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 java.awt.Color;
  10 import java.util.List;
  11
  12 import org.testng.annotations.BeforeMethod;
  13 import org.testng.annotations.BeforeTest;
  14 import org.testng.annotations.Test;
  15
  16 import jalview.api.FeatureColourI;
  17 import jalview.datamodel.SequenceFeature;
  18 import jalview.datamodel.SequenceI;
  19 import jalview.gui.AlignFrame;
  20 import jalview.gui.AlignViewport;
  21 import jalview.io.DataSourceType;
  22 import jalview.io.FileLoader;
  23 import jalview.schemes.FeatureColour;
  24 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  25 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  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 FeatureRendererModel 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, DataSourceType.PASTE);
  62     av = af.getViewport();
  63     seq = av.getAlignment().getSequenceAt(0);
  64     fr = af.getFeatureRenderer();
  65     finder = new FeatureColourFinder(fr);
  66   }
  67
  68   /**
  69    * Clear down any sequence features before each test (not as easy as it
  70    * sounds...)
  71    */
  72   @BeforeMethod(alwaysRun = true)
  73   public void setUpBeforeTest()
  74   {
  75     List<SequenceFeature> sfs = seq.getSequenceFeatures();
  76     for (SequenceFeature sf : sfs)
  77     {
  78       seq.deleteFeature(sf);
  79     }
  80     fr.findAllFeatures(true);
  81
  82     /*
  83      * reset all feature groups to visible
  84      */
  85     for (String group : fr.getGroups(false))
  86     {
  87       fr.setGroupVisibility(group, true);
  88     }
  89
  90     fr.clearRenderOrder();
  91     av.setShowSequenceFeatures(true);
  92   }
  93
  94   @Test(groups = "Functional")
  95   public void testFindFeatureColour_noFeatures()
  96   {
  97     av.setShowSequenceFeatures(false);
  98     Color c = finder.findFeatureColour(Color.blue, seq, 10);
  99     assertEquals(c, Color.blue);
 100
 101     av.setShowSequenceFeatures(true);
 102     c = finder.findFeatureColour(Color.blue, seq, 10);
 103     assertEquals(c, Color.blue);
 104   }
 105
 106   @Test(groups = "Functional")
 107   public void testFindFeatureColour_noFeaturesShown()
 108   {
 109     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 110             Float.NaN, "MetalGroup"));
 111     fr.featuresAdded();
 112     av.setShowSequenceFeatures(false);
 113     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 114     assertEquals(c, Color.blue);
 115   }
 116
 117   @Test(groups = "Functional")
 118   public void testFindFeatureColour_singleFeatureAtPosition()
 119   {
 120     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 121             Float.NaN, "MetalGroup"));
 122     fr.setColour("Metal", new FeatureColour(Color.red));
 123     fr.featuresAdded();
 124     av.setShowSequenceFeatures(true);
 125     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 126     assertEquals(c, Color.red);
 127   }
 128
 129   /**
 130    * feature colour at a gap is null (not white) - a user defined colour scheme
 131    * can then provide a bespoke gap colour if configured to do so
 132    */
 133   @Test(groups = "Functional")
 134   public void testFindFeatureColour_gapPosition()
 135   {
 136     seq.addSequenceFeature(
 137             new SequenceFeature("Metal", "Metal", 2, 12, 0f, null));
 138     fr.setColour("Metal", new FeatureColour(Color.red));
 139     fr.featuresAdded();
 140     av.setShowSequenceFeatures(true);
 141     Color c = finder.findFeatureColour(null, seq, 6);
 142     assertNull(c);
 143   }
 144
 145   /**
 146    * Nested features coloured by label - expect the colour of the enclosed
 147    * feature
 148    */
 149   @Test(groups = "Functional")
 150   public void testFindFeatureColour_nestedFeatures()
 151   {
 152     SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, 0f, null);
 153     seq.addSequenceFeature(sf1);
 154     SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20,
 155             0f, null);
 156     seq.addSequenceFeature(sf2);
 157     FeatureColourI fc = new FeatureColour(Color.red);
 158     fc.setColourByLabel(true);
 159     fr.setColour("domain", fc);
 160     fr.featuresAdded();
 161     av.setShowSequenceFeatures(true);
 162     Color c = finder.findFeatureColour(null, seq, 15);
 163     assertEquals(c, fr.getColor(sf2, fc));
 164   }
 165
 166   @Test(groups = "Functional")
 167   public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
 168   {
 169     /*
 170      * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
 171      * new features 'on top' (but reverses the order of any added features)
 172      */
