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  1. Project Clover database Thu Dec 4 2025 16:11:35 GMT
  2. Package jalview.structure

File StructureSelectionManagerTest.java

 

Code metrics

40
200
11
1
593
427
33
0.17
18.18
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3

Classes

Class Line # Actions
StructureSelectionManagerTest 64 200 33
0.4541832845.4%
 

Contributing tests

This file is covered by 9 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.structure;
22   
23    import static org.junit.Assert.assertArrayEquals;
24    import static org.mockito.Mockito.*;
25    import static org.testng.Assert.assertNotNull;
26    import static org.testng.AssertJUnit.assertEquals;
27    import static org.testng.AssertJUnit.assertTrue;
28   
29    import java.util.*;
30   
31    import org.testng.Assert;
32    import org.testng.annotations.BeforeClass;
33    import org.testng.annotations.BeforeMethod;
34    import org.testng.annotations.DataProvider;
35    import org.testng.annotations.Test;
36   
37    import jalview.analysis.AlignmentUtils;
38    import jalview.api.structures.JalviewStructureDisplayI;
39    import jalview.bin.Cache;
40    import jalview.datamodel.AlignedCodonFrame;
41    import jalview.datamodel.AlignmentAnnotation;
42    import jalview.datamodel.AlignmentI;
43    import jalview.datamodel.Annotation;
44    import jalview.datamodel.PDBEntry;
45    import jalview.datamodel.Sequence;
46    import jalview.datamodel.SequenceFeature;
47    import jalview.datamodel.SequenceI;
48    import jalview.ext.jmol.JmolCommands;
49    import jalview.gui.AlignFrame;
50    import jalview.gui.Desktop;
51    import jalview.gui.JvOptionPane;
52    import jalview.gui.SequenceRenderer;
53    import jalview.gui.StructureChooser;
54    import jalview.io.DataSourceType;
55    import jalview.io.FileLoader;
56    import jalview.io.Jalview2xmlBase;
57    import jalview.io.StructureFile;
58    import jalview.util.Constants;
59    import jalview.util.MapList;
60    import jalview.ws.DBRefFetcher;
61    import jalview.ws.sifts.SiftsSettings;
62   
63    @Test(singleThreaded = true)
 
64    public class StructureSelectionManagerTest extends Jalview2xmlBase
65    {
66   
 
67  1 toggle @Override
68    @BeforeClass(alwaysRun = true)
69    public void setUpJvOptionPane()
70    {
71  1 JvOptionPane.setInteractiveMode(false);
72  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
73    }
74   
75    private StructureSelectionManager ssm;
76   
 
77  9 toggle @BeforeMethod(alwaysRun = true)
78    public void setUp()
79    {
80  9 StructureImportSettings.setShowSeqFeatures(true);
81  9 ssm = StructureSelectionManager.getStructureSelectionManager(null);
82  9 ssm.resetAll();
83    }
84   
 
85  1 toggle @Test(groups = { "Functional" })
86    public void testRegisterMapping()
87    {
88  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
89  1 acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
90    new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
91  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
92  1 acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
93    new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
94   
95  1 ssm.registerMapping(acf1);
96  1 assertEquals(1, ssm.getSequenceMappings().size());
97  1 assertTrue(ssm.getSequenceMappings().contains(acf1));
98   
99  1 ssm.registerMapping(acf2);
100  1 assertEquals(2, ssm.getSequenceMappings().size());
101  1 assertTrue(ssm.getSequenceMappings().contains(acf1));
102  1 assertTrue(ssm.getSequenceMappings().contains(acf2));
103   
104    /*
105    * Re-adding the first mapping does nothing
106    */
107  1 ssm.registerMapping(acf1);
108  1 assertEquals(2, ssm.getSequenceMappings().size());
109  1 assertTrue(ssm.getSequenceMappings().contains(acf1));
110  1 assertTrue(ssm.getSequenceMappings().contains(acf2));
111    }
112   
 
