test/jalview/renderer/seqfeatures/FeatureRendererTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.renderer.seqfeatures;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.Assert.assertFalse;
  25 import static org.testng.Assert.assertNotNull;
  26 import static org.testng.Assert.assertNull;
  27 import static org.testng.Assert.assertSame;
  28 import static org.testng.Assert.assertTrue;
  29
  30 import jalview.analysis.GeneticCodes;
  31 import jalview.api.AlignViewportI;
  32 import jalview.api.FeatureColourI;
  33 import jalview.bin.Jalview;
  34 import jalview.datamodel.MappedFeatures;
  35 import jalview.datamodel.SequenceFeature;
  36 import jalview.datamodel.SequenceI;
  37 import jalview.datamodel.features.FeatureMatcher;
  38 import jalview.datamodel.features.FeatureMatcherSet;
  39 import jalview.datamodel.features.FeatureMatcherSetI;
  40 import jalview.gui.AlignFrame;
  41 import jalview.gui.AlignViewport;
  42 import jalview.gui.Desktop;
  43 import jalview.io.DataSourceType;
  44 import jalview.io.FileLoader;
  45 import jalview.schemes.FeatureColour;
  46 import jalview.util.matcher.Condition;
  47 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  48
  49 import java.awt.Color;
  50 import java.util.ArrayList;
  51 import java.util.Arrays;
  52 import java.util.HashMap;
  53 import java.util.List;
  54 import java.util.Map;
  55
  56 import org.testng.annotations.Test;
  57
  58 public class FeatureRendererTest
  59 {
  60
  61   @Test(groups = "Functional")
  62   public void testFindAllFeatures()
  63   {
  64     String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
  65     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
  66             DataSourceType.PASTE);
  67     AlignViewportI av = af.getViewport();
  68     FeatureRenderer fr = new FeatureRenderer(av);
  69
  70     /*
  71      * with no features
  72      */
  73     fr.findAllFeatures(true);
  74     assertTrue(fr.getRenderOrder().isEmpty());
  75     assertTrue(fr.getFeatureGroups().isEmpty());
  76
  77     List<SequenceI> seqs = av.getAlignment().getSequences();
  78
  79     // add a non-positional feature - should be ignored by FeatureRenderer
  80     SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
  81             "Group");
  82     seqs.get(0).addSequenceFeature(sf1);
  83     fr.findAllFeatures(true);
  84     // ? bug - types and groups added for non-positional features
  85     List<String> types = fr.getRenderOrder();
  86     List<String> groups = fr.getFeatureGroups();
  87     assertEquals(types.size(), 0);
  88     assertFalse(types.contains("Type"));
  89     assertEquals(groups.size(), 0);
  90     assertFalse(groups.contains("Group"));
  91
  92     // add some positional features
  93     seqs.get(1).addSequenceFeature(
  94             new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
  95     seqs.get(2).addSequenceFeature(
  96             new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
  97     // bug in findAllFeatures - group not checked for a known feature type
  98     seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9,
  99             Float.NaN, "RfamGroup"));
 100     // existing feature type with null group
 101     seqs.get(3).addSequenceFeature(
 102             new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
 103     // new feature type with null group
 104     seqs.get(3).addSequenceFeature(
 105             new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
 106     // null value for type produces NullPointerException
 107     fr.findAllFeatures(true);
 108     types = fr.getRenderOrder();
 109     groups = fr.getFeatureGroups();
 110     assertEquals(types.size(), 3);
 111     assertFalse(types.contains("Type"));
 112     assertTrue(types.contains("Pfam"));
 113     assertTrue(types.contains("Rfam"));
 114     assertTrue(types.contains("Scop"));
 115     assertEquals(groups.size(), 2);
 116     assertFalse(groups.contains("Group"));
 117     assertTrue(groups.contains("PfamGroup"));
 118     assertTrue(groups.contains("RfamGroup"));
 119     assertFalse(groups.contains(null)); // null group is ignored
 120
 121     /*
 122      * check min-max values
 123      */
 124     Map<String, float[][]> minMax = fr.getMinMax();
 125     assertEquals(minMax.size(), 1); // non-positional and NaN not stored
 126     assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
 127     assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
 128
 129     // increase max for Pfam, add scores for Rfam
