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  1. Project Clover database Thu Nov 7 2024 17:01:39 GMT
  2. Package jalview.structure

File StructureSelectionManagerTest.java

 

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24
167
9
1
499
350
23
0.14
18.56
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Classes

Class Line # Actions
StructureSelectionManagerTest 66 167 23
0.00%
 

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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.testng.Assert.assertNotNull;
25    import static org.testng.AssertJUnit.assertEquals;
26    import static org.testng.AssertJUnit.assertTrue;
27   
28    import java.util.ArrayList;
29    import java.util.LinkedHashMap;
30    import java.util.List;
31    import java.util.Map;
32    import java.util.SortedMap;
33    import java.util.TreeMap;
34   
35    import org.testng.Assert;
36    import org.testng.annotations.BeforeClass;
37    import org.testng.annotations.BeforeMethod;
38    import org.testng.annotations.Test;
39   
40    import jalview.analysis.AlignmentUtils;
41    import jalview.api.structures.JalviewStructureDisplayI;
42    import jalview.bin.Cache;
43    import jalview.datamodel.AlignedCodonFrame;
44    import jalview.datamodel.AlignmentAnnotation;
45    import jalview.datamodel.AlignmentI;
46    import jalview.datamodel.Annotation;
47    import jalview.datamodel.PDBEntry;
48    import jalview.datamodel.Sequence;
49    import jalview.datamodel.SequenceFeature;
50    import jalview.datamodel.SequenceI;
51    import jalview.ext.jmol.JmolCommands;
52    import jalview.gui.AlignFrame;
53    import jalview.gui.Desktop;
54    import jalview.gui.JvOptionPane;
55    import jalview.gui.SequenceRenderer;
56    import jalview.gui.StructureChooser;
57    import jalview.io.DataSourceType;
58    import jalview.io.FileLoader;
59    import jalview.io.Jalview2xmlBase;
60    import jalview.io.StructureFile;
61    import jalview.util.MapList;
62    import jalview.ws.DBRefFetcher;
63    import jalview.ws.sifts.SiftsSettings;
64   
65    @Test(singleThreaded = true)
 
66    public class StructureSelectionManagerTest extends Jalview2xmlBase
67    {
68   
 
69  0 toggle @Override
70    @BeforeClass(alwaysRun = true)
71    public void setUpJvOptionPane()
72    {
73  0 JvOptionPane.setInteractiveMode(false);
74  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
75    }
76   
77    private StructureSelectionManager ssm;
78   
 
79  0 toggle @BeforeMethod(alwaysRun = true)
80    public void setUp()
81    {
82  0 StructureImportSettings.setShowSeqFeatures(true);
83  0 ssm = new StructureSelectionManager();
84    }
85   
 
86  0 toggle @Test(groups = { "Functional" })
87    public void testRegisterMapping()
88    {
89  0 AlignedCodonFrame acf1 = new AlignedCodonFrame();
90  0 acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
91    new MapList(new int[]
92    { 1, 3 }, new int[] { 1, 1 }, 1, 1));
93  0 AlignedCodonFrame acf2 = new AlignedCodonFrame();
94  0 acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
95    new MapList(new int[]
96    { 1, 3 }, new int[] { 1, 1 }, 1, 1));
97   
98  0 ssm.registerMapping(acf1);
99  0 assertEquals(1, ssm.getSequenceMappings().size());
100  0 assertTrue(ssm.getSequenceMappings().contains(acf1));
101   
102  0 ssm.registerMapping(acf2);
103  0 assertEquals(2, ssm.getSequenceMappings().size());
104  0 assertTrue(ssm.getSequenceMappings().contains(acf1));
105  0 assertTrue(ssm.getSequenceMappings().contains(acf2));
106   
107    /*
108    * Re-adding the first mapping does nothing
109    */
110  0 ssm.registerMapping(acf1);
111  0 assertEquals(2, ssm.getSequenceMappings().size());
112  0 assertTrue(ssm.getSequenceMappings().contains(acf1));
113  0 assertTrue(ssm.getSequenceMappings().contains(acf2));
114    }
115   
 
