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.testng.Assert.assertNotNull;
  24 import static org.testng.AssertJUnit.assertEquals;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import jalview.analysis.AlignmentUtils;
  28 import jalview.datamodel.AlignedCodonFrame;
  29 import jalview.datamodel.AlignmentAnnotation;
  30 import jalview.datamodel.AlignmentI;
  31 import jalview.datamodel.Annotation;
  32 import jalview.datamodel.PDBEntry;
  33 import jalview.datamodel.Sequence;
  34 import jalview.datamodel.SequenceFeature;
  35 import jalview.datamodel.SequenceI;
  36 import jalview.gui.AlignFrame;
  37 import jalview.gui.Desktop;
  38 import jalview.gui.JvOptionPane;
  39 import jalview.gui.StructureChooser;
  40 import jalview.io.DataSourceType;
  41 import jalview.io.FileLoader;
  42 import jalview.io.Jalview2xmlBase;
  43 import jalview.io.StructureFile;
  44 import jalview.util.MapList;
  45 import jalview.ws.sifts.SiftsSettings;
  46
  47 import java.util.ArrayList;
  48 import java.util.LinkedHashMap;
  49 import java.util.List;
  50 import java.util.Map;
  51 import java.util.SortedMap;
  52 import java.util.TreeMap;
  53
  54 import org.testng.Assert;
  55 import org.testng.annotations.BeforeClass;
  56 import org.testng.annotations.BeforeMethod;
  57 import org.testng.annotations.Test;
  58
  59 public class StructureSelectionManagerTest extends Jalview2xmlBase
  60 {
  61
  62   @Override
  63   @BeforeClass(alwaysRun = true)
  64   public void setUpJvOptionPane()
  65   {
  66     JvOptionPane.setInteractiveMode(false);
  67     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  68   }
  69
  70   private StructureSelectionManager ssm;
  71
  72   @BeforeMethod(alwaysRun = true)
  73   public void setUp()
  74   {
  75     StructureImportSettings.setShowSeqFeatures(true);
  76     ssm = new StructureSelectionManager();
  77   }
  78
  79   @Test(groups = { "Functional" })
  80   public void testRegisterMapping()
  81   {
  82     AlignedCodonFrame acf1 = new AlignedCodonFrame();
  83     acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
  84             new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
  85     AlignedCodonFrame acf2 = new AlignedCodonFrame();
  86     acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
  87             new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
  88
  89     ssm.registerMapping(acf1);
  90     assertEquals(1, ssm.getSequenceMappings().size());
  91     assertTrue(ssm.getSequenceMappings().contains(acf1));
  92
  93     ssm.registerMapping(acf2);
  94     assertEquals(2, ssm.getSequenceMappings().size());
  95     assertTrue(ssm.getSequenceMappings().contains(acf1));
  96     assertTrue(ssm.getSequenceMappings().contains(acf2));
  97
  98     /*
  99      * Re-adding the first mapping does nothing
 100      */
 101     ssm.registerMapping(acf1);
 102     assertEquals(2, ssm.getSequenceMappings().size());
 103     assertTrue(ssm.getSequenceMappings().contains(acf1));
 104     assertTrue(ssm.getSequenceMappings().contains(acf2));
 105   }
 106
 107   @Test(groups = { "Functional" })
 108   public void testRegisterMappings()
 109   {
 110     AlignedCodonFrame acf1 = new AlignedCodonFrame();
 111     acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
 112             new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 113     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 114     acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
 115             new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 116     AlignedCodonFrame acf3 = new AlignedCodonFrame();
 117     acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
 118             new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 119
 120     List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
 121     set1.add(acf1);
 122     set1.add(acf2);
 123     List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
 124     set2.add(acf2);
 125     set2.add(acf3);
 126
 127     /*
 128      * Add both sets twice; each mapping should be added once only
 129      */
 130     ssm.registerMappings(set1);
 131     ssm.registerMappings(set1);
 132     ssm.registerMappings(set2);
 133     ssm.registerMappings(set2);
 134
 135     assertEquals(3, ssm.getSequenceMappings().size());
 136     assertTrue(ssm.getSequenceMappings().contains(acf1));
 137     assertTrue(ssm.getSequenceMappings().contains(acf2));
 138     assertTrue(ssm.getSequenceMappings().contains(acf3));
 139   }
 140
 141   /**
 142    * Verify that RESNUM sequence features are present after creating a PDB
 143    * mapping
 144    */
 145   @Test(groups = { "Functional" })
 146   public void testSetMapping_seqFeatures()
 147   {
 148     SequenceI seq = new Sequence(
 149             "1GAQ|B",
 150             "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
 151     StructureSelectionManager sm = new StructureSelectionManager();
 152     sm.setProcessSecondaryStructure(true);
 153     sm.setAddTempFacAnnot(true);
 154     StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
 155             new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
 156     assertTrue(pmap != null);
 157
 158     assertEquals(3, pmap.getSeqs().size());
 159     assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
 160     assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
 161     assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
 162
 163     /*
 164      * Verify a RESNUM sequence feature in the PDBfile sequence
 165      */
 166     SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures().get(0);
 167     assertEquals("RESNUM", sf.getType());
 168     assertEquals("1gaq", sf.getFeatureGroup());
 169     assertEquals("GLU:  19  1gaqA", sf.getDescription());
 170
 171     /*
 172      * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
 173      * sequence
 174      */
 175     StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
 176     sf = map.sequence.getSequenceFeatures().get(0);
 177     assertEquals("RESNUM", sf.getType());
 178     assertEquals("1gaq", sf.getFeatureGroup());
