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