2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.renderer.seqfeatures;
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertFalse;
25 import static org.testng.Assert.assertNotEquals;
26 import static org.testng.Assert.assertNull;
27 import static org.testng.Assert.assertTrue;
29 import java.awt.Color;
30 import java.util.List;
32 import org.testng.annotations.BeforeMethod;
33 import org.testng.annotations.BeforeTest;
34 import org.testng.annotations.Test;
36 import jalview.api.FeatureColourI;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceI;
39 import jalview.gui.AlignFrame;
40 import jalview.gui.AlignViewport;
41 import jalview.io.DataSourceType;
42 import jalview.io.FileLoader;
43 import jalview.schemes.FeatureColour;
44 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
45 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
48 * Unit tests for feature colour determination, including but not limited to
50 * <li>gap position</li>
51 * <li>no features present</li>
52 * <li>features present but show features turned off</li>
53 * <li>features displayed but selected feature turned off</li>
54 * <li>features displayed but feature group turned off</li>
55 * <li>feature displayed but none at the specified position</li>
56 * <li>multiple features at position, with no transparency</li>
57 * <li>multiple features at position, with transparency</li>
58 * <li>score graduated feature colour</li>
59 * <li>contact feature start at the selected position</li>
60 * <li>contact feature end at the selected position</li>
61 * <li>contact feature straddling the selected position (not shown)</li>
64 public class FeatureColourFinderTest
66 private AlignViewport av;
68 private SequenceI seq;
70 private FeatureColourFinder finder;
72 private AlignFrame af;
74 private FeatureRendererModel fr;
76 @BeforeTest(alwaysRun = true)
79 // aligned column 8 is sequence position 6
80 String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
81 af = new FileLoader().LoadFileWaitTillLoaded(s, DataSourceType.PASTE);
82 av = af.getViewport();
83 seq = av.getAlignment().getSequenceAt(0);
84 fr = af.getFeatureRenderer();
85 finder = new FeatureColourFinder(fr);
89 * Clear down any sequence features before each test (not as easy as it
92 @BeforeMethod(alwaysRun = true)
93 public void setUpBeforeTest()
95 List<SequenceFeature> sfs = seq.getSequenceFeatures();
96 for (SequenceFeature sf : sfs)
98 seq.deleteFeature(sf);
100 fr.findAllFeatures(true);
103 * reset all feature groups to visible
105 for (String group : fr.getGroups(false))
107 fr.setGroupVisibility(group, true);
110 fr.clearRenderOrder();
111 av.setShowSequenceFeatures(true);
114 @Test(groups = "Functional")
115 public void testFindFeatureColour_noFeatures()
117 av.setShowSequenceFeatures(false);
118 Color c = finder.findFeatureColour(Color.blue, seq, 10);
119 assertEquals(c, Color.blue);
121 av.setShowSequenceFeatures(true);
122 c = finder.findFeatureColour(Color.blue, seq, 10);
123 assertEquals(c, Color.blue);
126 @Test(groups = "Functional")
127 public void testFindFeatureColour_noFeaturesShown()
129 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
130 Float.NaN, "MetalGroup"));
132 av.setShowSequenceFeatures(false);
133 Color c = finder.findFeatureColour(Color.blue, seq, 10);
134 assertEquals(c, Color.blue);
137 @Test(groups = "Functional")
138 public void testFindFeatureColour_singleFeatureAtPosition()
140 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
141 Float.NaN, "MetalGroup"));
142 fr.setColour("Metal", new FeatureColour(Color.red));
144 av.setShowSequenceFeatures(true);
145 Color c = finder.findFeatureColour(Color.blue, seq, 10);
146 assertEquals(c, Color.red);
150 * feature colour at a gap is null (not white) - a user defined colour scheme
151 * can then provide a bespoke gap colour if configured to do so
153 @Test(groups = "Functional")
154 public void testFindFeatureColour_gapPosition()
156 seq.addSequenceFeature(
157 new SequenceFeature("Metal", "Metal", 2, 12, 0f, null));
158 fr.setColour("Metal", new FeatureColour(Color.red));
160 av.setShowSequenceFeatures(true);
161 Color c = finder.findFeatureColour(null, seq, 6);
166 * Nested features coloured by label - expect the colour of the enclosed
169 @Test(groups = "Functional")
170 public void testFindFeatureColour_nestedFeatures()
172 SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120,
174 seq.addSequenceFeature(sf1);
