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  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.structures.models

File AAStructureBindingModelTest.java

 

Code metrics

18
133
23
1
517
357
32
0.24
5.78
23
1.39

Classes

Class Line # Actions
AAStructureBindingModelTest 71 133 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.StructureCommandsI.AtomSpecType;
61    import jalview.structure.StructureMapping;
62    import jalview.structure.StructureSelectionManager;
63    import junit.extensions.PA;
64   
65    /**
66    * Unit tests for non-abstract methods of abstract base class
67    *
68    * @author gmcarstairs
69    *
70    */
 
71    public class AAStructureBindingModelTest
72    {
73   
 
74  1 toggle @BeforeClass(alwaysRun = true)
75    public void setUpJvOptionPane()
76    {
77  1 JvOptionPane.setInteractiveMode(false);
78  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
79    }
80   
81    /*
82    * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
83    */
84    private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
85    + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
86    + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
87    + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
88    + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
89    // artificial jump in residue numbering to prove it is correctly
90    // mapped:
91    + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
92    + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
93    + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
94    + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
95    + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
96    + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
97   
98    private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
99    + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
100    + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
101    + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
102    + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
103    + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
104   
105    private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
106    + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
107    + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
108    + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
109    + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
110    + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
111   
112    /**
113    * Multichain PDB with identical sequences imported - Binding should correctly
114    * recover chain mappings for each derived sequence
115    */
116    private static final String PDB_4_MC = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
117    + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
118    + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
119    + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
120    + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
121    + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n"
122    + "ATOM 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n"
123    + "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n"
124    + "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n"
125    + "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n"
126    + "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n";
127   
128    // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
129   
 
130  1 toggle @Test(groups = { "Functional" })
131    public void testImportPDBPreservesChainMappings() throws IOException
132    {
133  1 AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
134    PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance()
135    .forName(jalview.io.FileFormat.PDB.toString()));
136    // ideally, we would match on the actual data for the 'File' handle for
137    // pasted files,
138    // see JAL-623 - pasting is still not correctly handled...
139  1 PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "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(
170    AlignmentViewPanel alignment)
171    {
172  0 return null;
173    }
174   
 
175  0 toggle @Override
176    protected List<String> executeCommand(StructureCommandI command,
177    boolean getReply)
178    {
179  0 return null;
180    }
181   
 
182  0 toggle @Override
183    protected String getModelIdForFile(String chainId)
184    {
185  0 return "";
186    }
187   
 
188  0 toggle @Override
189    protected ViewerType getViewerType()
190    {
191  0 return null;
192    }
193    };
194  1 String[][] chains = binder.getChains();
195  1 assertFalse(chains == null || chains[0] == null,
196    "No chains discovered by binding");
197  1 assertEquals(chains[0].length, 2);
198  1 assertEquals(chains[0][0], "A");
199  1 assertEquals(chains[0][1], "B");
200    }
201   
202    AAStructureBindingModel testee;
203   
204    AlignmentI al = null;
205   
206    /**
207    * Set up test conditions with three aligned sequences,
208    */
 
209  4 toggle @BeforeMethod(alwaysRun = true)
210    public void setUp()
211    {
212  4 SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
213  4 SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
214  4 SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
215  4 SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
216  4 al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
217  4 al.setDataset(null);
218   
219    /*
220    * give pdb files the name generated by Jalview for PASTE source
221    */
222  4 PDBEntry[] pdbFiles = new PDBEntry[3];
223  4 pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
224  4 pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
225  4 pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
226  4 SequenceI[][] seqs = new SequenceI[3][];
227  4 seqs[0] = new SequenceI[] { seq1a, seq1b };
228  4 seqs[1] = new SequenceI[] { seq2 };
229  4 seqs[2] = new SequenceI[] { seq3 };
230  4 StructureSelectionManager ssm = new StructureSelectionManager();
231   
232  4 ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
233    DataSourceType.PASTE, null);
234  4 ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
235    DataSourceType.PASTE, null);
236  4 ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
237    DataSourceType.PASTE, null);
238   
239  4 testee = newBindingModel(pdbFiles, seqs, ssm, null);
240    }
241   
242    /**
243    * A helper method to construct the test target object
244    *
245    * @param pdbFiles
246    * @param seqs
247    * @param ssm
248    * @param alignPanel
249    */
 