113  1 toggle @Test(groups = { "Functional" })
114    public void testRegisterMappings()
115    {
116  1 AlignedCodonFrame acf1 = new AlignedCodonFrame();
117  1 acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
118    new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
119  1 AlignedCodonFrame acf2 = new AlignedCodonFrame();
120  1 acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
121    new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
122  1 AlignedCodonFrame acf3 = new AlignedCodonFrame();
123  1 acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
124    new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
125   
126  1 List<AlignedCodonFrame> set1 = new ArrayList<>();
127  1 set1.add(acf1);
128  1 set1.add(acf2);
129  1 List<AlignedCodonFrame> set2 = new ArrayList<>();
130  1 set2.add(acf2);
131  1 set2.add(acf3);
132   
133    /*
134    * Add both sets twice; each mapping should be added once only
135    */
136  1 ssm.registerMappings(set1);
137  1 ssm.registerMappings(set1);
138  1 ssm.registerMappings(set2);
139  1 ssm.registerMappings(set2);
140   
141  1 List<AlignedCodonFrame> mappings = ssm.getSequenceMappings();
142  1 assertEquals(3, mappings.size());
143  1 assertTrue(mappings.contains(acf1));
144  1 assertTrue(mappings.contains(acf2));
145  1 assertTrue(mappings.contains(acf3));
146    }
147   
148    /**
149    * Verify that RESNUM sequence features are present after creating a PDB
150    * mapping
151    */
 
152  1 toggle @Test(groups = { "Functional" })
153    public void testSetMapping_seqFeatures()
154    {
155  1 SequenceI seq = new Sequence(
156    "1GAQ|B",
157    "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
158  1 StructureSelectionManager sm = StructureSelectionManager.getStructureSelectionManager(null);
159  1 sm.setProcessSecondaryStructure(true);
160  1 sm.setAddTempFacAnnot(true);
161  1 StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
162    new String[]
163    { null }, "examples/1gaq.txt", DataSourceType.FILE, null, null);
164  1 assertTrue(pmap != null);
165   
166  1 assertEquals(3, pmap.getSeqs().size());
167  1 assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
168  1 assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
169  1 assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
170   
171    /*
172    * Verify a RESNUM sequence feature in the PDBfile sequence
173    */
174  1 SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
175  1 assertEquals("RESNUM", sf.getType());
176  1 assertEquals("1gaq", sf.getFeatureGroup());
177  1 assertEquals("GLU: 19 1gaqA", sf.getDescription());
178   
179    /*
180    * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
181    * sequence
182    */
183  1 StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
184  1 sf = map.sequence.getSequenceFeatures().get(0);
185  1 assertEquals("RESNUM", sf.getType());
186  1 assertEquals("1gaq", sf.getFeatureGroup());
187  1 assertEquals("ALA: 1 1gaqB", sf.getDescription());
188    }
189   
190    /**
191    * Verify that RESNUM sequence features are present after creating a PDB
192    * mapping from a local file, then that everything stays in the same place
193    * when the file is viewed. The corner case is that 4IM2 is a fragment of a
194    * PDB file, which still includes the 'ID' field - a bug in Jalview 2.10.3
195    * causes features, annotation and positions to be remapped to the wrong place
196    * on viewing the structure
197    */
 