 173     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 174             Float.NaN, "MetalGroup"));
 175     FeatureColour red = new FeatureColour(Color.red);
 176     fr.setColour("Metal", red);
 177     fr.featuresAdded();
 178     seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
 179             Float.NaN, "DomainGroup"));
 180     FeatureColour green = new FeatureColour(Color.green);
 181     fr.setColour("Domain", green);
 182     fr.featuresAdded();
 183     av.setShowSequenceFeatures(true);
 184
 185     /*
 186      * expect Domain (green) to be rendered above Metal (red)
 187      */
 188     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 189     assertEquals(c, Color.green);
 190
 191     /*
 192      * now promote Metal above Domain
 193      * - currently no way other than mimicking reordering of
 194      * table in Feature Settings
 195      */
 196     FeatureSettingsBean[] data = new FeatureSettingsBean[2];
 197     data[0] = new FeatureSettingsBean("Metal", red, null, true);
 198     data[1] = new FeatureSettingsBean("Domain", green, null, true);
 199     fr.setFeaturePriority(data);
 200     c = finder.findFeatureColour(Color.blue, seq, 10);
 201     assertEquals(c, Color.red);
 202
 203     /*
 204      * ..and turn off display of Metal
 205      */
 206     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 207     fr.setFeaturePriority(data);
 208     c = finder.findFeatureColour(Color.blue, seq, 10);
 209     assertEquals(c, Color.green);
 210   }
 211
 212   @Test(groups = "Functional")
 213   public void testFindFeatureColour_singleFeatureNotAtPosition()
 214   {
 215     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
 216             Float.NaN, "MetalGroup"));
 217     fr.setColour("Metal", new FeatureColour(Color.red));
 218     fr.featuresAdded();
 219     av.setShowSequenceFeatures(true);
 220     // column 2 = sequence position 3
 221     Color c = finder.findFeatureColour(Color.blue, seq, 2);
 222     assertEquals(c, Color.blue);
 223   }
 224
 225   @Test(groups = "Functional")
 226   public void testFindFeatureColour_featureTypeNotDisplayed()
 227   {
 228     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 229             Float.NaN, "MetalGroup"));
 230     FeatureColour red = new FeatureColour(Color.red);
 231     fr.setColour("Metal", red);
 232     fr.featuresAdded();
 233     av.setShowSequenceFeatures(true);
 234     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 235     assertEquals(c, Color.red);
 236
 237     /*
 238      * turn off display of Metal - is this the easiest way to do it??
 239      */
 240     FeatureSettingsBean[] data = new FeatureSettingsBean[1];
 241     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 242     fr.setFeaturePriority(data);
 243     c = finder.findFeatureColour(Color.blue, seq, 10);
 244     assertEquals(c, Color.blue);
 245
 246     /*
 247      * turn display of Metal back on
 248      */
 249     data[0] = new FeatureSettingsBean("Metal", red, null, true);
 250     fr.setFeaturePriority(data);
 251     c = finder.findFeatureColour(Color.blue, seq, 10);
 252     assertEquals(c, Color.red);
 253   }
 254
 255   @Test(groups = "Functional")
 256   public void testFindFeatureColour_featureGroupNotDisplayed()
 257   {
 258     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 259             Float.NaN, "MetalGroup"));
 260     FeatureColour red = new FeatureColour(Color.red);
 261     fr.setColour("Metal", red);
 262     fr.featuresAdded();
 263     av.setShowSequenceFeatures(true);
 264     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 265     assertEquals(c, Color.red);
 266
 267     /*
 268      * turn off display of MetalGroup
 269      */
 270     fr.setGroupVisibility("MetalGroup", false);
 271     c = finder.findFeatureColour(Color.blue, seq, 10);
 272     assertEquals(c, Color.blue);
 273
 274     /*
 275      * turn display of MetalGroup back on
 276      */
 277     fr.setGroupVisibility("MetalGroup", true);
 278     c = finder.findFeatureColour(Color.blue, seq, 10);
 279     assertEquals(c, Color.red);
 280   }
 281
 282   @Test(groups = "Functional")
 283   public void testFindFeatureColour_contactFeature()
 284   {
 285     /*
 286      * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
 287      */
 288     seq.addSequenceFeature(new SequenceFeature("Disulphide Bond", "Contact",
 289             2, 12, Float.NaN, "Disulphide"));
 290     fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
 291     fr.featuresAdded();
 292     av.setShowSequenceFeatures(true);
 293
 294     /*
 295      * Contact positions are residues 2 and 12
 296      * which are columns 1 and 14
 297      * positions in between don't count for a contact feature!