175 SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20,
177 seq.addSequenceFeature(sf2);
178 FeatureColourI fc = new FeatureColour(Color.red);
179 fc.setColourByLabel(true);
180 fr.setColour("domain", fc);
182 av.setShowSequenceFeatures(true);
183 Color c = finder.findFeatureColour(null, seq, 15);
184 assertEquals(c, fr.getColor(sf2, fc));
187 @Test(groups = "Functional")
188 public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
191 * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
192 * new features 'on top' (but reverses the order of any added features)
194 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
195 Float.NaN, "MetalGroup"));
196 FeatureColour red = new FeatureColour(Color.red);
197 fr.setColour("Metal", red);
199 seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
200 Float.NaN, "DomainGroup"));
201 FeatureColour green = new FeatureColour(Color.green);
202 fr.setColour("Domain", green);
204 av.setShowSequenceFeatures(true);
207 * expect Domain (green) to be rendered above Metal (red)
209 Color c = finder.findFeatureColour(Color.blue, seq, 10);
210 assertEquals(c, Color.green);
213 * now promote Metal above Domain
214 * - currently no way other than mimicking reordering of
215 * table in Feature Settings
217 FeatureSettingsBean[] data = new FeatureSettingsBean[2];
218 data[0] = new FeatureSettingsBean("Metal", red, null, true);
219 data[1] = new FeatureSettingsBean("Domain", green, null, true);
220 fr.setFeaturePriority(data);
221 c = finder.findFeatureColour(Color.blue, seq, 10);
222 assertEquals(c, Color.red);
225 * ..and turn off display of Metal
227 data[0] = new FeatureSettingsBean("Metal", red, null, false);
228 fr.setFeaturePriority(data);
229 c = finder.findFeatureColour(Color.blue, seq, 10);
230 assertEquals(c, Color.green);
233 @Test(groups = "Functional")
234 public void testFindFeatureColour_singleFeatureNotAtPosition()
236 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
237 Float.NaN, "MetalGroup"));
238 fr.setColour("Metal", new FeatureColour(Color.red));
240 av.setShowSequenceFeatures(true);
241 // column 2 = sequence position 3
242 Color c = finder.findFeatureColour(Color.blue, seq, 2);
243 assertEquals(c, Color.blue);
246 @Test(groups = "Functional")
247 public void testFindFeatureColour_featureTypeNotDisplayed()
249 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
250 Float.NaN, "MetalGroup"));
251 FeatureColour red = new FeatureColour(Color.red);
252 fr.setColour("Metal", red);
254 av.setShowSequenceFeatures(true);
255 Color c = finder.findFeatureColour(Color.blue, seq, 10);
256 assertEquals(c, Color.red);
259 * turn off display of Metal - is this the easiest way to do it??
261 FeatureSettingsBean[] data = new FeatureSettingsBean[1];
262 data[0] = new FeatureSettingsBean("Metal", red, null, false);
263 fr.setFeaturePriority(data);
264 c = finder.findFeatureColour(Color.blue, seq, 10);
265 assertEquals(c, Color.blue);
268 * turn display of Metal back on
270 data[0] = new FeatureSettingsBean("Metal", red, null, true);
271 fr.setFeaturePriority(data);
272 c = finder.findFeatureColour(Color.blue, seq, 10);
273 assertEquals(c, Color.red);
276 @Test(groups = "Functional")
277 public void testFindFeatureColour_featureGroupNotDisplayed()
279 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
280 Float.NaN, "MetalGroup"));
281 FeatureColour red = new FeatureColour(Color.red);
282 fr.setColour("Metal", red);
284 av.setShowSequenceFeatures(true);
285 Color c = finder.findFeatureColour(Color.blue, seq, 10);
286 assertEquals(c, Color.red);
289 * turn off display of MetalGroup
291 fr.setGroupVisibility("MetalGroup", false);
292 c = finder.findFeatureColour(Color.blue, seq, 10);
293 assertEquals(c, Color.blue);
296 * turn display of MetalGroup back on
298 fr.setGroupVisibility("MetalGroup", true);
299 c = finder.findFeatureColour(Color.blue, seq, 10);
300 assertEquals(c, Color.red);
303 @Test(groups = "Functional")
304 public void testFindFeatureColour_contactFeature()
307 * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
309 seq.addSequenceFeature(new SequenceFeature("Disulphide Bond", "Contact",
310 2, 12, Float.NaN, "Disulphide"));
311 fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
313 av.setShowSequenceFeatures(true);
316 * Contact positions are residues 2 and 12
317 * which are columns 1 and 14
318 * positions in between don't count for a contact feature!
