");
332 assertEquals(Arrays.toString(structs[1].pdbResNo),
333 "[0, 2, 0, 3, 4, 5]");
334 assertEquals(Arrays.toString(structs[2].pdbResNo),
335 "[0, 8, 0, 0, 10, 12]");
338 @Test(groups = { "Functional" })
339 public void testFindSuperposableResidues_hiddenColumn()
341 AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
343 for (int i = 0; i < structs.length; i++)
345 structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
349 * initialise BitSet of 'superposable columns' to true (would be false for
352 BitSet matched = new BitSet();
353 for (int i = 0; i < al.getWidth(); i++)
358 // treat column 5 of the alignment as hidden
361 int refStructure = testee.findSuperposableResidues(al, matched,
364 assertEquals(refStructure, 0);
366 // only ungapped, structure-mapped columns are not superposable
367 assertFalse(matched.get(0));
368 assertTrue(matched.get(1));
369 assertFalse(matched.get(2));
370 assertFalse(matched.get(3));
371 assertFalse(matched.get(4)); // superposable, but hidden, column
372 assertTrue(matched.get(5));
375 @Test(groups = { "Functional" })
376 public void testBuildColoursMap()
379 * load these sequences, coloured by Strand propensity,
380 * with columns 2-4 hidden
382 String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS";
383 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
384 DataSourceType.PASTE);
385 AlignmentI al = af.getViewport().getAlignment();
386 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
387 ColumnSelection cs = new ColumnSelection();
391 af.getViewport().setColumnSelection(cs);
392 af.hideSelColumns_actionPerformed(null);
393 SequenceI seq1 = al.getSequenceAt(0);
394 SequenceI seq2 = al.getSequenceAt(1);
395 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
396 PDBEntry[] pdbFiles = new PDBEntry[2];
397 pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
398 pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
399 StructureSelectionManager ssm = new StructureSelectionManager();
402 * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
404 HashMap<Integer, int[]> map = new HashMap<>();
405 for (int pos = 1; pos <= seq1.getLength(); pos++)
407 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
409 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
411 ssm.addStructureMapping(sm1);
412 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
414 ssm.addStructureMapping(sm2);
416 AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
420 * method under test builds a map of structures residues by colour
421 * verify the map holds what it should
423 Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
425 ChimeraCommands helper = new ChimeraCommands();
428 * M colour is #82827d (see strand.html help page)
429 * sequence residue 1 mapped to structure residue 21
431 Color mColor = new Color(0x82827d);
432 AtomSpecModel atomSpec = colours.get(mColor);
433 assertNotNull(atomSpec);
434 assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
437 * H colour is #60609f, seq1.2 mapped to structure 0 residue 22
439 Color hColor = new Color(0x60609f);
440 atomSpec = colours.get(hColor);
441 assertNotNull(atomSpec);
442 assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
445 * V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
447 Color vColor = new Color(0xffff00);
448 atomSpec = colours.get(vColor);
449 assertNotNull(atomSpec);
450 assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
453 * hidden columns are Gray (128, 128, 128)
454 * sequence positions 3-5 mapped to structure residues 23-25
456 Color gray = new Color(128, 128, 128);
457 atomSpec = colours.get(gray);
458 assertNotNull(atomSpec);
459 assertEquals(helper.getAtomSpec(atomSpec, false),
460 "#0:23-25.A|#1:23-25.B");
463 * S and G are both coloured #4949b6, structure residues 26-30
465 Color sgColour = new Color(0x4949b6);
466 atomSpec = colours.get(sgColour);
467 assertNotNull(atomSpec);
468 assertEquals(helper.getAtomSpec(atomSpec, false),
469 "#0:26-30.A|#1:26-30.B");
472 @Test(groups = { "Functional" })
473 public void testGetShownResidues()
476 * load these sequences, with columns 2-4 (third, fourth, fifth) hidden
478 String fasta = ">seq1/12-21\nMHRSQSSSGG\n>seq2/12-21\nMVRSNGGSSS";
479 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
480 DataSourceType.PASTE);
481 AlignmentI al = af.getViewport().getAlignment();
482 ColumnSelection cs = new ColumnSelection();
486 af.getViewport().setColumnSelection(cs);
487 af.hideSelColumns_actionPerformed(null);
488 SequenceI seq1 = al.getSequenceAt(0);
489 SequenceI seq2 = al.getSequenceAt(1);
490 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
491 PDBEntry[] pdbFiles = new PDBEntry[2];
492 pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
493 pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
494 StructureSelectionManager ssm = new StructureSelectionManager();
497 * map residues 12-21 to residues 21-30 (atoms 105-150) in structures
499 HashMap<Integer, int[]> map = new HashMap<>();
500 for (int pos = 1; pos <= seq1.getLength(); pos++)
502 map.put(pos + 11, new int[] { 20 + pos, 5 * (20 + pos) });
504 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
506 ssm.addStructureMapping(sm1);
507 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
509 ssm.addStructureMapping(sm2);
511 AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
515 * with hidden columns shown on structure
517 binding.setShowAlignmentOnly(true);
518 AtomSpecModel model = binding.getShownResidues(af.getViewport());
519 assertEquals(model.getModelCount(), 2);
521 for (String modelId : model.getModels())
523 assertEquals(modelId, String.valueOf(modelNo));
524 Iterable<String> chains = model.getChains(modelId);
525 String expectedChain = (modelNo == 0) ? "A" : "B";
526 for (String chain : chains)
528 assertEquals(chain, expectedChain);
529 List<int[]> ranges = model.getRanges(modelId, chain);
530 assertEquals(ranges.size(), 1);
531 assertEquals(ranges.get(0)[0], 21);
532 assertEquals(ranges.get(0)[1], 30);
538 * with hidden columns hidden on structure
539 * columns 2-4 correspond to residues 23-25 on structure - now omitted
541 binding.setHideHiddenRegions(true);
542 model = binding.getShownResidues(af.getViewport());
543 assertEquals(model.getModelCount(), 2);
545 for (String modelId : model.getModels())
547 assertEquals(modelId, String.valueOf(modelNo));
548 Iterable<String> chains = model.getChains(modelId);
549 String expectedChain = (modelNo == 0) ? "A" : "B";
550 for (String chain : chains)
552 assertEquals(chain, expectedChain);
553 List<int[]> ranges = model.getRanges(modelId, chain);
554 assertEquals(ranges.size(), 2);
555 assertEquals(ranges.get(0)[0], 21);
556 assertEquals(ranges.get(0)[1], 22);
557 assertEquals(ranges.get(1)[0], 26);
558 assertEquals(ranges.get(1)[1], 30);