 130     seqs.get(0).addSequenceFeature(
 131             new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
 132     seqs.get(1).addSequenceFeature(
 133             new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
 134     fr.findAllFeatures(true);
 135     // note minMax is not a defensive copy, shouldn't expose this
 136     assertEquals(minMax.size(), 2);
 137     assertEquals(minMax.get("Pfam")[0][0], 1f);
 138     assertEquals(minMax.get("Pfam")[0][1], 8f);
 139     assertEquals(minMax.get("Rfam")[0][0], 6f);
 140     assertEquals(minMax.get("Rfam")[0][1], 6f);
 141
 142     /*
 143      * check render order (last is on top)
 144      */
 145     List<String> renderOrder = fr.getRenderOrder();
 146     assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
 147
 148     /*
 149      * change render order (todo: an easier way)
 150      * nb here last comes first in the data array
 151      */
 152     FeatureSettingsBean[] data = new FeatureSettingsBean[3];
 153     FeatureColourI colour = new FeatureColour(Color.RED);
 154     data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
 155     data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
 156     data[2] = new FeatureSettingsBean("Scop", colour, null, false);
 157     fr.setFeaturePriority(data);
 158     assertEquals(fr.getRenderOrder(),
 159             Arrays.asList("Scop", "Pfam", "Rfam"));
 160     assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
 161
 162     /*
 163      * add a new feature type: should go on top of render order as visible,
 164      * other feature ordering and visibility should be unchanged
 165      */
 166     seqs.get(2).addSequenceFeature(
 167             new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
 168     fr.findAllFeatures(true);
 169     assertEquals(fr.getRenderOrder(),
 170             Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
 171     assertEquals(fr.getDisplayedFeatureTypes(),
 172             Arrays.asList("Rfam", "Metal"));
 173   }
 174
 175   @Test(groups = "Functional")
 176   public void testFindFeaturesAtColumn()
 177   {
 178     String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
 179     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
 180             DataSourceType.PASTE);
 181     AlignViewportI av = af.getViewport();
 182     FeatureRenderer fr = new FeatureRenderer(av);
 183     SequenceI seq = av.getAlignment().getSequenceAt(0);
 184
 185     /*
 186      * with no features
 187      */
 188     List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
 189     assertTrue(features.isEmpty());
 190
 191     /*
 192      * add features
 193      */
 194     SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
 195             "Group"); // non-positional
 196     seq.addSequenceFeature(sf1);
 197     SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
 198             "Group1");
 199     seq.addSequenceFeature(sf2);
 200     SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
 201             "Group2");
 202     seq.addSequenceFeature(sf3);
 203     SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
 204             null); // null group is always treated as visible
 205     seq.addSequenceFeature(sf4);
 206
 207     /*
 208      * add contact features
 209      */
 210     SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
 211             15, 1f, "Group1");
 212     seq.addSequenceFeature(sf5);
 213     SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
 214             15, 1f, "Group2");
 215     seq.addSequenceFeature(sf6);
 216     SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
 217             15, 1f, null);
 218     seq.addSequenceFeature(sf7);
 219
 220     // feature spanning B--C
 221     SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
 222             "Group");
 223     seq.addSequenceFeature(sf8);
 224     // contact feature B/C
 225     SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
 226             6, 1f, "Group");
 227     seq.addSequenceFeature(sf9);
 228
 229     /*
 230      * let feature renderer discover features (and make visible)
 231      */
 232     fr.findAllFeatures(true);
 233     features = fr.findFeaturesAtColumn(seq, 15); // all positional
 234     assertEquals(features.size(), 6);
 235     assertTrue(features.contains(sf2));
 236     assertTrue(features.contains(sf3));
 237     assertTrue(features.contains(sf4));
 238     assertTrue(features.contains(sf5));
 239     assertTrue(features.contains(sf6));