320 Color c = finder.findFeatureColour(Color.blue, seq, 10);
321 assertEquals(c, Color.blue);
322 c = finder.findFeatureColour(Color.blue, seq, 8);
323 assertEquals(c, Color.blue);
324 c = finder.findFeatureColour(Color.blue, seq, 1);
325 assertEquals(c, Color.red);
326 c = finder.findFeatureColour(Color.blue, seq, 14);
327 assertEquals(c, Color.red);
330 @Test(groups = "Functional")
331 public void testFindFeatureAtEnd()
334 * terminal residue feature
336 seq.addSequenceFeature(new SequenceFeature("PDBRESNUM", "pdb res 1",
337 seq.getEnd(), seq.getEnd(), Float.NaN, "1seq.pdb"));
338 fr.setColour("PDBRESNUM", new FeatureColour(Color.red));
340 av.setShowSequenceFeatures(true);
343 * final column should have PDBRESNUM feature, the others not
345 Color c = finder.findFeatureColour(Color.blue, seq,
346 seq.getLength() - 2);
347 assertNotEquals(c, Color.red);
348 c = finder.findFeatureColour(Color.blue, seq, seq.getLength() - 1);
349 assertEquals(c, Color.red);
352 @Test(groups = "Functional")
353 public void testFindFeatureColour_graduatedFeatureColour()
355 seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2, 2,
357 seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4, 4,
359 seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7, 7,
363 * graduated colour from 0 to 10
365 Color min = new Color(100, 50, 150);
366 Color max = new Color(200, 0, 100);
367 FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
368 fr.setColour("kd", fc);
370 av.setShowSequenceFeatures(true);
373 * position 2, column 1, score 0 - minimum colour in range
375 Color c = finder.findFeatureColour(Color.blue, seq, 1);
376 assertEquals(c, min);
379 * position 7, column 9, score 10 - maximum colour in range
381 c = finder.findFeatureColour(Color.blue, seq, 9);
382 assertEquals(c, max);
385 * position 4, column 3, score 5 - half way from min to max
387 c = finder.findFeatureColour(Color.blue, seq, 3);
388 assertEquals(c, new Color(150, 25, 125));
391 @Test(groups = "Functional")
392 public void testFindFeatureColour_transparencySingleFeature()
394 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
395 Float.NaN, "MetalGroup"));
396 FeatureColour red = new FeatureColour(Color.red);
397 fr.setColour("Metal", red);
399 av.setShowSequenceFeatures(true);
402 * the FeatureSettings transparency slider has range 0-70 which
403 * corresponds to a transparency value of 1 - 0.3
404 * A value of 0.4 gives a combination of
405 * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
407 fr.setTransparency(0.4f);
408 Color c = finder.findFeatureColour(Color.cyan, seq, 10);
409 assertEquals(c, new Color(102, 153, 153));
412 @Test(groups = "Functional")
413 public void testFindFeatureColour_transparencyTwoFeatures()
415 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
416 Float.NaN, "MetalGroup"));
417 FeatureColour red = new FeatureColour(Color.red);
418 fr.setColour("Metal", red);
420 seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
421 Float.NaN, "DomainGroup"));
422 FeatureColour green = new FeatureColour(Color.green);
423 fr.setColour("Domain", green);
425 av.setShowSequenceFeatures(true);
428 * Domain (green) rendered above Metal (red) above background (cyan)
429 * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
430 * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
432 fr.setTransparency(0.6f);
433 Color c = finder.findFeatureColour(Color.cyan, seq, 10);
434 assertEquals(c, new Color(61, 194, 41));
437 * now promote Metal above Domain
438 * - currently no way other than mimicking reordering of
439 * table in Feature Settings
