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.HiddenColumns;
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.BitSet;
48 import java.util.List;
50 import org.testng.annotations.BeforeClass;
51 import org.testng.annotations.BeforeMethod;
52 import org.testng.annotations.Test;
55 * Unit tests for non-abstract methods of abstract base class
60 public class AAStructureBindingModelTest
63 @BeforeClass(alwaysRun = true)
64 public void setUpJvOptionPane()
66 JvOptionPane.setInteractiveMode(false);
67 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
71 * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
73 private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
74 + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
75 + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
76 + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
77 + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
78 // artificial jump in residue numbering to prove it is correctly
80 + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
81 + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
82 + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
83 + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
84 + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
85 + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
87 private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
88 + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
89 + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
90 + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
91 + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
92 + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
94 private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
95 + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
96 + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
97 + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
98 + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
99 + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
101 AAStructureBindingModel testee;
103 AlignmentI al = null;
106 * Set up test conditions with three aligned sequences,
108 @BeforeMethod(alwaysRun = true)
111 SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
112 SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
113 SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
114 SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
115 al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
119 * give pdb files the name generated by Jalview for PASTE source
121 PDBEntry[] pdbFiles = new PDBEntry[3];
122 pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
123 pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
124 pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
125 SequenceI[][] seqs = new SequenceI[3][];
126 seqs[0] = new SequenceI[] { seq1a, seq1b };
127 seqs[1] = new SequenceI[] { seq2 };
128 seqs[2] = new SequenceI[] { seq3 };
129 StructureSelectionManager ssm = new StructureSelectionManager();
131 ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
132 DataSourceType.PASTE);
133 ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
134 DataSourceType.PASTE);
135 ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
136 DataSourceType.PASTE);
138 testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
141 public String[] getPdbFile()
143 return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
147 public void updateColours(Object source)
152 public void releaseReferences(Object svl)
157 public void highlightAtoms(List<AtomSpec> atoms)
162 public List<String> getChainNames()
168 public void setJalviewColourScheme(ColourSchemeI cs)
173 public String superposeStructures(AlignmentI[] als, int[] alm,
180 public void setBackgroundColour(Color col)
185 protected StructureMappingcommandSet[] getColourBySequenceCommands(
186 String[] files, SequenceRenderer sr, AlignmentViewPanel avp)
192 public SequenceRenderer getSequenceRenderer(
193 AlignmentViewPanel alignment)
199 protected void colourBySequence(
200 StructureMappingcommandSet[] colourBySequenceCommands)
205 public void colourByChain()
210 public void colourByCharge()
215 public FeatureRenderer getFeatureRenderer(
216 AlignmentViewPanel alignment)
224 * Verify that the method determines that columns 2, 5 and 6 of the alignment
225 * are alignable in structure
227 @Test(groups = { "Functional" })
228 public void testFindSuperposableResidues()
231 * create a data bean to hold data per structure file
233 SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
234 for (int i = 0; i < structs.length; i++)
236 structs[i] = testee.new SuperposeData(al.getWidth());
239 * initialise BitSet of 'superposable columns' to true (would be false for
242 BitSet matched = new BitSet();
243 for (int i = 0; i < al.getWidth(); i++)
248 int refStructure = testee
249 .findSuperposableResidues(al, matched, structs);
251 assertEquals(0, refStructure);
254 * only ungapped, structure-mapped columns are superposable
256 assertFalse(matched.get(0)); // gap in first sequence
257 assertTrue(matched.get(1));
258 assertFalse(matched.get(2)); // gap in third sequence
259 assertFalse(matched.get(3)); // gap in fourth sequence
260 assertTrue(matched.get(4));
261 assertTrue(matched.get(5)); // gap in second sequence
263 assertEquals("1YCS", structs[0].pdbId);
264 assertEquals("3A6S", structs[1].pdbId);
265 assertEquals("1OOT", structs[2].pdbId);
266 assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
267 assertEquals("B", structs[1].chain);
268 assertEquals("A", structs[2].chain);
269 // the 0's for unsuperposable positions propagate down the columns:
270 assertEquals("[0, 97, 98, 99, 100, 102]",
271 Arrays.toString(structs[0].pdbResNo));
272 assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
273 assertEquals("[0, 8, 0, 0, 10, 12]",
274 Arrays.toString(structs[2].pdbResNo));
277 @Test(groups = { "Functional" })
278 public void testFindSuperposableResidues_hiddenColumn()
280 SuperposeData[] structs = new SuperposeData[al.getHeight()];
281 for (int i = 0; i < structs.length; i++)
283 structs[i] = testee.new SuperposeData(al.getWidth());
286 * initialise BitSet of 'superposable columns' to true (would be false for
289 BitSet matched = new BitSet();
290 for (int i = 0; i < al.getWidth(); i++)
295 // treat column 5 of the alignment as hidden
298 int refStructure = testee
299 .findSuperposableResidues(al, matched, structs);
301 assertEquals(0, refStructure);
303 // only ungapped, structure-mapped columns are not superposable
304 assertFalse(matched.get(0));
305 assertTrue(matched.get(1));
306 assertFalse(matched.get(2));
307 assertFalse(matched.get(3));
308 assertFalse(matched.get(4)); // superposable, but hidden, column
309 assertTrue(matched.get(5));