198  0 toggle @Test(groups = { "Network" })
199    public void testMapping_EqualsFeatures()
200    {
201    // for some reason 'BeforeMethod' (which should be inherited from
202    // Jalview2XmlBase isn't always called)...
203  0 Desktop.getInstance().closeAll_actionPerformed(null);
204  0 try {
205  0 Thread.sleep(200);
206  0 } catch (Exception foo) {};
207  0 SequenceI seq = new Sequence("4IM2|A",
208    "LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
209  0 String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
210  0 StructureSelectionManager sm = StructureSelectionManager.getStructureSelectionManager(null);
211  0 sm.setProcessSecondaryStructure(true);
212  0 sm.setAddTempFacAnnot(true);
213  0 StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
214    new String[]
215    { null }, P4IM2_MISSING, DataSourceType.FILE, null, null);
216  0 assertTrue(pmap != null);
217   
218  0 assertEquals(1, pmap.getSeqs().size());
219  0 assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
220   
221  0 List<int[]> structuremap1 = new ArrayList<>(
222    sm.getMapping(P4IM2_MISSING)[0]
223    .getPDBResNumRanges(seq.getStart(), seq.getEnd()));
224   
225    /*
226    * Verify a RESNUM sequence feature in the PDBfile sequence
227    * LEU468 - start+0
228    * VAL479 - start+11
229    * MET486 - start+12
230    * GLY496 - start+13
231    * GLU516 - start+33 (last)
232    *
233    * Expect features and mapping to resolve to same residues.
234    * Also try creating a view and test again
235    *
236    */
237  0 String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET",
238    "486", "GLY", "496", "GLU", "516" };
239  0 int[] offset = new int[] { 0, 11, 12, 13, 33 };
240   
241  0 List<String> fdesc = new ArrayList<>();
242  0 for (int f = 0; f < feats.length; f += 2)
243    {
244  0 fdesc.add(feats[f] + ": " + feats[f + 1] + " 4im2A");
245    }
246  0 SequenceI pdbseq = pmap.getSeqs().get(0);
247  0 verifySeqFeats(pdbseq, offset, fdesc);
248   
249    /// Now load as a view
250   
251  0 AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
252    "examples/testdata/4IM2_missing.pdb", DataSourceType.FILE);
253  0 Desktop.addInternalFrame(alf, "examples/testdata/4IM2_missing.pdb", 800,
254    400);
255  0 AlignmentI pdbal = alf.getViewport().getAlignment();
256  0 SequenceI pdb_viewseq = pdbal.getSequenceAt(0);
257  0 assertEquals(pdb_viewseq.getSequenceAsString(),
258    seq.getSequenceAsString());
259    // verify the feature location on the sequence when pdb imported as an
260    // alignment
261  0 verifySeqFeats(pdb_viewseq, offset, fdesc);
262   
263   
264  0 JalviewStructureDisplayI viewr = openStructureViaChooser(alf,
265    pdb_viewseq, "4IM2");
266   
267    // and check all is good with feature location still
268  0 verifySeqFeats(pdb_viewseq, offset, fdesc);
269   
270    // finally check positional mapping for sequence and structure
271  0 PDBEntry pdbe = seq.getPDBEntry("4IM2");
272  0 StructureSelectionManager apssm = alf.alignPanel
273    .getStructureSelectionManager();
274  0 StructureMapping[] smap = apssm
275    .getMapping(pdbe.getFile());
276  0 assertNotNull(smap);
277  0 assertNotNull(smap[0]);
278    // find the last position in the alignment sequence - this is not
279    // 'SequenceI.getEnd()' - which gets the last PDBRESNUM rather than
280    // SequenceI.getStart() + number of residues in file...
281  0 int realSeqEnd = pdb_viewseq.findPosition(pdb_viewseq.getLength());
282  0 List<int[]> ranges = smap[0].getPDBResNumRanges(pdb_viewseq.getStart(),
283    realSeqEnd);
284  0 assertEquals(structuremap1.size(), ranges.size());
285  0 int tot_mapped = 0;
286  0 for (int p = 0; p < ranges.size(); p++)
287    {
288  0 assertArrayEquals(structuremap1.get(p), ranges.get(p));
289  0 tot_mapped += 1 + (structuremap1.get(p)[1] - structuremap1.get(p)[0]);
290    }
291   
292  0 assertEquals(pdb_viewseq.getLength(), tot_mapped);
293   
294  0 int lastmappedp = StructureMapping.UNASSIGNED_VALUE;
295  0 for (int rp = pdb_viewseq.getStart(), rpEnd = pdb_viewseq
296  0 .findPosition(pdb_viewseq.getLength() - 1); rp <= rpEnd; rp++)
297    {
298  0 int mappedp = smap[0].getPDBResNum(rp);
299  0 if (mappedp != StructureMapping.UNASSIGNED_VALUE)
300    {
301  0 tot_mapped--;
302  0 if (lastmappedp == mappedp)
303    {
304  0 Assert.fail("Duplicate mapped position at " + rp + " (dupe = "
305    + mappedp + ")");
306    }
307    }
308    }
309   
310  0 Assert.assertEquals(tot_mapped, 0,
311    "Different number of mapped residues compared to ranges of mapped residues");
312   
313    // positional mapping to atoms for color by structure is still wrong, even
314    // though panel looks correct.
315   
316  0 String[] smcr = new JmolCommands().colourBySequence(apssm,
317    new String[]
318    { pdbe.getFile() },
319    new SequenceI[][]
320    { new SequenceI[] { pdb_viewseq } },
321    new SequenceRenderer(alf.alignPanel.getAlignViewport()),
322    alf.alignPanel);
323    // Expected - all residues are white
324  0 for (String c : smcr)
325    {
326  0 assertTrue(c.contains("color[255,255,255]"));
327  0 System.out.println(c);
328    }
329    }
330   
 
