test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java

   1 package jalview.renderer.seqfeatures;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertFalse;
   5 import static org.testng.Assert.assertNotEquals;
   6 import static org.testng.Assert.assertNull;
   7 import static org.testng.Assert.assertTrue;
   8
   9 import jalview.api.FeatureColourI;
  10 import jalview.datamodel.SequenceFeature;
  11 import jalview.datamodel.SequenceI;
  12 import jalview.gui.AlignFrame;
  13 import jalview.gui.AlignViewport;
  14 import jalview.gui.FeatureRenderer;
  15 import jalview.io.DataSourceType;
  16 import jalview.io.FileLoader;
  17 import jalview.schemes.FeatureColour;
  18 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  19
  20 import java.awt.Color;
  21 import java.util.List;
  22
  23 import org.testng.annotations.BeforeMethod;
  24 import org.testng.annotations.BeforeTest;
  25 import org.testng.annotations.Test;
  26
  27 /**
  28  * Unit tests for feature colour determination, including but not limited to
  29  * <ul>
  30  * <li>gap position</li>
  31  * <li>no features present</li>
  32  * <li>features present but show features turned off</li>
  33  * <li>features displayed but selected feature turned off</li>
  34  * <li>features displayed but feature group turned off</li>
  35  * <li>feature displayed but none at the specified position</li>
  36  * <li>multiple features at position, with no transparency</li>
  37  * <li>multiple features at position, with transparency</li>
  38  * <li>score graduated feature colour</li>
  39  * <li>contact feature start at the selected position</li>
  40  * <li>contact feature end at the selected position</li>
  41  * <li>contact feature straddling the selected position (not shown)</li>
  42  * </ul>
  43  */
  44 public class FeatureColourFinderTest
  45 {
  46   private AlignViewport av;
  47
  48   private SequenceI seq;
  49
  50   private FeatureColourFinder finder;
  51
  52   private AlignFrame af;
  53
  54   private FeatureRenderer fr;
  55
  56   @BeforeTest(alwaysRun = true)
  57   public void setUp()
  58   {
  59     // aligned column 8 is sequence position 6
  60     String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
  61     af = new FileLoader().LoadFileWaitTillLoaded(s,
  62             DataSourceType.PASTE);
  63     av = af.getViewport();
  64     seq = av.getAlignment().getSequenceAt(0);
  65     fr = af.getFeatureRenderer();
  66     finder = new FeatureColourFinder(fr);
  67   }
  68
  69   /**
  70    * Clear down any sequence features before each test (not as easy as it
  71    * sounds...)
  72    */
  73   @BeforeMethod(alwaysRun = true)
  74   public void setUpBeforeTest()
  75   {
  76     List<SequenceFeature> sfs = seq.getSequenceFeatures();
  77     for (SequenceFeature sf : sfs)
  78     {
  79       seq.deleteFeature(sf);
  80     }
  81     fr.findAllFeatures(true);
  82
  83     /*
  84      * reset all feature groups to visible
  85      */
  86     for (String group : fr.getGroups(false))
  87     {
  88       fr.setGroupVisibility(group, true);
  89     }
  90
  91     fr.clearRenderOrder();
  92     av.setShowSequenceFeatures(true);
  93   }
  94
  95   @Test(groups = "Functional")
  96   public void testFindFeatureColour_noFeatures()
  97   {
  98     av.setShowSequenceFeatures(false);
  99     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 100     assertEquals(c, Color.blue);
 101
 102     av.setShowSequenceFeatures(true);
 103     c = finder.findFeatureColour(Color.blue, seq, 10);
 104     assertEquals(c, Color.blue);
 105   }
 106
 107   @Test(groups = "Functional")
 108   public void testFindFeatureColour_noFeaturesShown()
 109   {
 110     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 111             Float.NaN, "MetalGroup"));
 112     fr.featuresAdded();
 113     fr.setColour("Metal",  new FeatureColour(Color.red));
 114
 115     /*
 116      * global show features flag is _not_ checked by findFeatureColour
 117      */
 118     av.setShowSequenceFeatures(false);
