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