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