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