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.assertFalse;
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.SequenceRenderer;
29 import jalview.datamodel.Alignment;
30 import jalview.datamodel.AlignmentI;
31 import jalview.datamodel.PDBEntry;
32 import jalview.datamodel.PDBEntry.Type;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceI;
35 import jalview.gui.JvOptionPane;
36 import jalview.gui.StructureViewer.ViewerType;
37 import jalview.io.DataSourceType;
38 import jalview.io.FileFormats;
39 import jalview.structure.AtomSpec;
40 import jalview.structure.StructureCommandsI.SuperposeData;
41 import jalview.structure.StructureSelectionManager;
43 import java.io.IOException;
44 import java.util.Arrays;
45 import java.util.BitSet;
46 import java.util.List;
48 import org.testng.annotations.BeforeClass;
49 import org.testng.annotations.BeforeMethod;
50 import org.testng.annotations.Test;
53 * Unit tests for non-abstract methods of abstract base class
58 public class AAStructureBindingModelTest
61 @BeforeClass(alwaysRun = true)
62 public void setUpJvOptionPane()
64 JvOptionPane.setInteractiveMode(false);
65 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
69 * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
71 private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
72 + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
73 + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
74 + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
75 + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
76 // artificial jump in residue numbering to prove it is correctly
78 + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
79 + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
80 + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
81 + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
82 + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
83 + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
85 private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
86 + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
87 + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
88 + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
89 + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
90 + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
92 private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
93 + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
94 + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
95 + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
96 + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
97 + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
100 * Multichain PDB with identical sequences imported - Binding should correctly
101 * recover chain mappings for each derived sequence
103 private static final String PDB_4_MC = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
104 + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
105 + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
106 + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
107 + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
108 + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n"
109 + "ATOM 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n"
110 + "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n"
111 + "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n"
112 + "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n"
113 + "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n";
115 // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
117 @Test(groups= {"Functional"})
118 public void testImportPDBPreservesChainMappings() throws IOException
120 AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
121 PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance()
122 .forName(jalview.io.FileFormat.PDB.toString()));
123 // ideally, we would match on the actual data for the 'File' handle for
125 // see JAL-623 - pasting is still not correctly handled...
126 PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB,
128 AAStructureBindingModel binder = new AAStructureBindingModel(
129 new StructureSelectionManager(), new PDBEntry[]
132 { importedAl.getSequencesArray() }, null)
136 public void updateColours(Object source)
141 public void releaseReferences(Object svl)
146 public String[] getStructureFiles()
152 public void highlightAtoms(List<AtomSpec> atoms)
157 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
163 protected List<String> executeCommand(String command,
170 protected int getModelNoForFile(String chainId)
176 protected ViewerType getViewerType()
181 String[][] chains = binder.getChains();
182 assertFalse(chains == null || chains[0] == null,
183 "No chains discovered by binding");
184 assertEquals(2, chains[0].length);
185 assertEquals("A", chains[0][0]);
186 assertEquals("B", chains[0][1]);
188 AAStructureBindingModel testee;
190 AlignmentI al = null;
193 * Set up test conditions with three aligned sequences,
195 @BeforeMethod(alwaysRun = true)
198 SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
199 SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
200 SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
201 SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
202 al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
206 * give pdb files the name generated by Jalview for PASTE source
208 PDBEntry[] pdbFiles = new PDBEntry[3];
209 pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
210 pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
211 pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
212 SequenceI[][] seqs = new SequenceI[3][];
213 seqs[0] = new SequenceI[] { seq1a, seq1b };
214 seqs[1] = new SequenceI[] { seq2 };
215 seqs[2] = new SequenceI[] { seq3 };
216 StructureSelectionManager ssm = new StructureSelectionManager();
218 ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
219 DataSourceType.PASTE, null);
220 ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
221 DataSourceType.PASTE, null);
222 ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
223 DataSourceType.PASTE, null);
225 testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
228 public String[] getStructureFiles()
230 return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
234 public void updateColours(Object source)
239 public void releaseReferences(Object svl)
244 public void highlightAtoms(List<AtomSpec> atoms)
249 public SequenceRenderer getSequenceRenderer(
250 AlignmentViewPanel alignment)
256 protected List<String> executeCommand(String command,
263 protected int getModelNoForFile(String chainId)
269 protected ViewerType getViewerType()
277 * Verify that the method determines that columns 2, 5 and 6 of the alignment
278 * are alignable in structure
280 @Test(groups = { "Functional" })
281 public void testFindSuperposableResidues()
284 * create a data bean to hold data per structure file
286 SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().length];
287 for (int i = 0; i < structs.length; i++)
289 structs[i] = new SuperposeData(al.getWidth(), 0);
292 * initialise BitSet of 'superposable columns' to true (would be false for
295 BitSet matched = new BitSet();
296 for (int i = 0; i < al.getWidth(); i++)
301 int refStructure = testee
302 .findSuperposableResidues(al, matched, structs);
304 assertEquals(0, refStructure);
307 * only ungapped, structure-mapped columns are superposable
309 assertFalse(matched.get(0)); // gap in first sequence
310 assertTrue(matched.get(1));
311 assertFalse(matched.get(2)); // gap in third sequence
312 assertFalse(matched.get(3)); // gap in fourth sequence
313 assertTrue(matched.get(4));
314 assertTrue(matched.get(5)); // gap in second sequence
316 assertEquals("1YCS", structs[0].pdbId);
317 assertEquals("3A6S", structs[1].pdbId);
318 assertEquals("1OOT", structs[2].pdbId);
319 assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
320 assertEquals("B", structs[1].chain);
321 assertEquals("A", structs[2].chain);
322 // the 0's for unsuperposable positions propagate down the columns:
323 assertEquals("[0, 97, 98, 99, 100, 102]",
324 Arrays.toString(structs[0].pdbResNo));
325 assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
326 assertEquals("[0, 8, 0, 0, 10, 12]",
327 Arrays.toString(structs[2].pdbResNo));
330 @Test(groups = { "Functional" })
331 public void testFindSuperposableResidues_hiddenColumn()
333 SuperposeData[] structs = new SuperposeData[al.getHeight()];
334 for (int i = 0; i < structs.length; i++)
336 structs[i] = new SuperposeData(al.getWidth(), 0);
339 * initialise BitSet of 'superposable columns' to true (would be false for
342 BitSet matched = new BitSet();
343 for (int i = 0; i < al.getWidth(); i++)
348 // treat column 5 of the alignment as hidden
351 int refStructure = testee
352 .findSuperposableResidues(al, matched, structs);
354 assertEquals(0, refStructure);
356 // only ungapped, structure-mapped columns are not superposable
357 assertFalse(matched.get(0));
358 assertTrue(matched.get(1));
359 assertFalse(matched.get(2));
360 assertFalse(matched.get(3));
361 assertFalse(matched.get(4)); // superposable, but hidden, column
362 assertTrue(matched.get(5));