250  5 toggle protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
251    SequenceI[][] seqs, StructureSelectionManager ssm,
252    AlignmentViewPanel avp)
253    {
254  5 AAStructureBindingModel model = new AAStructureBindingModel(ssm,
255    pdbFiles, seqs, null)
256    {
 
257  4 toggle @Override
258    public String[] getStructureFiles()
259    {
260  4 String[] files = new String[getPdbCount()];
261  15 for (int i = 0; i < this.getPdbCount(); i++)
262    {
263  11 files[i] = getPdbEntry(i).getFile();
264    }
265  4 return files;
266    }
267   
 
268  0 toggle @Override
269    public void updateColours(Object source)
270    {
271    }
272   
 
273  0 toggle @Override
274    public void releaseReferences(Object svl)
275    {
276    }
277   
 
278  0 toggle @Override
279    public void highlightAtoms(List<AtomSpec> atoms)
280    {
281    }
282   
 
283  1 toggle @Override
284    public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
285    {
286  1 return avp == null ? null
287    : new jalview.gui.SequenceRenderer(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
335    .getStructureFiles().length];
336  4 for (int i = 0; i < structs.length; i++)
337    {
338  3 structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
339    "0");
340    }
341    /*
342    * initialise BitSet of 'superposable columns' to true (would be false for
343    * hidden columns)
344    */
345  1 BitSet matched = new BitSet();
346  7 for (int i = 0; i < al.getWidth(); i++)
347    {
348  6 matched.set(i);
349    }
350   
351  1 int refStructure = testee.findSuperposableResidues(al, matched,
352    structs);
353   
354  1 assertEquals(refStructure, 0);
355   
356    /*
357    * only ungapped, structure-mapped columns are superposable
358    */
359  1 assertFalse(matched.get(0)); // gap in first sequence
360  1 assertTrue(matched.get(1));
361  1 assertFalse(matched.get(2)); // gap in third sequence
362  1 assertFalse(matched.get(3)); // gap in fourth sequence
363  1 assertTrue(matched.get(4));
364  1 assertTrue(matched.get(5)); // gap in second sequence
365   
366  1 assertEquals(structs[0].pdbId, "1YCS");
367  1 assertEquals(structs[1].pdbId, "3A6S");
368  1 assertEquals(structs[2].pdbId, "1OOT");
369  1 assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B
370  1 assertEquals(structs[1].chain, "B");
371  1 assertEquals(structs[2].chain, "A");
372    // the 0's for unsuperposable positions propagate down the columns:
373  1 assertEquals(Arrays.toString(structs[0].pdbResNo),
374    "[0, 97, 98, 99, 100, 102]");
375  1 assertEquals(Arrays.toString(structs[1].pdbResNo),
376    "[0, 2, 0, 3, 4, 5]");
377  1 assertEquals(Arrays.toString(structs[2].pdbResNo),
378    "[0, 8, 0, 0, 10, 12]");
379    }
380   
 
381  1 toggle @Test(groups = { "Functional" })
382    public void testFindSuperposableResidues_hiddenColumn()
383    {
384  1 AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
385    .getHeight()];
386  5 for (int i = 0; i < structs.length; i++)
387    {
388  4 structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
389    "0");
390    }
391    /*
392    * initialise BitSet of 'superposable columns' to true (would be false for
393    * hidden columns)
394    */
395  1 BitSet matched = new BitSet();
396  7 for (int i = 0; i < al.getWidth(); i++)
397    {
398  6 matched.set(i);
399    }
400   
401    // treat column 5 of the alignment as hidden
402  1 matched.clear(4);
403   
404  1 int refStructure = testee.findSuperposableResidues(al, matched,
405    structs);
406   
407  1 assertEquals(refStructure, 0);
408   
409    // only ungapped, structure-mapped columns are not superposable
410  1 assertFalse(matched.get(0));
411  1 assertTrue(matched.get(1));
412  1 assertFalse(matched.get(2));
413  1 assertFalse(matched.get(3));
414  1 assertFalse(matched.get(4)); // superposable, but hidden, column
415  1 assertTrue(matched.get(5));
416    }
417   
 