 119     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 120     assertEquals(c, Color.red);
 121   }
 122
 123   @Test(groups = "Functional")
 124   public void testFindFeatureColour_singleFeatureAtPosition()
 125   {
 126     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 127             Float.NaN, "MetalGroup"));
 128     fr.setColour("Metal", new FeatureColour(Color.red));
 129     fr.featuresAdded();
 130     av.setShowSequenceFeatures(true);
 131     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 132     assertEquals(c, Color.red);
 133   }
 134
 135   /**
 136    * feature colour at a gap is null (not white) - a user defined colour scheme
 137    * can then provide a bespoke gap colour if configured to do so
 138    */
 139   @Test(groups = "Functional")
 140   public void testFindFeatureColour_gapPosition()
 141   {
 142     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
 143             null));
 144     fr.setColour("Metal", new FeatureColour(Color.red));
 145     fr.featuresAdded();
 146     av.setShowSequenceFeatures(true);
 147     Color c = finder.findFeatureColour(null, seq, 6);
 148     assertNull(c);
 149   }
 150
 151   @Test(groups = "Functional")
 152   public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
 153   {
 154     /*
 155      * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
 156      * new features 'on top' (but reverses the order of any added features)
 157      */
 158     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 159             Float.NaN, "MetalGroup"));
 160     FeatureColour red = new FeatureColour(Color.red);
 161     fr.setColour("Metal", red);
 162     fr.featuresAdded();
 163     seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
 164             Float.NaN, "DomainGroup"));
 165     FeatureColour green = new FeatureColour(Color.green);
 166     fr.setColour("Domain", green);
 167     fr.featuresAdded();
 168     av.setShowSequenceFeatures(true);
 169
 170     /*
 171      * expect Domain (green) to be rendered above Metal (red)
 172      */
 173     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 174     assertEquals(c, Color.green);
 175
 176     /*
 177      * now promote Metal above Domain
 178      * - currently no way other than mimicking reordering of
 179      * table in Feature Settings
 180      */
 181     FeatureSettingsBean[] data = new FeatureSettingsBean[2];
 182     data[0] = new FeatureSettingsBean("Metal", red, null, true);
 183     data[1] = new FeatureSettingsBean("Domain", green, null, true);
 184     fr.setFeaturePriority(data);
 185     c = finder.findFeatureColour(Color.blue, seq, 10);
 186     assertEquals(c, Color.red);
 187
 188     /*
 189      * ..and turn off display of Metal
 190      */
 191     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 192     fr.setFeaturePriority(data);
 193     c = finder.findFeatureColour(Color.blue, seq, 10);
 194     assertEquals(c, Color.green);
 195   }
 196
 197   @Test(groups = "Functional")
 198   public void testFindFeatureColour_singleFeatureNotAtPosition()
 199   {
 200     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
 201             Float.NaN, "MetalGroup"));
 202     fr.setColour("Metal", new FeatureColour(Color.red));
 203     fr.featuresAdded();
 204     av.setShowSequenceFeatures(true);
 205     // column 2 = sequence position 3
 206     Color c = finder.findFeatureColour(Color.blue, seq, 2);
 207     assertEquals(c, Color.blue);
 208   }
 209
 210   @Test(groups = "Functional")
 211   public void testFindFeatureColour_featureTypeNotDisplayed()
 212   {
 213     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 214             Float.NaN, "MetalGroup"));
 215     FeatureColour red = new FeatureColour(Color.red);
 216     fr.setColour("Metal", red);
 217     fr.featuresAdded();
 218     av.setShowSequenceFeatures(true);
 219     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 220     assertEquals(c, Color.red);
 221
 222     /*
 223      * turn off display of Metal - is this the easiest way to do it??
