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