418  1 toggle @Test(groups = { "Functional" })
419    public void testBuildColoursMap()
420    {
421    /*
422    * load these sequences, coloured by Strand propensity,
423    * with columns 2-4 hidden
424    */
425  1 String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS";
426  1 AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
427    DataSourceType.PASTE);
428  1 AlignmentI al = af.getViewport().getAlignment();
429  1 af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
430  1 ColumnSelection cs = new ColumnSelection();
431  1 cs.addElement(2);
432  1 cs.addElement(3);
433  1 cs.addElement(4);
434  1 af.getViewport().setColumnSelection(cs);
435  1 af.hideSelColumns_actionPerformed(null);
436  1 SequenceI seq1 = al.getSequenceAt(0);
437  1 SequenceI seq2 = al.getSequenceAt(1);
438  1 SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
439  1 PDBEntry[] pdbFiles = new PDBEntry[2];
440  1 pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
441  1 pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
442  1 StructureSelectionManager ssm = new StructureSelectionManager();
443   
444    /*
445    * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
446    */
447  1 HashMap<Integer, int[]> map = new HashMap<>();
448  11 for (int pos = 1; pos <= seq1.getLength(); pos++)
449    {
450  10 map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
451    }
452  1 StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
453    "A", map, null);
454  1 ssm.addStructureMapping(sm1);
455  1 StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
456    "B", map, null);
457  1 ssm.addStructureMapping(sm2);
458   
459  1 AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
460    af.alignPanel);
461   
462    /*
463    * method under test builds a map of structures residues by colour
464    * verify the map holds what it should
465    */
466  1 Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
467    af.alignPanel);
468  1 ChimeraCommands helper = new ChimeraCommands();
469   
470    /*
471    * M colour is #82827d (see strand.html help page)
472    * sequence residue 1 mapped to structure residue 21
473    */
474  1 Color mColor = new Color(0x82827d);
475  1 AtomSpecModel atomSpec = colours.get(mColor);
476  1 assertNotNull(atomSpec);
477  1 assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
478    "#0:21.A|#1:21.B");
479   
480    /*
481    * H colour is #60609f, seq1.2 mapped to structure 0 residue 22
482    */
483  1 Color hColor = new Color(0x60609f);
484  1 atomSpec = colours.get(hColor);
485  1 assertNotNull(atomSpec);
486  1 assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
487    "#0:22.A");
488   
489    /*
490    * V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
491    */
492  1 Color vColor = new Color(0xffff00);
493  1 atomSpec = colours.get(vColor);
494  1 assertNotNull(atomSpec);
495  1 assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
496    "#1:22.B");
497   
498    /*
499    * hidden columns are Gray (128, 128, 128)
500    * sequence positions 3-5 mapped to structure residues 23-25
501    */
502  1 Color gray = new Color(128, 128, 128);
503  1 atomSpec = colours.get(gray);
504  1 assertNotNull(atomSpec);
505  1 assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
506    "#0:23-25.A|#1:23-25.B");
507   
508    /*
509    * S and G are both coloured #4949b6, structure residues 26-30
510    */
511  1 Color sgColour = new Color(0x4949b6);
512  1 atomSpec = colours.get(sgColour);
513  1 assertNotNull(atomSpec);
514  1 assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
515    "#0:26-30.A|#1:26-30.B");
516    }
517    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 17:34:35 GMT using coverage data from Mon Nov 11 2024 17:34:16 GMT.
  • OpenClover is free and open-source software.