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