 298      */
 299     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 300     assertEquals(c, Color.blue);
 301     c = finder.findFeatureColour(Color.blue, seq, 8);
 302     assertEquals(c, Color.blue);
 303     c = finder.findFeatureColour(Color.blue, seq, 1);
 304     assertEquals(c, Color.red);
 305     c = finder.findFeatureColour(Color.blue, seq, 14);
 306     assertEquals(c, Color.red);
 307   }
 308
 309   @Test(groups = "Functional")
 310   public void testFindFeatureAtEnd()
 311   {
 312     /*
 313      * terminal residue feature
 314      */
 315     seq.addSequenceFeature(new SequenceFeature("PDBRESNUM", "pdb res 1",
 316             seq.getEnd(), seq.getEnd(), Float.NaN, "1seq.pdb"));
 317     fr.setColour("PDBRESNUM", new FeatureColour(Color.red));
 318     fr.featuresAdded();
 319     av.setShowSequenceFeatures(true);
 320
 321     /*
 322      * final column should have PDBRESNUM feature, the others not
 323      */
 324     Color c = finder.findFeatureColour(Color.blue, seq,
 325             seq.getLength() - 2);
 326     assertNotEquals(c, Color.red);
 327     c = finder.findFeatureColour(Color.blue, seq, seq.getLength() - 1);
 328     assertEquals(c, Color.red);
 329   }
 330
 331   @Test(groups = "Functional")
 332   public void testFindFeatureColour_graduatedFeatureColour()
 333   {
 334     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2, 2,
 335             0f, "KdGroup"));
 336     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4, 4,
 337             5f, "KdGroup"));
 338     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7, 7,
 339             10f, "KdGroup"));
 340
 341     /*
 342      * graduated colour from 0 to 10
 343      */
 344     Color min = new Color(100, 50, 150);
 345     Color max = new Color(200, 0, 100);
 346     FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
 347     fr.setColour("kd", fc);
 348     fr.featuresAdded();
 349     av.setShowSequenceFeatures(true);
 350
 351     /*
 352      * position 2, column 1, score 0 - minimum colour in range
 353      */
 354     Color c = finder.findFeatureColour(Color.blue, seq, 1);
 355     assertEquals(c, min);
 356
 357     /*
 358      * position 7, column 9, score 10 - maximum colour in range
 359      */
 360     c = finder.findFeatureColour(Color.blue, seq, 9);
 361     assertEquals(c, max);
 362
 363     /*
 364      * position 4, column 3, score 5 - half way from min to max
 365      */
 366     c = finder.findFeatureColour(Color.blue, seq, 3);
 367     assertEquals(c, new Color(150, 25, 125));
 368   }
 369
 370   @Test(groups = "Functional")
 371   public void testFindFeatureColour_transparencySingleFeature()
 372   {
 373     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 374             Float.NaN, "MetalGroup"));
 375     FeatureColour red = new FeatureColour(Color.red);
 376     fr.setColour("Metal", red);
 377     fr.featuresAdded();
 378     av.setShowSequenceFeatures(true);
 379
 380     /*
 381      * the FeatureSettings transparency slider has range 0-70 which
 382      * corresponds to a transparency value of 1 - 0.3
 383      * A value of 0.4 gives a combination of
 384      * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
 385      */
 386     fr.setTransparency(0.4f);
 387     Color c = finder.findFeatureColour(Color.cyan, seq, 10);
 388     assertEquals(c, new Color(102, 153, 153));
 389   }
 390
 391   @Test(groups = "Functional")
 392   public void testFindFeatureColour_transparencyTwoFeatures()
 393   {
 394     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 395             Float.NaN, "MetalGroup"));
 396     FeatureColour red = new FeatureColour(Color.red);
 397     fr.setColour("Metal", red);
 398     fr.featuresAdded();
 399     seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
 400             Float.NaN, "DomainGroup"));
 401     FeatureColour green = new FeatureColour(Color.green);
 402     fr.setColour("Domain", green);
 403     fr.featuresAdded();
 404     av.setShowSequenceFeatures(true);
 405
 406     /*
 407      * Domain (green) rendered above Metal (red) above background (cyan)
 408      * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
 409      * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
 410      */
 411     fr.setTransparency(0.6f);
 412     Color c = finder.findFeatureColour(Color.cyan, seq, 10);
 413     assertEquals(c, new Color(61, 194, 41));
 414
 415     /*
 416      * now promote Metal above Domain
 417      * - currently no way other than mimicking reordering of
 418      * table in Feature Settings
 419      * Metal (red) rendered above Domain (green) above background (cyan)
 420      * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
 421      * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
 422      */
 423     FeatureSettingsBean[] data = new FeatureSettingsBean[2];
 424     data[0] = new FeatureSettingsBean("Metal", red, null, true);
 425     data[1] = new FeatureSettingsBean("Domain", green, null, true);
 426     fr.setFeaturePriority(data);
 427     c = finder.findFeatureColour(Color.cyan, seq, 10);
