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