 240     assertTrue(features.contains(sf7));
 241
 242     /*
 243      * at a non-contact position
 244      */
 245     features = fr.findFeaturesAtColumn(seq, 14);
 246     assertEquals(features.size(), 3);
 247     assertTrue(features.contains(sf2));
 248     assertTrue(features.contains(sf3));
 249     assertTrue(features.contains(sf4));
 250
 251     /*
 252      * make "Type2" not displayed
 253      */
 254     FeatureColourI colour = new FeatureColour(Color.RED);
 255     FeatureSettingsBean[] data = new FeatureSettingsBean[4];
 256     data[0] = new FeatureSettingsBean("Type1", colour, null, true);
 257     data[1] = new FeatureSettingsBean("Type2", colour, null, false);
 258     data[2] = new FeatureSettingsBean("Type3", colour, null, true);
 259     data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
 260             true);
 261     fr.setFeaturePriority(data);
 262
 263     features = fr.findFeaturesAtColumn(seq, 15);
 264     assertEquals(features.size(), 5); // no sf2
 265     assertTrue(features.contains(sf3));
 266     assertTrue(features.contains(sf4));
 267     assertTrue(features.contains(sf5));
 268     assertTrue(features.contains(sf6));
 269     assertTrue(features.contains(sf7));
 270
 271     /*
 272      * make "Group2" not displayed
 273      */
 274     fr.setGroupVisibility("Group2", false);
 275
 276     features = fr.findFeaturesAtColumn(seq, 15);
 277     assertEquals(features.size(), 3); // no sf2, sf3, sf6
 278     assertTrue(features.contains(sf4));
 279     assertTrue(features.contains(sf5));
 280     assertTrue(features.contains(sf7));
 281
 282     // features 'at' a gap between b and c
 283     // - returns enclosing feature BC but not contact feature B/C
 284     features = fr.findFeaturesAtColumn(seq, 4);
 285     assertEquals(features.size(), 1);
 286     assertTrue(features.contains(sf8));
 287     features = fr.findFeaturesAtColumn(seq, 5);
 288     assertEquals(features.size(), 1);
 289     assertTrue(features.contains(sf8));
 290
 291     /*
 292      * give "Type3" features a graduated colour scheme
 293      * - first with no threshold
 294      */
 295     FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
 296             Color.red, null, 0f, 10f);
 297     fr.getFeatureColours().put("Type3", gc);
 298     features = fr.findFeaturesAtColumn(seq, 8);
 299     assertTrue(features.contains(sf4));
 300     // now with threshold > 2f - feature score of 1f is excluded
 301     gc.setAboveThreshold(true);
 302     gc.setThreshold(2f);
 303     features = fr.findFeaturesAtColumn(seq, 8);
 304     assertFalse(features.contains(sf4));
 305
 306     /*
 307      * make "Type3" graduated colour by attribute "AF"
 308      * - first with no attribute held - feature should be excluded
 309      */
 310     gc.setAttributeName("AF");
 311     features = fr.findFeaturesAtColumn(seq, 8);
 312     assertFalse(features.contains(sf4));
 313     // now with the attribute above threshold - should be included
 314     sf4.setValue("AF", "2.4");
 315     features = fr.findFeaturesAtColumn(seq, 8);
 316     assertTrue(features.contains(sf4));
 317     // now with the attribute below threshold - should be excluded
 318     sf4.setValue("AF", "1.4");
 319     features = fr.findFeaturesAtColumn(seq, 8);
 320     assertFalse(features.contains(sf4));
 321   }
 322
 323   @Test(groups = "Functional")
 324   public void testFilterFeaturesForDisplay()
 325   {
 326     String seqData = ">s1\nabcdef\n";
 327     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
 328             DataSourceType.PASTE);
 329     AlignViewportI av = af.getViewport();
 330     FeatureRenderer fr = new FeatureRenderer(av);
 331
 332     List<SequenceFeature> features = new ArrayList<>();
 333     fr.filterFeaturesForDisplay(features); // empty list, does nothing
 334
 335     SequenceI seq = av.getAlignment().getSequenceAt(0);
 336     SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
 337             "group1");
 338     SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
 339             "group2");
 340     SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
 341             "group3");
 342     SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
 343             "group4");
 344     SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
 345             "group4");
 346     seq.addSequenceFeature(sf1);
 347     seq.addSequenceFeature(sf2);
 348     seq.addSequenceFeature(sf3);
 349     seq.addSequenceFeature(sf4);
