test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java

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