331  0 toggle private void verifySeqFeats(SequenceI pdbseq, int[] offset,
332    List<String> fdesc)
333    {
334  0 for (int o = 0; o < offset.length; o++)
335    {
336  0 int res = pdbseq.findPosition(offset[o]);
337  0 List<SequenceFeature> sf = pdbseq.getFeatures().findFeatures(res, res,
338    "RESNUM");
339  0 assertEquals("Expected sequence feature at position " + res + "("
340    + offset[o] + ")", 1, sf.size());
341  0 assertEquals("Wrong description at " + res + "(" + offset[o] + ")",
342    fdesc.get(o), sf.get(0).getDescription());
343    }
344   
345    }
346   
 
347  0 toggle @Test(groups = { "Network" })
348    public void testAssociatedMappingToSubSeq() throws Exception
349    {
350   
351    // currently this test fails if trimming is enabled
352  0 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
353    Boolean.FALSE.toString());
354  0 String TEMP_FACTOR_AA="Temperature Factor";
355  0 String PDBID = "4IM2";
356  0 String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" +
357    "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" +
358    "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" +
359    "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" +
360    "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" +
361    "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" +
362    "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" +
363    "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" +
364    "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" +
365    "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" +
366    "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" +
367    "GGLRNVDCL";
368    /*
369    * annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
370    *
371    * Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
372    */
373  0 String FullLengthAnnot = "JALVIEW_ANNOTATION\n" +
374    "# Created: Mon Feb 05 15:30:20 GMT 2018\n" +
375    "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" +
376    "\n" +
377    "\n" +
378    "SEQUENCE_REF\tTBK1_HUMAN\n"
379    + "LINE_GRAPH\tTemperature Factor\tTemperature Factor for 4im2A\t125.22|128.51|120.35|113.12|122.6|114.44|91.49|102.53|98.22|111.41|111.32|116.64|103.55|100.53|95.07|105.55|114.76|128.29|133.55|142.14|121.12|110.36|95.79|95.39|87.14|99.56|93.55|94.21|100.33|110.68|97.85|82.37|75.87|76.53|77.85|82.49|80.92|96.88|122.58|133.31|160.15|180.51|||||242.88|258.97|247.01|227.12|223.24|211.62|184.65|183.51|168.96|160.04|150.88|131.68|130.43|139.87|148.59|136.57|125.7|96.51|74.49|74.08|85.87|70.93|86.47|101.59|97.51|97.39|117.19|114.27|129.5|112.98|147.52|170.26|154.98|168.18|157.51|131.95|105.85|97.78|97.35|76.51|76.31|72.55|71.43|78.82|79.94|75.04|79.54|77.95|83.56|88.5|71.51|71.73|75.96|82.36|81.75|66.51|67.23|69.35|67.92|54.75|71.19|61.85|65.34|67.97|64.51|67.41|62.28|72.85|72.76|70.64|65.23|71.07|67.73|87.72|64.93|75.92|94.02|99.35|93.71|103.59|106.29|115.46|118.69|147.18|130.62|171.64|158.95|164.11||107.42|88.53|83.52|88.06|94.06|80.82|59.01|59.73|78.89|69.21|70.34|81.95|74.53|60.92|64.65|55.79|75.71|68.86|70.95|75.08|87.76|85.43|105.84|||||||||||||||||137.46|151.33|145.17|122.79|111.