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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.structures.models

File AAStructureBindingModelTest.java

 

Code metrics

18
133
23
1
509
350
32
0.24
5.78
23
1.39

Classes

Class Line # Actions
AAStructureBindingModelTest 70 133 32
0.867816186.8%
 

Contributing tests

This file is covered by 4 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.structures.models;
22   
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.Assert.assertTrue;
27   
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;
34    import java.util.Map;
35   
36    import org.testng.annotations.BeforeClass;
37    import org.testng.annotations.BeforeMethod;
38    import org.testng.annotations.Test;
39   
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;
63   
64    /**
65    * Unit tests for non-abstract methods of abstract base class
66    *
67    * @author gmcarstairs
68    *
69    */
 
70    public class AAStructureBindingModelTest
71    {
72   
 
73  1 toggle @BeforeClass(alwaysRun = true)
74    public void setUpJvOptionPane()
75    {
76  1 JvOptionPane.setInteractiveMode(false);
77  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
78    }
79   
80    /*
81    * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
82    */
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
89    // mapped:
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";
96   
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";
103   
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";
110   
111    /**
112    * Multichain PDB with identical sequences imported - Binding should correctly
113    * recover chain mappings for each derived sequence
114    */
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";
126   
127    // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
128   
 
129  1 toggle @Test(groups= {"Functional"})
130    public void testImportPDBPreservesChainMappings() throws IOException
131    {
132  1 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
136    // pasted files,
137    // see JAL-623 - pasting is still not correctly handled...
138  1 PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB,
139    "Paste");
140  1 AAStructureBindingModel binder = new AAStructureBindingModel(
141    new StructureSelectionManager(), new PDBEntry[]
142    { importedPDB },
143    new SequenceI[][]
144    { importedAl.getSequencesArray() }, null)
145    {
146   
 
147  0 toggle @Override
148    public void updateColours(Object source)
149    {
150    }
151   
 
152  0 toggle @Override
153    public void releaseReferences(Object svl)
154    {
155    }
156   
 
157  0 toggle @Override
158    public String[] getStructureFiles()
159    {
160  0 return null;
161    }
162   
 
163  0 toggle @Override
164    public void highlightAtoms(List<AtomSpec> atoms)
165    {
166    }
167   
 
168  0 toggle @Override
169    public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
170    {
171  0 return null;
172    }
173   
 
174  0 toggle @Override
175    protected List<String> executeCommand(StructureCommandI command,
176    boolean getReply)
177    {
178  0 return null;
179    }
180   
 
181  0 toggle @Override
182    protected String getModelIdForFile(String chainId)
183    {
184  0 return "";
185    }
186   
 
187  0 toggle @Override
188    protected ViewerType getViewerType()
189    {
190  0 return null;
191    }
192    };
193  1 String[][] chains = binder.getChains();
194  1 assertFalse(chains == null || chains[0] == null,
195    "No chains discovered by binding");
196  1 assertEquals(chains[0].length, 2);
197  1 assertEquals(chains[0][0], "A");
198  1 assertEquals(chains[0][1], "B");
199    }
200    AAStructureBindingModel testee;
201   
202    AlignmentI al = null;
203   
204    /**
205    * Set up test conditions with three aligned sequences,
206    */
 
207  4 toggle @BeforeMethod(alwaysRun = true)
208    public void setUp()
209    {
210  4 SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
211  4 SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
212  4 SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
213  4 SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
214  4 al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
215  4 al.setDataset(null);
216   
217    /*
218    * give pdb files the name generated by Jalview for PASTE source
219    */
220  4 PDBEntry[] pdbFiles = new PDBEntry[3];
221  4 pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
222  4 pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
223  4 pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
224  4 SequenceI[][] seqs = new SequenceI[3][];
225  4 seqs[0] = new SequenceI[] { seq1a, seq1b };
226  4 seqs[1] = new SequenceI[] { seq2 };
227  4 seqs[2] = new SequenceI[] { seq3 };
228  4 StructureSelectionManager ssm = new StructureSelectionManager();
229   
230  4 ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
231    DataSourceType.PASTE, null);
232  4 ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
233    DataSourceType.PASTE, null);
234  4 ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
235    DataSourceType.PASTE, null);
236   
237  4 testee = newBindingModel(pdbFiles, seqs, ssm, null);
238    }
239   
240    /**
241    * A helper method to construct the test target object
242    *
243    * @param pdbFiles
244    * @param seqs
245    * @param ssm
246    * @param alignPanel
247    */
 
