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.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.FeatureRenderer;
29 import jalview.api.SequenceRenderer;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.ColumnSelection;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.PDBEntry.Type;
35 import jalview.datamodel.Sequence;
36 import jalview.datamodel.SequenceI;
37 import jalview.gui.JvOptionPane;
38 import jalview.io.DataSourceType;
39 import jalview.schemes.ColourSchemeI;
40 import jalview.structure.AtomSpec;
41 import jalview.structure.StructureMappingcommandSet;
42 import jalview.structure.StructureSelectionManager;
43 import jalview.structures.models.AAStructureBindingModel.SuperposeData;
45 import java.awt.Color;
46 import java.util.Arrays;
47 import java.util.List;
49 import org.testng.annotations.BeforeClass;
50 import org.testng.annotations.BeforeMethod;
51 import org.testng.annotations.Test;
54 * Unit tests for non-abstract methods of abstract base class
59 public class AAStructureBindingModelTest
62 @BeforeClass(alwaysRun = true)
63 public void setUpJvOptionPane()
65 JvOptionPane.setInteractiveMode(false);
66 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
70 * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
72 private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
73 + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
74 + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
75 + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
76 + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
77 // artificial jump in residue numbering to prove it is correctly
79 + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
80 + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
81 + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
82 + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
83 + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
84 + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
86 private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
87 + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
88 + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
89 + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
90 + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
91 + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
93 private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
94 + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
95 + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
96 + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
97 + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
98 + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
100 AAStructureBindingModel testee;
102 AlignmentI al = null;
105 * Set up test conditions with three aligned sequences,
107 @BeforeMethod(alwaysRun = true)
110 SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
111 SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
112 SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
113 SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
114 al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
118 * give pdb files the name generated by Jalview for PASTE source
120 PDBEntry[] pdbFiles = new PDBEntry[3];
121 pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
122 pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
123 pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
124 SequenceI[][] seqs = new SequenceI[3][];
125 seqs[0] = new SequenceI[] { seq1a, seq1b };
126 seqs[1] = new SequenceI[] { seq2 };
127 seqs[2] = new SequenceI[] { seq3 };
128 StructureSelectionManager ssm = new StructureSelectionManager();
130 ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
131 DataSourceType.PASTE);
132 ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
133 DataSourceType.PASTE);
134 ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
135 DataSourceType.PASTE);
137 testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
140 public String[] getPdbFile()
142 return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
146 public void updateColours(Object source)
151 public void releaseReferences(Object svl)
156 public void highlightAtoms(List<AtomSpec> atoms)
161 public List<String> getChainNames()
167 public void setJalviewColourScheme(ColourSchemeI cs)
172 public void superposeStructures(AlignmentI[] als, int[] alm,
173 ColumnSelection[] alc)
178 public void setBackgroundColour(Color col)
183 protected StructureMappingcommandSet[] getColourBySequenceCommands(
184 String[] files, SequenceRenderer sr, FeatureRenderer fr,
185 AlignmentI alignment)
191 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
197 public SequenceRenderer getSequenceRenderer(
198 AlignmentViewPanel alignment)
204 protected void colourBySequence(
205 StructureMappingcommandSet[] colourBySequenceCommands)
210 public void colourByChain()
215 public void colourByCharge()
222 * Verify that the method determines that columns 2, 5 and 6 of the alignment
223 * are alignable in structure
225 @Test(groups = { "Functional" })
226 public void testFindSuperposableResidues()
229 * create a data bean to hold data per structure file
231 SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
232 for (int i = 0; i < structs.length; i++)
234 structs[i] = testee.new SuperposeData(al.getWidth());
237 * initialise array of 'superposable columns' to true (would be false for
240 boolean[] matched = new boolean[al.getWidth()];
241 Arrays.fill(matched, true);
243 int refStructure = testee
244 .findSuperposableResidues(al, matched, structs);
246 assertEquals(0, refStructure);
249 * only ungapped, structure-mapped columns are superposable
251 assertFalse(matched[0]); // gap in first sequence
252 assertTrue(matched[1]);
253 assertFalse(matched[2]); // gap in third sequence
254 assertFalse(matched[3]); // gap in fourth sequence
255 assertTrue(matched[4]);
256 assertTrue(matched[5]); // gap in second sequence
258 assertEquals("1YCS", structs[0].pdbId);
259 assertEquals("3A6S", structs[1].pdbId);
260 assertEquals("1OOT", structs[2].pdbId);
261 assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
262 assertEquals("B", structs[1].chain);
263 assertEquals("A", structs[2].chain);
264 // the 0's for unsuperposable positions propagate down the columns:
265 assertEquals("[0, 97, 98, 99, 100, 102]",
266 Arrays.toString(structs[0].pdbResNo));
267 assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
268 assertEquals("[0, 8, 0, 0, 10, 12]",
269 Arrays.toString(structs[2].pdbResNo));
272 @Test(groups = { "Functional" })
273 public void testFindSuperposableResidues_hiddenColumn()
275 SuperposeData[] structs = new SuperposeData[al.getHeight()];
276 for (int i = 0; i < structs.length; i++)
278 structs[i] = testee.new SuperposeData(al.getWidth());
281 * initialise array of 'superposable columns' to true (would be false for
284 boolean[] matched = new boolean[al.getWidth()];
285 Arrays.fill(matched, true);
286 // treat column 5 of the alignment as hidden
289 int refStructure = testee
290 .findSuperposableResidues(al, matched, structs);
292 assertEquals(0, refStructure);
294 // only ungapped, structure-mapped columns are not superposable
295 assertFalse(matched[0]);
296 assertTrue(matched[1]);
297 assertFalse(matched[2]);
298 assertFalse(matched[3]);
299 assertFalse(matched[4]); // superposable, but hidden, column
300 assertTrue(matched[5]);
303 public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
308 public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)