116  0 toggle @Test(groups = { "Functional" })
117    public void testRegisterMappings()
118    {
119  0 AlignedCodonFrame acf1 = new AlignedCodonFrame();
120  0 acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
121    new MapList(new int[]
122    { 1, 3 }, new int[] { 1, 1 }, 1, 1));
123  0 AlignedCodonFrame acf2 = new AlignedCodonFrame();
124  0 acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
125    new MapList(new int[]
126    { 1, 3 }, new int[] { 1, 1 }, 1, 1));
127  0 AlignedCodonFrame acf3 = new AlignedCodonFrame();
128  0 acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
129    new MapList(new int[]
130    { 1, 3 }, new int[] { 1, 1 }, 1, 1));
131   
132  0 List<AlignedCodonFrame> set1 = new ArrayList<>();
133  0 set1.add(acf1);
134  0 set1.add(acf2);
135  0 List<AlignedCodonFrame> set2 = new ArrayList<>();
136  0 set2.add(acf2);
137  0 set2.add(acf3);
138   
139    /*
140    * Add both sets twice; each mapping should be added once only
141    */
142  0 ssm.registerMappings(set1);
143  0 ssm.registerMappings(set1);
144  0 ssm.registerMappings(set2);
145  0 ssm.registerMappings(set2);
146   
147  0 assertEquals(3, ssm.getSequenceMappings().size());
148  0 assertTrue(ssm.getSequenceMappings().contains(acf1));
149  0 assertTrue(ssm.getSequenceMappings().contains(acf2));
150  0 assertTrue(ssm.getSequenceMappings().contains(acf3));
151    }
152   
153    /**
154    * Verify that RESNUM sequence features are present after creating a PDB
155    * mapping
156    */
 
157  0 toggle @Test(groups = { "Functional" })
158    public void testSetMapping_seqFeatures()
159    {
160  0 SequenceI seq = new Sequence("1GAQ|B",
161    "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
162  0 StructureSelectionManager sm = new StructureSelectionManager();
163  0 sm.setProcessSecondaryStructure(true);
164  0 sm.setAddTempFacAnnot(true);
165  0 StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
166    new String[]
167    { null }, "examples/1gaq.txt", DataSourceType.FILE, null, null);
168  0 assertTrue(pmap != null);
169   
170  0 assertEquals(3, pmap.getSeqs().size());
171  0 assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
172  0 assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
173  0 assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
174   
175    /*
176    * Verify a RESNUM sequence feature in the PDBfile sequence
177    */
178  0 SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
179  0 assertEquals("RESNUM", sf.getType());
180  0 assertEquals("1gaq", sf.getFeatureGroup());
181  0 assertEquals("GLU: 19 1gaqA", sf.getDescription());
182   
183    /*
184    * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
185    * sequence
186    */
187  0 StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
188  0 sf = map.sequence.getSequenceFeatures().get(0);
189  0 assertEquals("RESNUM", sf.getType());
190  0 assertEquals("1gaq", sf.getFeatureGroup());
191  0 assertEquals("ALA: 1 1gaqB", sf.getDescription());
192    }
193   
194    /**
195    * Verify that RESNUM sequence features are present after creating a PDB
196    * mapping from a local file, then that everything stays in the same place
197    * when the file is viewed. The corner case is that 4IM2 is a fragment of a
198    * PDB file, which still includes the 'ID' field - a bug in Jalview 2.10.3
199    * causes features, annotation and positions to be remapped to the wrong place
200    * on viewing the structure
201    */
 