 350     seq.addSequenceFeature(sf5);
 351
 352     fr.findAllFeatures(true);
 353
 354     features = seq.getSequenceFeatures();
 355     assertEquals(features.size(), 5);
 356     assertTrue(features.contains(sf1));
 357     assertTrue(features.contains(sf2));
 358     assertTrue(features.contains(sf3));
 359     assertTrue(features.contains(sf4));
 360     assertTrue(features.contains(sf5));
 361
 362     /*
 363      * filter out duplicate (co-located) features
 364      * note: which gets removed is not guaranteed
 365      */
 366     fr.filterFeaturesForDisplay(features);
 367     assertEquals(features.size(), 3);
 368     assertTrue(features.contains(sf1) || features.contains(sf4));
 369     assertFalse(features.contains(sf1) && features.contains(sf4));
 370     assertTrue(features.contains(sf2) || features.contains(sf3));
 371     assertFalse(features.contains(sf2) && features.contains(sf3));
 372     assertTrue(features.contains(sf5));
 373
 374     /*
 375      * features in hidden groups are removed
 376      */
 377     fr.setGroupVisibility("group2", false);
 378     fr.setGroupVisibility("group3", false);
 379     features = seq.getSequenceFeatures();
 380     fr.filterFeaturesForDisplay(features);
 381     assertEquals(features.size(), 2);
 382     assertTrue(features.contains(sf1) || features.contains(sf4));
 383     assertFalse(features.contains(sf1) && features.contains(sf4));
 384     assertFalse(features.contains(sf2));
 385     assertFalse(features.contains(sf3));
 386     assertTrue(features.contains(sf5));
 387
 388     /*
 389      * no filtering if transparency is applied
 390      */
 391     fr.setTransparency(0.5f);
 392     features = seq.getSequenceFeatures();
 393     fr.filterFeaturesForDisplay(features);
 394     assertEquals(features.size(), 5);
 395   }
 396
 397   @Test(groups = "Functional")
 398   public void testGetColour()
 399   {
 400     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n",
 401             DataSourceType.PASTE);
 402     AlignViewportI av = af.getViewport();
 403     FeatureRenderer fr = new FeatureRenderer(av);
 404
 405     /*
 406      * simple colour, feature type and group displayed
 407      */
 408     FeatureColourI fc = new FeatureColour(Color.red);
 409     fr.getFeatureColours().put("Cath", fc);
 410     SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
 411             "group1");
 412     assertEquals(fr.getColour(sf1), Color.red);
 413
 414     /*
 415      * hide feature type, then unhide
 416      * - feature type visibility should not affect the result
 417      */
 418     FeatureSettingsBean[] data = new FeatureSettingsBean[1];
 419     data[0] = new FeatureSettingsBean("Cath", fc, null, false);
 420     fr.setFeaturePriority(data);
 421     assertEquals(fr.getColour(sf1), Color.red);
 422     data[0] = new FeatureSettingsBean("Cath", fc, null, true);
 423     fr.setFeaturePriority(data);
 424     assertEquals(fr.getColour(sf1), Color.red);
 425
 426     /*
 427      * hide feature group, then unhide
 428      */
 429     fr.setGroupVisibility("group1", false);
 430     assertNull(fr.getColour(sf1));
 431     fr.setGroupVisibility("group1", true);
 432     assertEquals(fr.getColour(sf1), Color.red);
 433
 434     /*
 435      * graduated colour by score, no threshold, no score
 436      *
 437      */
 438     FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
 439             Color.red, Color.green, 1f, 11f);
 440     fr.getFeatureColours().put("Cath", gc);
 441     assertEquals(fr.getColour(sf1), Color.green);
 442
 443     /*
 444      * graduated colour by score, no threshold, with score value
 445      */
 446     SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
 447             "group1");
 448     // score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
 449     Color expected = new Color(255, 128, 0);
 450     assertEquals(fr.getColour(sf2), expected);
 451
 452     /*
 453      * above threshold, score is above threshold - no change
 454      */
 455     gc.setAboveThreshold(true);
 456     gc.setThreshold(5f);
 457     assertEquals(fr.getColour(sf2), expected);
 458
 459     /*
 460      * threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
 461      * or from yellow(255, 255, 0) to red(255, 0, 0)
 462      */
 463     gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
 464             5f, 11f);
 465     fr.getFeatureColours().put("Cath", gc);
 466     gc.setAutoScaled(false); // this does little other than save a checkbox setting!
