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.BeforeMethod;
  20 import org.testng.annotations.BeforeTest;
  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   @BeforeTest(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 (not as easy as it
  67    * sounds...)
  68    */
  69   @BeforeMethod(alwaysRun = true)
  70   public void setUpBeforeTest()
  71   {
  72     SequenceFeature[] sfs = seq.getSequenceFeatures();
  73     if (sfs != null)
  74     {
  75       for (SequenceFeature sf : sfs)
  76       {
  77         seq.deleteFeature(sf);
  78       }
  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   @Test(groups = "Functional")
 130   public void testFindFeatureColour_gapPosition()
 131   {
 132     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
 133             null));
 134     fr.setColour("Metal", new FeatureColour(Color.red));
 135     fr.featuresAdded();
 136     av.setShowSequenceFeatures(true);
 137     Color c = finder.findFeatureColour(null, seq, 6);
 138     assertEquals(c, Color.white);
 139   }
 140
 141   @Test(groups = "Functional")
 142   public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
 143   {
 144     /*
 145      * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
 146      * new features 'on top' (but reverses the order of any added features)
 147      */
 148     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 149             Float.NaN, "MetalGroup"));
 150     FeatureColour red = new FeatureColour(Color.red);
 151     fr.setColour("Metal", red);
 152     fr.featuresAdded();
 153     seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
 154             Float.NaN, "DomainGroup"));
 155     FeatureColour green = new FeatureColour(Color.green);
 156     fr.setColour("Domain", green);
 157     fr.featuresAdded();
 158     av.setShowSequenceFeatures(true);
 159
 160     /*
 161      * expect Domain (green) to be rendered above Metal (red)
 162      */
 163     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 164     assertEquals(c, Color.green);
 165
 166     /*
 167      * now promote Metal above Domain
 168      * - currently no way other than mimicking reordering of
 169      * table in Feature Settings
 170      */
 171     Object[][] data = new Object[2][];
 172     data[0] = new Object[] { "Metal", red, true };
 173     data[1] = new Object[] { "Domain", green, true };
 174     fr.setFeaturePriority(data);
 175     c = finder.findFeatureColour(Color.blue, seq, 10);
 176     assertEquals(c, Color.red);
 177
 178     /*
 179      * ..and turn off display of Metal
 180      */
 181     data[0][2] = false;
 182     fr.setFeaturePriority(data);
 183     c = finder.findFeatureColour(Color.blue, seq, 10);
 184     assertEquals(c, Color.green);
 185   }
 186
 187   @Test(groups = "Functional")
 188   public void testFindFeatureColour_singleFeatureNotAtPosition()
 189   {
 190     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
 191             Float.NaN, "MetalGroup"));
 192     fr.setColour("Metal", new FeatureColour(Color.red));
 193     fr.featuresAdded();
 194     av.setShowSequenceFeatures(true);
 195     // column 2 = sequence position 3
 196     Color c = finder.findFeatureColour(Color.blue, seq, 2);
 197     assertEquals(c, Color.blue);
 198   }
 199
 200   @Test(groups = "Functional")
 201   public void testFindFeatureColour_featureTypeNotDisplayed()
 202   {
 203     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 204             Float.NaN, "MetalGroup"));
 205     FeatureColour red = new FeatureColour(Color.red);
 206     fr.setColour("Metal", red);
 207     fr.featuresAdded();
 208     av.setShowSequenceFeatures(true);
 209     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 210     assertEquals(c, Color.red);
 211
 212     /*
 213      * turn off display of Metal - is this the easiest way to do it??