202  0 toggle @Test(groups = { "Network" })
203    public void testMapping_EqualsFeatures()
204    {
205    // for some reason 'BeforeMethod' (which should be inherited from
206    // Jalview2XmlBase isn't always called)...
207  0 if (Desktop.instance != null)
208  0 Desktop.instance.closeAll_actionPerformed(null);
209  0 try
210    {
211  0 Thread.sleep(200);
212    } catch (Exception foo)
213    {
214    }
215  0 ;
216  0 SequenceI seq = new Sequence("4IM2|A",
217    "LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
218  0 String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
219  0 StructureSelectionManager sm = new StructureSelectionManager();
220  0 sm.setProcessSecondaryStructure(true);
221  0 sm.setAddTempFacAnnot(true);
222  0 StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
223    new String[]
224    { null }, P4IM2_MISSING, DataSourceType.FILE, null, null);
225  0 assertTrue(pmap != null);
226   
227  0 assertEquals(1, pmap.getSeqs().size());
228  0 assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
229   
230  0 List<int[]> structuremap1 = new ArrayList<>(
231    sm.getMapping(P4IM2_MISSING)[0]
232    .getPDBResNumRanges(seq.getStart(), seq.getEnd()));
233   
234    /*
235    * Verify a RESNUM sequence feature in the PDBfile sequence
236    * LEU468 - start+0
237    * VAL479 - start+11
238    * MET486 - start+12
239    * GLY496 - start+13
240    * GLU516 - start+33 (last)
241    *
242    * Expect features and mapping to resolve to same residues.
243    * Also try creating a view and test again
244    *
245    */
246  0 String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET",
247    "486", "GLY", "496", "GLU", "516" };
248  0 int[] offset = new int[] { 0, 11, 12, 13, 33 };
249   
250  0 List<String> fdesc = new ArrayList<>();
251  0 for (int f = 0; f < feats.length; f += 2)
252    {
253  0 fdesc.add(feats[f] + ": " + feats[f + 1] + " 4im2A");
254    }
255  0 SequenceI pdbseq = pmap.getSeqs().get(0);
256  0 verifySeqFeats(pdbseq, offset, fdesc);
257   
258    /// Now load as a view
259   
260  0 AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
261    "examples/testdata/4IM2_missing.pdb", DataSourceType.FILE);
262  0 Desktop.addInternalFrame(alf, "examples/testdata/4IM2_missing.pdb", 800,
263    400);
264  0 AlignmentI pdbal = alf.getViewport().getAlignment();
265  0 SequenceI pdb_viewseq = pdbal.getSequenceAt(0);
266  0 assertEquals(pdb_viewseq.getSequenceAsString(),
267    seq.getSequenceAsString());
268    // verify the feature location on the sequence when pdb imported as an
269    // alignment