248  5 toggle protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
249    SequenceI[][] seqs,
250    StructureSelectionManager ssm, AlignmentViewPanel avp)
251    {
252  5 AAStructureBindingModel model = new AAStructureBindingModel(ssm,
253    pdbFiles, seqs, null)
254    {
 
255  4 toggle @Override
256    public String[] getStructureFiles()
257    {
258  4 String[] files = new String[getPdbCount()];
259  15 for (int i = 0; i < this.getPdbCount(); i++)
260    {
261  11 files[i] = getPdbEntry(i).getFile();
262    }
263  4 return files;
264    }
265   
 
266  0 toggle @Override
267    public void updateColours(Object source)
268    {
269    }
270   
 
271  0 toggle @Override
272    public void releaseReferences(Object svl)
273    {
274    }
275   
 
276  0 toggle @Override
277    public void highlightAtoms(List<AtomSpec> atoms)
278    {
279    }
280   
 
281  1 toggle @Override
282    public SequenceRenderer getSequenceRenderer(
283    AlignmentViewPanel avp)
284    {
285  1 return avp == null ? null
286    : new jalview.gui.SequenceRenderer(
287    avp.getAlignViewport());
288    }
289   
 
290  0 toggle @Override
291    protected List<String> executeCommand(StructureCommandI command,
292    boolean getReply)
293    {
294  0 return null;
295    }
296   
297    /*
298    * for this test, let structure model ids be 0, 1, ...
299    * corresponding to first, second etc pdbfile
300    */
 
301  2 toggle @Override
302    protected String getModelIdForFile(String pdbfile)
303    {
304  3 for (int i = 0; i < this.getPdbCount(); i++)
305    {
306  3 if (pdbfile.equals(this.getPdbEntry(i).getFile()))
307    {
308  2 return String.valueOf(i);
309    }
310    }
311  0 return "";
312    }
313   
 
314  0 toggle @Override
315    protected ViewerType getViewerType()
316    {
317  0 return null;
318    }
319    };
320  5 PA.setValue(model, "commandGenerator", new ChimeraCommands());
321  5 return model;
322    }
323   
324    /**
325    * Verify that the method determines that columns 2, 5 and 6 of the alignment
326    * are alignable in structure
327    */
 
328  1 toggle @Test(groups = { "Functional" })
329    public void testFindSuperposableResidues()
330    {
331    /*
332    * create a data bean to hold data per structure file
333    */
334  1 AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee.getStructureFiles().length];
335  4 for (int i = 0; i < structs.length; i++)
336    {
337  3 structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
338    }
339    /*
340    * initialise BitSet of 'superposable columns' to true (would be false for
341    * hidden columns)
342    */
343  1 BitSet matched = new BitSet();
344  7 for (int i = 0; i < al.getWidth(); i++)
345    {
346  6 matched.set(i);
347    }
348   
349  1 int refStructure = testee
350    .findSuperposableResidues(al, matched, structs);
351   
352  1 assertEquals(refStructure, 0);
353   
354    /*
355    * only ungapped, structure-mapped columns are superposable
356    */
357  1 assertFalse(matched.get(0)); // gap in first sequence
358  1 assertTrue(matched.get(1));
359  1 assertFalse(matched.get(2)); // gap in third sequence
360  1 assertFalse(matched.get(3)); // gap in fourth sequence
361  1 assertTrue(matched.get(4));
362  1 assertTrue(matched.get(5)); // gap in second sequence
363   
364  1 assertEquals(structs[0].pdbId, "1YCS");
365  1 assertEquals(structs[1].pdbId, "3A6S");
366  1 assertEquals(structs[2].pdbId, "1OOT");
367  1 assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B
368  1 assertEquals(structs[1].chain, "B");
369  1 assertEquals(structs[2].chain, "A");
370    // the 0's for unsuperposable positions propagate down the columns:
371  1 assertEquals(Arrays.toString(structs[0].pdbResNo),
372    "[0, 97, 98, 99, 100, 102]");
373  1 assertEquals(Arrays.toString(structs[1].pdbResNo),
374    "[0, 2, 0, 3, 4, 5]");
375  1 assertEquals(Arrays.toString(structs[2].pdbResNo),
376    "[0, 8, 0, 0, 10, 12]");
377    }
378   
 