 428     assertEquals(c, new Color(153, 102, 41));
 429
 430     /*
 431      * ..and turn off display of Metal
 432      * Domain (green) above background (pink)
 433      * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
 434      */
 435     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 436     fr.setFeaturePriority(data);
 437     c = finder.findFeatureColour(Color.pink, seq, 10);
 438     assertEquals(c, new Color(102, 223, 70));
 439   }
 440
 441   @Test(groups = "Functional")
 442   public void testNoFeaturesDisplayed()
 443   {
 444     /*
 445      * no features on alignment to render
 446      */
 447     assertTrue(finder.noFeaturesDisplayed());
 448
 449     /*
 450      * add a feature
 451      * it will be automatically set visible but we leave
 452      * the viewport configured not to show features
 453      */
 454     av.setShowSequenceFeatures(false);
 455     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 456             Float.NaN, "MetalGroup"));
 457     FeatureColour red = new FeatureColour(Color.red);
 458     fr.setColour("Metal", red);
 459     fr.featuresAdded();
 460     assertTrue(finder.noFeaturesDisplayed());
 461
 462     /*
 463      * turn on feature display
 464      */
 465     av.setShowSequenceFeatures(true);
 466     assertFalse(finder.noFeaturesDisplayed());
 467
 468     /*
 469      * turn off display of Metal
 470      */
 471     FeatureSettingsBean[] data = new FeatureSettingsBean[1];
 472     data[0] = new FeatureSettingsBean("Metal", red, null, false);
 473     fr.setFeaturePriority(data);
 474     assertTrue(finder.noFeaturesDisplayed());
 475
 476     /*
 477      * turn display of Metal back on
 478      */
 479     fr.setVisible("Metal");
 480     assertFalse(finder.noFeaturesDisplayed());
 481
 482     /*
 483      * turn off MetalGroup - has no effect here since the group of a
 484      * sequence feature instance is independent of its type
 485      */
 486     fr.setGroupVisibility("MetalGroup", false);
 487     assertFalse(finder.noFeaturesDisplayed());
 488
 489     /*
 490      * a finder with no feature renderer
 491      */
 492     FeatureColourFinder finder2 = new FeatureColourFinder(null);
 493     assertTrue(finder2.noFeaturesDisplayed());
 494   }
 495
 496   @Test(groups = "Functional")
 497   public void testFindFeatureColour_graduatedWithThreshold()
 498   {
 499     String kdFeature = "kd";
 500     String metalFeature = "Metal";
 501     seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
 502             2, 2, 0f, "KdGroup"));
 503     seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
 504             4, 4, 5f, "KdGroup"));
 505     seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4, 5f,
 506             "MetalGroup"));
 507     seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
 508             7, 7, 10f, "KdGroup"));
 509
 510     /*
 511      * kd feature has graduated colour from 0 to 10
 512      * above threshold value of 5
 513      */
 514     Color min = new Color(100, 50, 150);
 515     Color max = new Color(200, 0, 100);
 516     FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
 517     fc.setAboveThreshold(true);
 518     fc.setThreshold(5f);
 519     fr.setColour(kdFeature, fc);
 520     FeatureColour green = new FeatureColour(Color.green);
 521     fr.setColour(metalFeature, green);
 522     fr.featuresAdded();
 523
 524     /*
 525      * render order is kd above Metal
 526      */
 527     FeatureSettingsBean[] data = new FeatureSettingsBean[2];
 528     data[0] = new FeatureSettingsBean(kdFeature, fc, null, true);
 529     data[1] = new FeatureSettingsBean(metalFeature, green, null, true);
 530     fr.setFeaturePriority(data);
 531
 532     av.setShowSequenceFeatures(true);
 533
 534     /*
 535      * position 2, column 1, score 0 - below threshold - default colour
 536      */
 537     Color c = finder.findFeatureColour(Color.blue, seq, 1);
 538     assertEquals(c, Color.blue);
 539
 540     /*
 541      * position 4, column 3, score 5 - at threshold
 542      * should return Green (colour of Metal feature)
 543      */
 544     c = finder.findFeatureColour(Color.blue, seq, 3);
 545     assertEquals(c, Color.green);
 546
 547     /*
 548      * position 7, column 9, score 10 - maximum colour in range
 549      */
 550     c = finder.findFeatureColour(Color.blue, seq, 9);
 551     assertEquals(c, max);
 552
 553     /*
 554      * now colour below threshold of 5
 555      */
 556     fc.setBelowThreshold(true);
 557
 558     /*
 559      * position 2, column 1, score 0 - min colour
 560      */
 561     c = finder.findFeatureColour(Color.blue, seq, 1);
 562     assertEquals(c, min);
 563
 564     /*
 565      * position 4, column 3, score 5 - at threshold
 566      * should return Green (colour of Metal feature)
 567      */
 568     c = finder.findFeatureColour(Color.blue, seq, 3);
 569     assertEquals(c, Color.green);
 570
 571     /*
 572      * position 7, column 9, score 10 - above threshold - default colour
 573      */
 574     c = finder.findFeatureColour(Color.blue, seq, 9);
 575     assertEquals(c, Color.blue);
 576   }
 577 }