270  0 verifySeqFeats(pdb_viewseq, offset, fdesc);
271   
272  0 JalviewStructureDisplayI viewr = openStructureViaChooser(alf,
273    pdb_viewseq, "4IM2");
274   
275    // and check all is good with feature location still
276  0 verifySeqFeats(pdb_viewseq, offset, fdesc);
277   
278    // finally check positional mapping for sequence and structure
279  0 PDBEntry pdbe = seq.getPDBEntry("4IM2");
280  0 StructureSelectionManager apssm = alf.alignPanel
281    .getStructureSelectionManager();
282  0 StructureMapping[] smap = apssm.getMapping(pdbe.getFile());
283  0 assertNotNull(smap);
284  0 assertNotNull(smap[0]);
285    // find the last position in the alignment sequence - this is not
286    // 'SequenceI.getEnd()' - which gets the last PDBRESNUM rather than
287    // SequenceI.getStart() + number of residues in file...
288  0 int realSeqEnd = pdb_viewseq.findPosition(pdb_viewseq.getLength());
289  0 List<int[]> ranges = smap[0].getPDBResNumRanges(pdb_viewseq.getStart(),
290    realSeqEnd);
291  0 assertEquals(structuremap1.size(), ranges.size());
292  0 int tot_mapped = 0;
293  0 for (int p = 0; p < ranges.size(); p++)
294    {
295  0 assertArrayEquals(structuremap1.get(p), ranges.get(p));
296  0 tot_mapped += 1 + (structuremap1.get(p)[1] - structuremap1.get(p)[0]);
297    }
298   
299  0 assertEquals(pdb_viewseq.getLength(), tot_mapped);
300   
301  0 int lastmappedp = StructureMapping.UNASSIGNED_VALUE;
302  0 for (int rp = pdb_viewseq.getStart(), rpEnd = pdb_viewseq
303  0 .findPosition(pdb_viewseq.getLength() - 1); rp <= rpEnd; rp++)
304    {
305  0 int mappedp = smap[0].getPDBResNum(rp);
306  0 if (mappedp != StructureMapping.UNASSIGNED_VALUE)
307    {
308  0 tot_mapped--;
309  0 if (lastmappedp == mappedp)
310    {
311  0 Assert.fail("Duplicate mapped position at " + rp + " (dupe = "
312    + mappedp + ")");
313    }
314    }
315    }
316   
317  0 Assert.assertEquals(tot_mapped, 0,
318    "Different number of mapped residues compared to ranges of mapped residues");
319   
320    // positional mapping to atoms for color by structure is still wrong, even
321    // though panel looks correct.
322   
323  0 String[] smcr = new JmolCommands().colourBySequence(apssm,
324    new String[]
325    { pdbe.getFile() },
326    new SequenceI[][]
327    { new SequenceI[] { pdb_viewseq } },
328    new SequenceRenderer(alf.alignPanel.getAlignViewport()),
329    alf.alignPanel);
330    // Expected - all residues are white
331  0 for (String c : smcr)
332    {
333  0 assertTrue(c.contains("color[255,255,255]"));
334  0 System.out.println(c);
335    }
336    }
337   
 