379  1 toggle @Test(groups = { "Functional" })
380    public void testFindSuperposableResidues_hiddenColumn()
381    {
382  1 AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al.getHeight()];
383  5 for (int i = 0; i < structs.length; i++)
384    {
385  4 structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
386    }
387    /*
388    * initialise BitSet of 'superposable columns' to true (would be false for
389    * hidden columns)
390    */
391  1 BitSet matched = new BitSet();
392  7 for (int i = 0; i < al.getWidth(); i++)
393    {
394  6 matched.set(i);
395    }
396   
397    // treat column 5 of the alignment as hidden
398  1 matched.clear(4);
399   
400  1 int refStructure = testee
401    .findSuperposableResidues(al, matched, structs);
402   
403  1 assertEquals(refStructure, 0);
404   
405    // only ungapped, structure-mapped columns are not superposable
406  1 assertFalse(matched.get(0));
407  1 assertTrue(matched.get(1));
408  1 assertFalse(matched.get(2));
409  1 assertFalse(matched.get(3));
410  1 assertFalse(matched.get(4)); // superposable, but hidden, column
411  1 assertTrue(matched.get(5));
412    }
413   
 
414  1 toggle @Test(groups = { "Functional" })
415    public void testBuildColoursMap()
416    {
417    /*
418    * load these sequences, coloured by Strand propensity,
419    * with columns 2-4 hidden
420    */
421  1 String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS";
422  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
423    DataSourceType.PASTE);
424  1 AlignmentI al = af.getViewport().getAlignment();
425  1 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
426  1 ColumnSelection cs = new ColumnSelection();
427  1 cs.addElement(2);
428  1 cs.addElement(3);
429  1 cs.addElement(4);
430  1 af.getViewport().setColumnSelection(cs);
431  1 af.hideSelColumns_actionPerformed(null);
432  1 SequenceI seq1 = al.getSequenceAt(0);
433  1 SequenceI seq2 = al.getSequenceAt(1);
434  1 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
435  1 PDBEntry[] pdbFiles = new PDBEntry[2];
436  1 pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
437  1 pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
438  1 StructureSelectionManager ssm = new StructureSelectionManager();
439   
440    /*
441    * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
442    */
443  1 HashMap<Integer, int[]> map = new HashMap<>();
444  11 for (int pos = 1; pos <= seq1.getLength(); pos++)
445    {
446  10 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
447    }
448  1 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
449    "A", map, null);
450  1 ssm.addStructureMapping(sm1);
451  1 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
452    "B", map, null);
453  1 ssm.addStructureMapping(sm2);
454   
455  1 AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
456    af.alignPanel);
457   
458    /*
459    * method under test builds a map of structures residues by colour
460    * verify the map holds what it should
461    */
462  1 Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
463    af.alignPanel);
464  1 ChimeraCommands helper = new ChimeraCommands();
465   
466    /*
467    * M colour is #82827d (see strand.html help page)
468    * sequence residue 1 mapped to structure residue 21
469    */
470  1 Color mColor = new Color(0x82827d);
471  1 AtomSpecModel atomSpec = colours.get(mColor);
472  1 assertNotNull(atomSpec);
473  1 assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
474   
475    /*
476    * H colour is #60609f, seq1.2 mapped to structure 0 residue 22
477    */
478  1 Color hColor = new Color(0x60609f);
479  1 atomSpec = colours.get(hColor);
480  1 assertNotNull(atomSpec);
481  1 assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
482   
483    /*
484    * V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
485    */
486  1 Color vColor = new Color(0xffff00);
487  1 atomSpec = colours.get(vColor);
488  1 assertNotNull(atomSpec);
489  1 assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
490   
491    /*
492    * hidden columns are Gray (128, 128, 128)
493    * sequence positions 3-5 mapped to structure residues 23-25
494    */
495  1 Color gray = new Color(128, 128, 128);
496  1 atomSpec = colours.get(gray);
497  1 assertNotNull(atomSpec);
498  1 assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
499   
500    /*
501    * S and G are both coloured #4949b6, structure residues 26-30
502    */
503  1 Color sgColour = new Color(0x4949b6);
504  1 atomSpec = colours.get(sgColour);
505  1 assertNotNull(atomSpec);
506  1 assertEquals(helper.getAtomSpec(atomSpec, false),
507    "#0:26-30.A|#1:26-30.B");
508    }
509    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.