 224      */
 225     FeatureSettingsBean[] data = new FeatureSettingsBean[1];
 226     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 227     fr.setFeaturePriority(data);
 228     c = finder.findFeatureColour(Color.blue, seq, 10);
 229     assertEquals(c, Color.blue);
 230
 231     /*
 232      * turn display of Metal back on
 233      */
 234     data[0] = new FeatureSettingsBean("Metal", red, null, true);
 235     fr.setFeaturePriority(data);
 236     c = finder.findFeatureColour(Color.blue, seq, 10);
 237     assertEquals(c, Color.red);
 238   }
 239
 240   @Test(groups = "Functional")
 241   public void testFindFeatureColour_featureGroupNotDisplayed()
 242   {
 243     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 244             Float.NaN, "MetalGroup"));
 245     FeatureColour red = new FeatureColour(Color.red);
 246     fr.setColour("Metal", red);
 247     fr.featuresAdded();
 248     av.setShowSequenceFeatures(true);
 249     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 250     assertEquals(c, Color.red);
 251
 252     /*
 253      * turn off display of MetalGroup
 254      */
 255     fr.setGroupVisibility("MetalGroup", false);
 256     c = finder.findFeatureColour(Color.blue, seq, 10);
 257     assertEquals(c, Color.blue);
 258
 259     /*
 260      * turn display of MetalGroup back on
 261      */
 262     fr.setGroupVisibility("MetalGroup", true);
 263     c = finder.findFeatureColour(Color.blue, seq, 10);
 264     assertEquals(c, Color.red);
 265   }
 266
 267   @Test(groups = "Functional")
 268   public void testFindFeatureColour_contactFeature()
 269   {
 270     /*
 271      * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
 272      */
 273     seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
 274             "Contact", 2, 12, Float.NaN, "Disulphide"));
 275     fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
 276     fr.featuresAdded();
 277     av.setShowSequenceFeatures(true);
 278
 279     /*
 280      * Contact positions are residues 2 and 12
 281      * which are columns 1 and 14
 282      * positions in between don't count for a contact feature!
 283      */
 284     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 285     assertEquals(c, Color.blue);
 286     c = finder.findFeatureColour(Color.blue, seq, 8);
 287     assertEquals(c, Color.blue);
 288     c = finder.findFeatureColour(Color.blue, seq, 1);
 289     assertEquals(c, Color.red);
 290     c = finder.findFeatureColour(Color.blue, seq, 14);
 291     assertEquals(c, Color.red);
 292   }
 293
 294   @Test(groups = "Functional")
 295   public void testFindFeatureAtEnd()
 296   {
 297     /*
 298      * terminal residue feature
 299      */
 300     seq.addSequenceFeature(new SequenceFeature("PDBRESNUM", "pdb res 1",
 301             seq.getEnd(), seq.getEnd(), Float.NaN, "1seq.pdb"));
 302     fr.setColour("PDBRESNUM", new FeatureColour(Color.red));
 303     fr.featuresAdded();
 304     av.setShowSequenceFeatures(true);
 305
 306     /*
 307      * final column should have PDBRESNUM feature, the others not
 308      */
 309     Color c = finder.findFeatureColour(Color.blue, seq,
 310             seq.getLength() - 2);
 311     assertNotEquals(c, Color.red);
 312     c = finder.findFeatureColour(Color.blue, seq, seq.getLength() - 1);
 313     assertEquals(c, Color.red);
 314   }
 315
 316   @Test(groups = "Functional")
 317   public void testFindFeatureColour_graduatedFeatureColour()
 318   {
 319     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
 320             2, 0f, "KdGroup"));
 321     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
 322             4, 5f, "KdGroup"));
 323     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
 324             7, 10f, "KdGroup"));
 325
 326     /*
 327      * graduated colour from 0 to 10
 328      */
 329     Color min = new Color(100, 50, 150);
 330     Color max = new Color(200, 0, 100);
 331     FeatureColourI fc = new FeatureColour(min, max, 0, 10);
 332     fr.setColour("kd", fc);
 333     fr.featuresAdded();
 334     av.setShowSequenceFeatures(true);
 335
 336     /*