338  0 toggle private void verifySeqFeats(SequenceI pdbseq, int[] offset,
339    List<String> fdesc)
340    {
341  0 for (int o = 0; o < offset.length; o++)
342    {
343  0 int res = pdbseq.findPosition(offset[o]);
344  0 List<SequenceFeature> sf = pdbseq.getFeatures().findFeatures(res, res,
345    "RESNUM");
346  0 assertEquals("Expected sequence feature at position " + res + "("
347    + offset[o] + ")", 1, sf.size());
348  0 assertEquals("Wrong description at " + res + "(" + offset[o] + ")",
349    fdesc.get(o), sf.get(0).getDescription());
350    }
351   
352    }
353   
 
354  0 toggle @Test(groups = { "Network" })
355    public void testAssociatedMappingToSubSeq() throws Exception
356    {
357   
358    // currently this test fails if trimming is enabled
359  0 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
360    Boolean.FALSE.toString());
361  0 String TEMP_FACTOR_AA = "Temperature Factor";
362  0 String PDBID = "4IM2";
363  0 String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n"
364    + "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n"
365    + "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n"
366    + "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n"
367    + "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n"
368    + "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n"
369    + "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n"
370    + "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n"
371    + "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n"
372    + "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n"
373    + "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n"
374    + "GGLRNVDCL";
375    /*
376    * annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
377    *
378    * Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
379    */
380  0 String FullLengthAnnot = "JALVIEW_ANNOTATION\n"
381    + "# Created: Mon Feb 05 15:30:20 GMT 2018\n"
382    + "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" + "\n" + "\n"
383    + "SEQUENCE_REF\tTBK1_HUMAN\n"
384    + "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"
385    + "\n" + "";
386  0 AlignFrame alf_full = new FileLoader(false)
387    .LoadFileWaitTillLoaded(FullLengthSeq, DataSourceType.PASTE);
388  0 alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE,
389    null, null);
390  0 AlignmentI al_full = alf_full.getViewport().getAlignment();
391  0 AlignmentAnnotation fullseq_tf = al_full
392    .findAnnotations(al_full.getSequences().get(0), null,
393    TEMP_FACTOR_AA)
394    .iterator().next();
395  0 assertNotNull(fullseq_tf);
396   
397    // getMappingFor
398    // AlignmentI al_full=alf_full.getViewport().getAlignment();
399    //
400    // // load 4IM2 (full length, SIFTS onto full alingnment)
401    // SiftsSettings.setMapWithSifts(true);
402    // StructureChooser schoose = new StructureChooser(selectedSeqs_full,
403    // seq_full,
404    // alf_full.getViewport().getAlignPanel());
405    // schoose.selectStructure(PDBID);
406    // schoose.ok_ActionPerformed();
407   
408  0 AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
409    ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
410    DataSourceType.PASTE);
411  0 Desktop.addInternalFrame(alf, "Foo", 800, 600);
412  0 ;
413  0 AlignmentI al = alf.getViewport().getAlignment();
414  0 SequenceI seq = al.getSequenceAt(0);
415  0 assertEquals(470, seq.getStart());
416    // load 4IM2 (full length, SIFTS)
417  0 SiftsSettings.setMapWithSifts(true);
418  0 StructureImportSettings.setProcessSecondaryStructure(true);
419  0 StructureImportSettings.setVisibleChainAnnotation(true);
420  0 JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq,
421    PDBID);
422   
423  0 AlignmentAnnotation subseq_tf = null;
424  0 assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
425   
426  0 if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
427    {
428    // FIXME JAL-2321 - don't see reference annotation on alignment the first
429    // time
430    // around
431  0 SortedMap<String, String> tipEntries = new TreeMap<>();
432  0 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
433   
434  0 AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
435    tipEntries, candidates, al);
436  0 AlignmentUtils.addReferenceAnnotations(candidates, al, null);
437    // FAILS BECAUSE LABEL HAS PDB ID STRING
438  0 if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
439    .hasNext())
440    {
441  0 Assert.fail(
442    "JAL-2321 or worse has occured. No secondary structure added to alignment.");
443    }
444    }
445  0 subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
446    .next();
447    // verify against annotation after loading 4IM2 to full length TBK1_HUMAN
448    // verify location of mapped residues
449    // verify location of secondary structure annotation
450    // Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
451    // GLU497 (helix),
452   
453    // check there is or is not a tempfactor for each mapped position, and that
454    // values are equal for those positions.
455  0 for (int p = seq.getStart(); p <= seq.getEnd(); p++)
456    {
457  0 Annotation orig, subseq;
458  0 orig = fullseq_tf.getAnnotationForPosition(p);
459  0 subseq = subseq_tf.getAnnotationForPosition(p);
460  0 if (orig == null)
461    {
462  0 Assert.assertNull(subseq,
463    "Expected no annotation transferred at position " + p);
464    }
465  0 ;
466  0 if (orig != null)
467    {
468  0 Assert.assertNotNull(subseq,
469    "Expected annotation transfer at position " + p);
470  0 assertEquals(orig.value, subseq.value);
471    }
472  0 ;
473   
474    }
475    }
476   
 
477  0 toggle private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,
478    SequenceI seq, String pDBID)
479    {
480   
481  0 SequenceI[] selectedSeqs = new SequenceI[] { seq };
482   
483  0 StructureChooser schoose = new StructureChooser(selectedSeqs, seq,
484    alf.getViewport().getAlignPanel());
485   
486  0 try
487    {
488  0 Thread.sleep(5000);
489    } catch (InterruptedException q)
490    {
491    }
492  0 ;
493  0 Assert.assertTrue(schoose.selectStructure(pDBID),
494    "Couldn't select structure via structure chooser: " + pDBID);
495  0 schoose.showStructures(true);
496  0 return schoose.getOpenedStructureViewer();
497    }
498   
499    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 17:02:19 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.