 214      */
 215     Object[][] data = new Object[1][];
 216     data[0] = new Object[] { "Metal", red, false };
 217     fr.setFeaturePriority(data);
 218     c = finder.findFeatureColour(Color.blue, seq, 10);
 219     assertEquals(c, Color.blue);
 220
 221     /*
 222      * turn display of Metal back on
 223      */
 224     data[0] = new Object[] { "Metal", red, true };
 225     fr.setFeaturePriority(data);
 226     c = finder.findFeatureColour(Color.blue, seq, 10);
 227     assertEquals(c, Color.red);
 228   }
 229
 230   @Test(groups = "Functional")
 231   public void testFindFeatureColour_featureGroupNotDisplayed()
 232   {
 233     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 234             Float.NaN, "MetalGroup"));
 235     FeatureColour red = new FeatureColour(Color.red);
 236     fr.setColour("Metal", red);
 237     fr.featuresAdded();
 238     av.setShowSequenceFeatures(true);
 239     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 240     assertEquals(c, Color.red);
 241
 242     /*
 243      * turn off display of MetalGroup
 244      */
 245     fr.setGroupVisibility("MetalGroup", false);
 246     c = finder.findFeatureColour(Color.blue, seq, 10);
 247     assertEquals(c, Color.blue);
 248
 249     /*
 250      * turn display of MetalGroup back on
 251      */
 252     fr.setGroupVisibility("MetalGroup", true);
 253     c = finder.findFeatureColour(Color.blue, seq, 10);
 254     assertEquals(c, Color.red);
 255   }
 256
 257   @Test(groups = "Functional")
 258   public void testFindFeatureColour_contactFeature()
 259   {
 260     /*
 261      * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
 262      */
 263     seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
 264             "Contact", 2, 12, Float.NaN, "Disulphide"));
 265     fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
 266     fr.featuresAdded();
 267     av.setShowSequenceFeatures(true);
 268
 269     /*
 270      * Contact positions are residues 2 and 12
 271      * which are columns 1 and 14
 272      * positions in between don't count for a contact feature!
 273      */
 274     Color c = finder.findFeatureColour(Color.blue, seq, 10);
 275     assertEquals(c, Color.blue);
 276     c = finder.findFeatureColour(Color.blue, seq, 8);
 277     assertEquals(c, Color.blue);
 278     c = finder.findFeatureColour(Color.blue, seq, 1);
 279     assertEquals(c, Color.red);
 280     c = finder.findFeatureColour(Color.blue, seq, 14);
 281     assertEquals(c, Color.red);
 282   }
 283
 284   @Test(groups = "Functional")
 285   public void testFindFeatureColour_graduatedFeatureColour()
 286   {
 287     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
 288             2, 0f, "KdGroup"));
 289     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
 290             4, 5f, "KdGroup"));
 291     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
 292             7, 10f, "KdGroup"));
 293
 294     /*
 295      * graduated colour from 0 to 10
 296      */
 297     Color min = new Color(100, 50, 150);
 298     Color max = new Color(200, 0, 100);
 299     FeatureColourI fc = new FeatureColour(min, max, 0, 10);
 300     fr.setColour("kd", fc);
 301     fr.featuresAdded();
 302     av.setShowSequenceFeatures(true);
 303
 304     /*
 305      * position 2, column 1, score 0 - minimum colour in range
 306      */
 307     Color c = finder.findFeatureColour(Color.blue, seq, 1);
 308     assertEquals(c, min);
 309
 310     /*
 311      * position 7, column 9, score 10 - maximum colour in range
 312      */
 313     c = finder.findFeatureColour(Color.blue, seq, 9);
 314     assertEquals(c, max);
 315
 316     /*
 317      * position 4, column 3, score 5 - half way from min to max
 318      */
 319     c = finder.findFeatureColour(Color.blue, seq, 3);
 320     assertEquals(c, new Color(150, 25, 125));
 321   }
 322
 323   @Test(groups = "Functional")
 324   public void testFindFeatureColour_transparencySingleFeature()
 325   {
 326     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 327             Float.NaN, "MetalGroup"));
 328     FeatureColour red = new FeatureColour(Color.red);
 329     fr.setColour("Metal", red);
 330     fr.featuresAdded();
 331     av.setShowSequenceFeatures(true);
 332
 333     /*
