test/jalview/structure/StructureSelectionManagerTest.java

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