 467     assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
 468
 469     /*
 470      * feature score is below threshold - no colour
 471      */
 472     gc.setAboveThreshold(true);
 473     gc.setThreshold(7f);
 474     assertNull(fr.getColour(sf2));
 475
 476     /*
 477      * feature score is above threshold - no colour
 478      */
 479     gc.setBelowThreshold(true);
 480     gc.setThreshold(3f);
 481     assertNull(fr.getColour(sf2));
 482
 483     /*
 484      * colour by feature attribute value
 485      * first with no value held
 486      */
 487     gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
 488             1f, 11f);
 489     fr.getFeatureColours().put("Cath", gc);
 490     gc.setAttributeName("AF");
 491     assertEquals(fr.getColour(sf2), Color.green);
 492
 493     // with non-numeric attribute value
 494     sf2.setValue("AF", "Five");
 495     assertEquals(fr.getColour(sf2), Color.green);
 496
 497     // with numeric attribute value
 498     sf2.setValue("AF", "6");
 499     assertEquals(fr.getColour(sf2), expected);
 500
 501     // with numeric value outwith threshold
 502     gc.setAboveThreshold(true);
 503     gc.setThreshold(10f);
 504     assertNull(fr.getColour(sf2));
 505
 506     // with filter on AF < 4
 507     gc.setAboveThreshold(false);
 508     assertEquals(fr.getColour(sf2), expected);
 509     FeatureMatcherSetI filter = new FeatureMatcherSet();
 510     filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
 511     fr.setFeatureFilter("Cath", filter);
 512     assertNull(fr.getColour(sf2));
 513
 514     // with filter on 'Consequence contains missense'
 515     filter = new FeatureMatcherSet();
 516     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
 517             "Consequence"));
 518     fr.setFeatureFilter("Cath", filter);
 519     // if feature has no Consequence attribute, no colour
 520     assertNull(fr.getColour(sf2));
 521     // if attribute does not match filter, no colour
 522     sf2.setValue("Consequence", "Synonymous");
 523     assertNull(fr.getColour(sf2));
 524     // attribute matches filter
 525     sf2.setValue("Consequence", "Missense variant");
 526     assertEquals(fr.getColour(sf2), expected);
 527
 528     // with filter on CSQ:Feature contains "ENST01234"
 529     filter = new FeatureMatcherSet();
 530     filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
 531             "CSQ", "Feature"));
 532     fr.setFeatureFilter("Cath", filter);
 533     // if feature has no CSQ data, no colour
 534     assertNull(fr.getColour(sf2));
 535     // if CSQ data does not include Feature, no colour
 536     Map<String, String> csqData = new HashMap<>();
 537     csqData.put("BIOTYPE", "Transcript");
 538     sf2.setValue("CSQ", csqData);
 539     assertNull(fr.getColour(sf2));
 540     // if attribute does not match filter, no colour
 541     csqData.put("Feature", "ENST9876");
 542     assertNull(fr.getColour(sf2));
 543     // attribute matches filter
 544     csqData.put("Feature", "ENST01234");
 545     assertEquals(fr.getColour(sf2), expected);
 546   }
 547
 548   @Test(groups = "Functional")
 549   public void testIsVisible()
 550   {
 551     String seqData = ">s1\nMLQGIFPRS\n";
 552     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
 553             DataSourceType.PASTE);
 554     AlignViewportI av = af.getViewport();
 555     FeatureRenderer fr = new FeatureRenderer(av);
 556     SequenceI seq = av.getAlignment().getSequenceAt(0);
 557     SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
 558             "Group");
 559     sf.setValue("AC", "11");
 560     sf.setValue("CLIN_SIG", "Likely Pathogenic");
 561     seq.addSequenceFeature(sf);
 562
 563     assertFalse(fr.isVisible(null));
 564
 565     /*
 566      * initial state FeatureRenderer hasn't 'found' feature
 567      * and so its feature type has not yet been set visible
 568      */
 569     assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
 570     assertFalse(fr.isVisible(sf));
 571
 572     fr.findAllFeatures(true);
 573     assertTrue(fr.isVisible(sf));
 574
 575     /*
 576      * feature group not visible