56|126.72|124.06|161.75|176.84|180.51|198.49|196.75|187.41||195.23|202.27|203.16|226.55|221.75|193.83||||||172.33|177.97|151.47|132.65|99.22|93.7|91.15|88.24|72.35|70.05|70.0|74.92|66.51|68.37|65.76|70.12|74.97|76.89|80.83|70.21|69.48|79.54|82.65|96.54|114.31|140.46|168.51|176.99|205.08|209.27|155.83|139.41|151.3|129.33|111.31|119.62|121.37|102.26|115.39|129.97|128.65|110.38|110.66|116.1|82.53|84.02|82.17|87.63|86.42|77.23|91.23|95.53|102.21|120.73|133.26|109.67|108.49|93.25|92.85|86.39|95.66|94.92|85.82|80.13|76.17|86.61|78.9|77.97|105.6|70.66|69.35|78.94|66.68|63.03|69.91|79.05|75.43|70.73|70.02|80.57|81.74|77.99|84.1|91.66|92.42|94.03|116.47|132.01|154.55|163.99|161.37|155.23|132.78|109.3|90.38|101.83|99.61|91.68|82.77|86.12|82.73|90.13|85.14|79.54|74.27|74.06|72.88|86.34|72.0|69.32|60.9|68.15|52.99|63.53|61.3|66.01|68.28|77.41|71.52|67.18|66.17|71.51|65.47|52.63|65.08|66.37|73.76|77.79|67.58|79.53|84.75|87.42|78.9|79.19|85.57|73.67|80.56|86.19|72.17|66.27|72.8|86.28|78.89|74.5|90.6|80.42|92.5|92.84|96.18|92.08|88.5|87.25|64.6|68.95|65.56|67.55|71.62|78.24|84.95|71.35|86.41|84.73|94.41|95.09|84.74|87.64|88.85|75.1|86.42|79.28|73.14|78.54|80.81|60.66|67.93|71.64|59.85|64.7|61.22|63.84|65.9|62.18|74.95|72.92|93.37|90.47|96.0|93.8|88.46|79.78|83.4|66.55|68.7|73.2|78.76|85.67|84.8|89.59|96.52|79.53|103.51|134.72|126.7|145.31|156.17|149.35|128.48|117.29|118.98|131.59|109.36|90.39|87.68|91.81|78.77|80.11|91.39|75.57|78.98|71.53|76.85|70.9|64.71|73.55|73.45|60.0|69.92|57.89|69.07|66.45|62.85|57.83|57.89|66.4|61.61|60.85|66.47|63.53|63.84|65.96|73.06|70.82|64.51|63.66|73.37|73.59|68.09|78.93|76.99|75.05|71.32|88.4|78.88|93.08|110.61|94.32|99.24|128.99|129.49|132.74|124.21|120.32|142.06|166.41|149.87|153.29|172.19|165.89|181.6|223.11|237.73|176.41|171.09|189.65|188.61|154.84|142.72|154.25|170.99|175.65|||||||110.61||||||||||158.07|170.73|167.93|198.47|212.36|181.71|157.69|163.31|138.96|120.29|131.63|152.26|125.06|136.66|148.97|129.68|120.52|135.31|136.05|119.39|124.18|128.94|123.02|103.37|128.44|134.12|118.88|120.94|130.38|124.67|112.21|113.69|123.65|132.06|114.97|110.75|92.38|101.2|103.25|94.84|85.3|82.19|89.81|98.81|83.03|68.91|65.24|70.31|63.49|86.38|71.07|62.65|63.95|66.98|58.06|68.28|62.11|63.86|67.4|68.69|69.57|68.03|74.23|75.66|70.67|81.08|81.31|82.49|88.15|95.99|92.97|100.01|113.18|122.37|110.99|122.19|159.27|147.74|133.96|111.2|115.64|126.55|107.15|102.85|117.06|116.56|109.55|96.82|98.92|96.53|86.0|88.11|92.76|85.77|79.41|93.06|86.96|76.35|72.37|74.19|68.6|67.46|74.47|76.25|66.73|73.18|75.2|88.21|84.93|75.04|71.09|82.6|80.03|76.22|75.76|83.72|75.85|79.36|90.35|86.9|78.24|95.64|97.38|86.41|85.02|91.87|87.36|77.56|81.25|91.66|83.65|77.67|85.07|89.21|92.66|92.46|89.0|100.83|96.71|94.81|101.37|111.28|124.48|119.73|127.81|134.41|132.4|140.32|140.86|166.52|160.16|168.39|176.74|174.63|172.86|168.55|155.9|132.71|113.44|113.49|123.9|151.11|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
380    +
381    "\n" +
382    "";
383  0 AlignFrame alf_full=new
384    FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE);
385  0 alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null);
386  0 AlignmentI al_full = alf_full.getViewport().getAlignment();