 179     assertEquals("ALA:   1  1gaqB", sf.getDescription());
 180   }
 181
 182   @Test(groups= {"Network"})
 183   public void testAssociatedMappingToSubSeq() throws Exception
 184   {
 185
 186     String TEMP_FACTOR_AA="Temperature Factor";
 187     String PDBID = "4IM2";
 188     String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" +
 189             "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" +
 190             "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" +
 191             "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" +
 192             "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" +
 193             "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" +
 194             "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" +
 195             "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" +
 196             "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" +
 197             "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" +
 198             "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" +
 199             "GGLRNVDCL";
 200     /*
 201      * annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
 202      *
 203      * Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
 204      */
 205     String FullLengthAnnot = "JALVIEW_ANNOTATION\n" +
 206             "# Created: Mon Feb 05 15:30:20 GMT 2018\n" +
 207             "\n" +
 208             "\n" +
 209             "SEQUENCE_REF\tTBK1_HUMAN\n"
 210             + "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"
 211             +
 212             "\n" +
 213             "";
 214     AlignFrame alf_full=new
 215      FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE);
 216     alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null);
 217     AlignmentI al_full = alf_full.getViewport().getAlignment();
 218     AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator()
 219             .next();
 220     assertNotNull(fullseq_tf);
 221
 222     // getMappingFor
 223     // AlignmentI al_full=alf_full.getViewport().getAlignment();
 224     //
 225     // // load 4IM2 (full length, SIFTS onto full alingnment)
 226     // SiftsSettings.setMapWithSifts(true);
 227     // StructureChooser schoose = new StructureChooser(selectedSeqs_full,
 228     // seq_full,
 229     // alf_full.getViewport().getAlignPanel());
 230     // schoose.selectStructure(PDBID);
 231     // schoose.ok_ActionPerformed();
 232
 233     AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
 234             ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
 235             DataSourceType.PASTE);
 236     Desktop.addInternalFrame(alf, "Foo", 800, 600);
 237     ;
 238     AlignmentI al = alf.getViewport().getAlignment();
 239     SequenceI seq = al.getSequenceAt(0);
 240     assertEquals(470, seq.getStart());
 241     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 242
 243     // load 4IM2 (full length, SIFTS)
 244     SiftsSettings.setMapWithSifts(true);
 245     StructureImportSettings.setProcessSecondaryStructure(true);
 246     StructureImportSettings.setVisibleChainAnnotation(true);
 247
 248     StructureChooser schoose = new StructureChooser(selectedSeqs, seq,
 249             alf.getViewport().getAlignPanel());
 250
 251     try
 252     {
 253       Thread.sleep(5000);
 254     } catch (InterruptedException q)
 255     {
 256     }
 257     ;
 258     schoose.selectStructure(PDBID);
 259     schoose.ok_ActionPerformed();
 260     try
 261     {
 262       Thread.sleep(10000);
 263     } catch (InterruptedException q)
 264     {
 265     }
 266     ;
 267
 268     AlignmentAnnotation subseq_tf=null;
 269     assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0);
 270
 271     if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
 272     {
 273       // FIXME JAL-2321 - don't see reference annotation on alignment the first
 274       // time
 275       // around
 276       SortedMap<String, String> tipEntries = new TreeMap<>();
 277       final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
 278
 279       AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
 280               tipEntries, candidates, al);
 281       AlignmentUtils.addReferenceAnnotations(candidates, al, null);
 282
 283       if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
 284               .hasNext())
 285       {
 286         Assert.fail(
 287                 "JAL-2321 or worse has occured. No secondary structure added to alignment.");
 288       }
 289     }
 290     subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
 291             .next();
 292     // verify against annotation after loading 4IM2 to full length TBK1_HUMAN
 293     // verify location of mapped residues
 294     // verify location of secondary structure annotation
 295     // Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
 296     // GLU497 (helix),
 297     PDBEntry pdbe = seq.getPDBEntry(PDBID);
 298     StructureMapping[] sm = alf.alignPanel.getStructureSelectionManager()
 299             .getMapping(pdbe.getFile());
 300     assertNotNull(sm);
 301     assertNotNull(sm[0]);
 302
 303     List<int[]> ranges = sm[0].getPDBResNumRanges(seq.getStart(),seq.getEnd());
 304     // check there is or is not a tempfactor for each mapped position, and that
 305     // values are equal for those positions.
 306     for (int p=seq.getStart();p<=seq.getEnd();p++)
 307     {
 308       Annotation orig,subseq;
 309       orig = fullseq_tf.getAnnotationForPosition(p);
 310       subseq = subseq_tf.getAnnotationForPosition(p);
 311       if (orig == null)
 312       {
 313         Assert.assertNull(subseq,
 314                 "Expected no annotation transferred at position " + p);
 315       }
 316       ;
 317       if (orig != null)
 318       {
 319         Assert.assertNotNull(subseq,
 320                 "Expected annotation transfer at position " + p);
 321         assertEquals(orig.value, subseq.value);
 322       }
 323       ;
 324
 325     }
 326
 327   }
 328
 329 }