 337      * position 2, column 1, score 0 - minimum colour in range
 338      */
 339     Color c = finder.findFeatureColour(Color.blue, seq, 1);
 340     assertEquals(c, min);
 341
 342     /*
 343      * position 7, column 9, score 10 - maximum colour in range
 344      */
 345     c = finder.findFeatureColour(Color.blue, seq, 9);
 346     assertEquals(c, max);
 347
 348     /*
 349      * position 4, column 3, score 5 - half way from min to max
 350      */
 351     c = finder.findFeatureColour(Color.blue, seq, 3);
 352     assertEquals(c, new Color(150, 25, 125));
 353   }
 354
 355   @Test(groups = "Functional")
 356   public void testFindFeatureColour_transparencySingleFeature()
 357   {
 358     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 359             Float.NaN, "MetalGroup"));
 360     FeatureColour red = new FeatureColour(Color.red);
 361     fr.setColour("Metal", red);
 362     fr.featuresAdded();
 363     av.setShowSequenceFeatures(true);
 364
 365     /*
 366      * the FeatureSettings transparency slider has range 0-70 which
 367      * corresponds to a transparency value of 1 - 0.3
 368      * A value of 0.4 gives a combination of
 369      * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
 370      */
 371     fr.setTransparency(0.4f);
 372     Color c = finder.findFeatureColour(Color.cyan, seq, 10);
 373     assertEquals(c, new Color(102, 153, 153));
 374   }
 375
 376   @Test(groups = "Functional")
 377   public void testFindFeatureColour_transparencyTwoFeatures()
 378   {
 379     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 380             Float.NaN, "MetalGroup"));
 381     FeatureColour red = new FeatureColour(Color.red);
 382     fr.setColour("Metal", red);
 383     fr.featuresAdded();
 384     seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
 385             Float.NaN, "DomainGroup"));
 386     FeatureColour green = new FeatureColour(Color.green);
 387     fr.setColour("Domain", green);
 388     fr.featuresAdded();
 389     av.setShowSequenceFeatures(true);
 390
 391     /*
 392      * Domain (green) rendered above Metal (red) above background (cyan)
 393      * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
 394      * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
 395      */
 396     fr.setTransparency(0.6f);
 397     Color c = finder.findFeatureColour(Color.cyan, seq, 10);
 398     assertEquals(c, new Color(61, 194, 41));
 399
 400     /*
 401      * now promote Metal above Domain
 402      * - currently no way other than mimicking reordering of
 403      * table in Feature Settings
 404      * Metal (red) rendered above Domain (green) above background (cyan)
 405      * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
 406      * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
 407      */
 408     FeatureSettingsBean[] data = new FeatureSettingsBean[2];
 409     data[0] = new FeatureSettingsBean("Metal", red, null, true);
 410     data[1] = new FeatureSettingsBean("Domain", green, null, true);
 411     fr.setFeaturePriority(data);
 412     c = finder.findFeatureColour(Color.cyan, seq, 10);
 413     assertEquals(c, new Color(153, 102, 41));
 414
 415     /*
 416      * ..and turn off display of Metal
 417      * Domain (green) above background (pink)
 418      * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
 419      */
 420     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 421     fr.setFeaturePriority(data);
 422     c = finder.findFeatureColour(Color.pink, seq, 10);
 423     assertEquals(c, new Color(102, 223, 70));
 424   }
 425
 426   @Test(groups = "Functional")
 427   public void testNoFeaturesDisplayed()
 428   {
 429     /*
 430      * no features on alignment to render
 431      */
 432     assertTrue(finder.noFeaturesDisplayed());
 433
 434     /*
 435      * add a feature
 436      * it will be automatically set visible but we leave
 437      * the viewport configured not to show features
 438      */
 439     av.setShowSequenceFeatures(false);
 440     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 441             Float.NaN, "MetalGroup"));