387  0 AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator()
388    .next();
389  0 assertNotNull(fullseq_tf);
390   
391    // getMappingFor
392    // AlignmentI al_full=alf_full.getViewport().getAlignment();
393    //
394    // // load 4IM2 (full length, SIFTS onto full alingnment)
395    // SiftsSettings.setMapWithSifts(true);
396    // StructureChooser schoose = new StructureChooser(selectedSeqs_full,
397    // seq_full,
398    // alf_full.getViewport().getAlignPanel());
399    // schoose.selectStructure(PDBID);
400    // schoose.ok_ActionPerformed();
401   
402  0 AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
403    ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
404    DataSourceType.PASTE);
405  0 Desktop.addInternalFrame(alf, "Foo", 800, 600);
406  0 ;
407  0 AlignmentI al = alf.getViewport().getAlignment();
408  0 SequenceI seq = al.getSequenceAt(0);
409  0 assertEquals(470, seq.getStart());
410    // load 4IM2 (full length, SIFTS)
411  0 SiftsSettings.setMapWithSifts(true);
412  0 StructureImportSettings.setProcessSecondaryStructure(true);
413  0 StructureImportSettings.setVisibleChainAnnotation(true);
414  0 JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq,
415    PDBID);
416   
417  0 AlignmentAnnotation subseq_tf=null;
418  0 assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
419   
420  0 if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
421    {
422    // FIXME JAL-2321 - don't see reference annotation on alignment the first
423    // time
424    // around
425  0 SortedMap<String, String> tipEntries = new TreeMap<>();
426  0 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
427   
428  0 AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
429    tipEntries, candidates, al);
430  0 AlignmentUtils.addReferenceAnnotations(candidates, al, null);
431    // FAILS BECAUSE LABEL HAS PDB ID STRING
432  0 if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
433    .hasNext())
434    {
435  0 Assert.fail(
436    "JAL-2321 or worse has occured. No secondary structure added to alignment.");
437    }
438    }
439  0 subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
440    .next();
441    // verify against annotation after loading 4IM2 to full length TBK1_HUMAN
442    // verify location of mapped residues
443    // verify location of secondary structure annotation
444    // Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
445    // GLU497 (helix),
446   
447    // check there is or is not a tempfactor for each mapped position, and that
448    // values are equal for those positions.
449  0 for (int p=seq.getStart();p<=seq.getEnd();p++)
450    {
451  0 Annotation orig,subseq;
452  0 orig = fullseq_tf.getAnnotationForPosition(p);
453  0 subseq = subseq_tf.getAnnotationForPosition(p);
454  0 if (orig == null)
455    {
456  0 Assert.assertNull(subseq,
457    "Expected no annotation transferred at position " + p);
458    }
459  0 ;
460  0 if (orig != null)
461    {
462  0 Assert.assertNotNull(subseq,
463    "Expected annotation transfer at position " + p);
464  0 assertEquals(orig.value, subseq.value);
465    }
466  0 ;
467   
468    }
469    }
470   
 
