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