 577      */
 578     fr.setGroupVisibility("Group", false);
 579     assertFalse(fr.isVisible(sf));
 580     fr.setGroupVisibility("Group", true);
 581     assertTrue(fr.isVisible(sf));
 582
 583     /*
 584      * feature score outwith colour threshold (score > 2)
 585      */
 586     FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
 587             Color.white, 0, 10);
 588     fc.setAboveThreshold(true);
 589     fc.setThreshold(2f);
 590     fr.setColour("METAL", fc);
 591     assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
 592     fc.setBelowThreshold(true);
 593     assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
 594
 595     /*
 596      * colour with threshold on attribute AC (value is 11)
 597      */
 598     fc.setAttributeName("AC");
 599     assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
 600     fc.setAboveThreshold(true);
 601     assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
 602
 603     fc.setAttributeName("AF"); // attribute AF is absent in sf
 604     assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
 605
 606     FeatureMatcherSetI filter = new FeatureMatcherSet();
 607     filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
 608             "CLIN_SIG"));
 609     fr.setFeatureFilter("METAL", filter);
 610     assertTrue(fr.isVisible(sf)); // feature matches filter
 611     filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
 612     assertFalse(fr.isVisible(sf)); // feature doesn't match filter
 613   }
 614
 615   @Test(groups = "Functional")
 616   public void testFindComplementFeaturesAtResidue()
 617   {
 618     Jalview.main(
 619             new String[]
 620             { "-nonews", "-props", "test/jalview/testProps.jvprops" });
 621
 622     // codons for MCWHSE
 623     String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";
 624     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(cdsSeq,
 625             DataSourceType.PASTE);
 626     af.showTranslation_actionPerformed(
 627             GeneticCodes.getInstance().getStandardCodeTable());
 628     af.closeMenuItem_actionPerformed(true);
 629
 630     /*
 631      * find the complement frames (ugly)
 632      */
 633     AlignFrame[] frames = Desktop.getAlignFrames();
 634     assertEquals(frames.length, 2);
 635     AlignViewport av1 = frames[0].getViewport();
 636     AlignViewport av2 = frames[1].getViewport();
 637     AlignViewport cds = av1.getAlignment().isNucleotide() ? av1 : av2;
 638     AlignViewport peptide = cds == av1 ? av2 : av1;
 639     assertNotNull(cds);
 640     assertNotNull(peptide);
 641
 642     /*
 643      * add features to CDS at first codon, positions 2-3
 644      */
 645     SequenceI seq1 = cds.getAlignment().getSequenceAt(0);
 646     SequenceFeature sf1 = new SequenceFeature("sequence_variant", "G,GT", 2,
 647             2, "ensembl");
 648     seq1.addSequenceFeature(sf1);
 649     SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA",
 650             3, 3, "ensembl");
 651     seq1.addSequenceFeature(sf2);
 652
 653     /*
 654      * 'find' mapped features from the peptide position
 655      * - first with CDS features _not_ shown on peptide alignment
 656      */
 657     SequenceI seq2 = peptide.getAlignment().getSequenceAt(0);
 658     FeatureRenderer frC = new FeatureRenderer(cds);
 659     frC.featuresAdded();
 660     MappedFeatures mf = frC.findComplementFeaturesAtResidue(seq2, 1);
 661     assertNotNull(mf);
 662     assertEquals(mf.features.size(), 2);
 663     assertSame(mf.features.get(0), sf1);
 664     assertSame(mf.features.get(1), sf2);
 665
 666     /*
 667      * add exon feature and verify it is only returned once for a
 668      * peptide position, even though it is on all 3 codon positions
 669      */
 670     SequenceFeature sf3 = new SequenceFeature("exon", "exon1", 4, 12,
 671             "ensembl");
 672     seq1.addSequenceFeature(sf3);
 673     frC.featuresAdded();
 674     mf = frC.findComplementFeaturesAtResidue(seq2, 3);
 675     assertNotNull(mf);
 676     assertEquals(mf.features.size(), 1);
 677     assertSame(mf.features.get(0), sf3);
 678   }
 679 }