471  0 toggle private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,
472    SequenceI seq,
473    String pDBID)
474    {
475   
476  0 SequenceI[] selectedSeqs = new SequenceI[] { seq };
477   
478  0 StructureChooser schoose = new StructureChooser(selectedSeqs, seq,
479    alf.getViewport().getAlignPanel());
480   
481  0 try
482    {
483  0 Thread.sleep(5000);
484    } catch (InterruptedException q)
485    {
486    }
487  0 ;
488  0 Assert.assertTrue(schoose.selectStructure(pDBID),
489    "Couldn't select structure via structure chooser: " + pDBID);
490  0 schoose.showStructures(true);
491  0 return schoose.getOpenedStructureViewer();
492    }
493   
 
494  1 toggle @DataProvider(name = "annotationProviderData")
495    public Object[][] annotationProviderData()
496    {
497  1 return new Object[][] {
498    { null, "desc", true, true, true, false, false }, // null PDB path
499    { "file.pdb", "desc", false, true, true, false, false }, // no pdb seq
500    { "file.pdb", "desc", true, false, true, false, false }, // no PDB entry
501    { "file.pdb", "desc", true, true, false, false, false }, // mismatched
502    // desc
503    { "file.pdb", "desc", true, true, true, true, false }, // valid provider
504    { "file.pdb", "desc", true, true, true, false, true }, // already has
505    // provider
506    };
507    }
508   
 
509  6 toggle @Test(dataProvider = "annotationProviderData", groups = { "Functional" })
510    public void testSaveAnnotationProvider(String pdbFilePath,
511    String ssAnnotDescriptionInPDB, boolean pdbSeqNotNull,
512    boolean pdbEntryNotNull, boolean sameDescInPDB,
513    boolean providerAvailableInPDBEntry,
514    boolean providerAlreadyPresent)
515    {
516   
517  6 SequenceI seq = mock(SequenceI.class);
518  6 SequenceI datasetSeq = mock(SequenceI.class);
519  6 StructureFile pdb = mock(StructureFile.class);
520  6 when(seq.getDatasetSequence()).thenReturn(datasetSeq);
521  6 when(pdb.getInFile()).thenReturn(pdbFilePath);
522   
523    // PDBEntry and datasequence object
524  6 if (pdbSeqNotNull)
525    {
526  5 SequenceI pdbSeq = mock(SequenceI.class);
527  5 AlignmentAnnotation pdbAnnotation = new AlignmentAnnotation(
528    "Secondary Structure", ssAnnotDescriptionInPDB,
529    new Annotation[] {});
530  5 AlignmentAnnotation[] pdbAnnotations = new AlignmentAnnotation[] {
531    pdbAnnotation };
532  5 when(pdbSeq.getAnnotation(Constants.SS_ANNOTATION_LABEL))
533    .thenReturn(pdbAnnotations);
534  5 Vector<SequenceI> pdbSeqs = new Vector<>();
535  5 pdbSeqs.add(pdbSeq);
536  5 when(pdb.getSeqs()).thenReturn(pdbSeqs);
537    }
538    else
539    {
540  1 when(pdb.getSeqs()).thenReturn(null);
541    }
542   
543  6 if (pdbEntryNotNull)
544    {
545  5 PDBEntry entry = mock(PDBEntry.class);
546  5 when(entry.getFile()).thenReturn("file.pdb");
547  5 when(entry.getProvider()).thenReturn("myprovider");
548   
549  5 Vector<PDBEntry> entries = new Vector<>();
550  5 entries.add(entry);
551  5 when(datasetSeq.getAllPDBEntries()).thenReturn(entries);
552    }
553    else
554    {
555  1 when(datasetSeq.getAllPDBEntries()).thenReturn(null);
556    }
557   
558    // Dataset annotation
559  6 AlignmentAnnotation datasetAnnotation = new AlignmentAnnotation(
560    "Secondary Structure", "", new Annotation[] {});
561  6 datasetAnnotation.description = sameDescInPDB ? ssAnnotDescriptionInPDB
562    : "desc2";
563  6 if (providerAlreadyPresent)
564    {
565  1 datasetAnnotation.setProperty(Constants.SS_PROVIDER_PROPERTY,
566    "myprovider2");
567    }
568   
569  6 when(datasetSeq.getAnnotation(Constants.SS_ANNOTATION_LABEL))
570    .thenReturn(new AlignmentAnnotation[]
571    { datasetAnnotation });
572   
573    // Call method
574  6 ssm.saveAnnotationProvider(pdb, seq);
575   
576    // Assert
577  6 Object result = datasetAnnotation
578    .getProperty(Constants.SS_PROVIDER_PROPERTY);
579  6 if (providerAvailableInPDBEntry)
580    {
581  1 assert "myprovider".equals(result) : "Result should be myprovider";
582    }
583  5 else if (providerAlreadyPresent)
584    {
585  1 assert "myprovider2".equals(result) : "Result should be myprovider2";
586    }
587    else
588    {
589  4 assert result == null : "Result should be null";
590    }
591    }
592   
593    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.