 334      * the FeatureSettings transparency slider has range 0-70 which
 335      * corresponds to a transparency value of 1 - 0.3
 336      * A value of 0.4 gives a combination of
 337      * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
 338      */
 339     fr.setTransparency(0.4f);
 340     Color c = finder.findFeatureColour(Color.cyan, seq, 10);
 341     assertEquals(c, new Color(102, 153, 153));
 342   }
 343
 344   @Test(groups = "Functional")
 345   public void testFindFeatureColour_transparencyTwoFeatures()
 346   {
 347     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 348             Float.NaN, "MetalGroup"));
 349     FeatureColour red = new FeatureColour(Color.red);
 350     fr.setColour("Metal", red);
 351     fr.featuresAdded();
 352     seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
 353             Float.NaN, "DomainGroup"));
 354     FeatureColour green = new FeatureColour(Color.green);
 355     fr.setColour("Domain", green);
 356     fr.featuresAdded();
 357     av.setShowSequenceFeatures(true);
 358
 359     /*
 360      * Domain (green) rendered above Metal (red) above background (cyan)
 361      * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
 362      * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
 363      */
 364     fr.setTransparency(0.6f);
 365     Color c = finder.findFeatureColour(Color.cyan, seq, 10);
 366     assertEquals(c, new Color(61, 194, 41));
 367
 368     /*
 369      * now promote Metal above Domain
 370      * - currently no way other than mimicking reordering of
 371      * table in Feature Settings
 372      * Metal (red) rendered above Domain (green) above background (cyan)
 373      * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
 374      * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
 375      */
 376     Object[][] data = new Object[2][];
 377     data[0] = new Object[] { "Metal", red, true };
 378     data[1] = new Object[] { "Domain", green, true };
 379     fr.setFeaturePriority(data);
 380     c = finder.findFeatureColour(Color.cyan, seq, 10);
 381     assertEquals(c, new Color(153, 102, 41));
 382
 383     /*
 384      * ..and turn off display of Metal
 385      * Domain (green) above background (pink)
 386      * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
 387      */
 388     data[0][2] = false;
 389     fr.setFeaturePriority(data);
 390     c = finder.findFeatureColour(Color.pink, seq, 10);
 391     assertEquals(c, new Color(102, 223, 70));
 392   }
 393
 394   @Test(groups = "Functional")
 395   public void testNoFeaturesDisplayed()
 396   {
 397     /*
 398      * no features on alignment to render
 399      */
 400     assertTrue(finder.noFeaturesDisplayed());
 401
 402     /*
 403      * add a feature
 404      * it will be automatically set visible but we leave
 405      * the viewport configured not to show features
 406      */
 407     av.setShowSequenceFeatures(false);
 408     seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
 409             Float.NaN, "MetalGroup"));
 410     FeatureColour red = new FeatureColour(Color.red);
 411     fr.setColour("Metal", red);
 412     fr.featuresAdded();
 413     assertTrue(finder.noFeaturesDisplayed());
 414
 415     /*
 416      * turn on feature display
 417      */
 418     av.setShowSequenceFeatures(true);
 419     assertFalse(finder.noFeaturesDisplayed());
 420
 421     /*
 422      * turn off display of Metal
 423      */
 424     Object[][] data = new Object[1][];
 425     data[0] = new Object[] { "Metal", red, false };
 426     fr.setFeaturePriority(data);
 427     assertTrue(finder.noFeaturesDisplayed());
 428
 429     /*
 430      * turn display of Metal back on
 431      */
 432     fr.setVisible("Metal");
 433     assertFalse(finder.noFeaturesDisplayed());
 434
 435     /*
 436      * turn off MetalGroup - has no effect here since the group of a
 437      * sequence feature instance is independent of its type
 438      */
 439     fr.setGroupVisibility("MetalGroup", false);
 440     assertFalse(finder.noFeaturesDisplayed());
 441
 442     /*
 443      * a finder with no feature renderer
 444      */
 445     FeatureColourFinder finder2 = new FeatureColourFinder(null);
 446     assertTrue(finder2.noFeaturesDisplayed());
 447   }
 448 }