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