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