 442     FeatureColour red = new FeatureColour(Color.red);
 443     fr.setColour("Metal", red);
 444     fr.featuresAdded();
 445     assertTrue(finder.noFeaturesDisplayed());
 446
 447     /*
 448      * turn on feature display
 449      */
 450     av.setShowSequenceFeatures(true);
 451     assertFalse(finder.noFeaturesDisplayed());
 452
 453     /*
 454      * turn off display of Metal
 455      */
 456     FeatureSettingsBean[] data = new FeatureSettingsBean[1];
 457     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 458     fr.setFeaturePriority(data);
 459     assertTrue(finder.noFeaturesDisplayed());
 460
 461     /*
 462      * turn display of Metal back on
 463      */
 464     fr.setVisible("Metal");
 465     assertFalse(finder.noFeaturesDisplayed());
 466
 467     /*
 468      * turn off MetalGroup - has no effect here since the group of a
 469      * sequence feature instance is independent of its type
 470      */
 471     fr.setGroupVisibility("MetalGroup", false);
 472     assertFalse(finder.noFeaturesDisplayed());
 473
 474     /*
 475      * a finder with no feature renderer
 476      */
 477     FeatureColourFinder finder2 = new FeatureColourFinder(null);
 478     assertTrue(finder2.noFeaturesDisplayed());
 479   }
 480
 481   @Test(groups = "Functional")
 482   public void testFindFeatureColour_graduatedWithThreshold()
 483   {
 484     String kdFeature = "kd";
 485     String metalFeature = "Metal";
 486     seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 2,
 487             2, 0f, "KdGroup"));
 488     seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 4,
 489             4, 5f, "KdGroup"));
 490     seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4,
 491             5f, "MetalGroup"));
 492     seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 7,
 493             7, 10f, "KdGroup"));
 494
 495     /*
 496      * kd feature has graduated colour from 0 to 10
 497      * above threshold value of 5
 498      */
 499     Color min = new Color(100, 50, 150);
 500     Color max = new Color(200, 0, 100);
 501     FeatureColourI fc = new FeatureColour(min, max, 0, 10);
 502     fc.setAboveThreshold(true);
 503     fc.setThreshold(5f);
 504     fr.setColour(kdFeature, fc);
 505     FeatureColour green = new FeatureColour(Color.green);
 506     fr.setColour(metalFeature, green);
 507     fr.featuresAdded();
 508
 509     /*
 510      * render order is kd above Metal
 511      */
 512     FeatureSettingsBean[] data = new FeatureSettingsBean[2];
 513     data[0] = new FeatureSettingsBean(kdFeature, fc, null, true);
 514     data[1] = new FeatureSettingsBean(metalFeature, green, null, true);
 515     fr.setFeaturePriority(data);
 516
 517     av.setShowSequenceFeatures(true);
 518
 519     /*
 520      * position 2, column 1, score 0 - below threshold - default colour
 521      */
 522     Color c = finder.findFeatureColour(Color.blue, seq, 1);
 523     assertEquals(c, Color.blue);
 524
 525     /*
 526      * position 4, column 3, score 5 - at threshold
 527      * should return Green (colour of Metal feature)
 528      */
 529     c = finder.findFeatureColour(Color.blue, seq, 3);
 530     assertEquals(c, Color.green);
 531
 532     /*
 533      * position 7, column 9, score 10 - maximum colour in range
 534      */
 535     c = finder.findFeatureColour(Color.blue, seq, 9);
 536     assertEquals(c, max);
 537
 538     /*
 539      * now colour below threshold of 5
 540      */
 541     fc.setBelowThreshold(true);
 542
 543     /*
 544      * position 2, column 1, score 0 - min colour
 545      */
 546     c = finder.findFeatureColour(Color.blue, seq, 1);
 547     assertEquals(c, min);
 548
 549     /*
 550      * position 4, column 3, score 5 - at threshold
 551      * should return Green (colour of Metal feature)
 552      */
 553     c = finder.findFeatureColour(Color.blue, seq, 3);
 554     assertEquals(c, Color.green);
 555
 556     /*
 557      * position 7, column 9, score 10 - above threshold - default colour
 558      */
 559     c = finder.findFeatureColour(Color.blue, seq, 9);
 560     assertEquals(c, Color.blue);
 561   }
 562 }