440 * Metal (red) rendered above Domain (green) above background (cyan)
441 * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
442 * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
444 FeatureSettingsBean[] data = new FeatureSettingsBean[2];
445 data[0] = new FeatureSettingsBean("Metal", red, null, true);
446 data[1] = new FeatureSettingsBean("Domain", green, null, true);
447 fr.setFeaturePriority(data);
448 c = finder.findFeatureColour(Color.cyan, seq, 10);
449 assertEquals(c, new Color(153, 102, 41));
452 * ..and turn off display of Metal
453 * Domain (green) above background (pink)
454 * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
456 data[0] = new FeatureSettingsBean("Metal", red, null, false);
457 fr.setFeaturePriority(data);
458 c = finder.findFeatureColour(Color.pink, seq, 10);
459 assertEquals(c, new Color(102, 223, 70));
462 @Test(groups = "Functional")
463 public void testNoFeaturesDisplayed()
466 * no features on alignment to render
468 assertTrue(finder.noFeaturesDisplayed());
472 * it will be automatically set visible but we leave
473 * the viewport configured not to show features
475 av.setShowSequenceFeatures(false);
476 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
477 Float.NaN, "MetalGroup"));
478 FeatureColour red = new FeatureColour(Color.red);
479 fr.setColour("Metal", red);
481 assertTrue(finder.noFeaturesDisplayed());
484 * turn on feature display
486 av.setShowSequenceFeatures(true);
487 assertFalse(finder.noFeaturesDisplayed());
490 * turn off display of Metal
492 FeatureSettingsBean[] data = new FeatureSettingsBean[1];
493 data[0] = new FeatureSettingsBean("Metal", red, null, false);
494 fr.setFeaturePriority(data);
495 assertTrue(finder.noFeaturesDisplayed());
498 * turn display of Metal back on
500 fr.setVisible("Metal");
501 assertFalse(finder.noFeaturesDisplayed());
504 * turn off MetalGroup - has no effect here since the group of a
505 * sequence feature instance is independent of its type
507 fr.setGroupVisibility("MetalGroup", false);
508 assertFalse(finder.noFeaturesDisplayed());
511 * a finder with no feature renderer
513 FeatureColourFinder finder2 = new FeatureColourFinder(null);
514 assertTrue(finder2.noFeaturesDisplayed());
517 @Test(groups = "Functional")
518 public void testFindFeatureColour_graduatedWithThreshold()
520 String kdFeature = "kd";
521 String metalFeature = "Metal";
522 seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
523 2, 2, 0f, "KdGroup"));
524 seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
525 4, 4, 5f, "KdGroup"));
526 seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4, 5f,
528 seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
529 7, 7, 10f, "KdGroup"));
532 * kd feature has graduated colour from 0 to 10
533 * above threshold value of 5
535 Color min = new Color(100, 50, 150);
536 Color max = new Color(200, 0, 100);
537 FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
538 fc.setAboveThreshold(true);
540 fr.setColour(kdFeature, fc);
541 FeatureColour green = new FeatureColour(Color.green);
542 fr.setColour(metalFeature, green);
546 * render order is kd above Metal
548 FeatureSettingsBean[] data = new FeatureSettingsBean[2];
549 data[0] = new FeatureSettingsBean(kdFeature, fc, null, true);
550 data[1] = new FeatureSettingsBean(metalFeature, green, null, true);
551 fr.setFeaturePriority(data);
553 av.setShowSequenceFeatures(true);
556 * position 2, column 1, score 0 - below threshold - default colour
558 Color c = finder.findFeatureColour(Color.blue, seq, 1);
559 assertEquals(c, Color.blue);
562 * position 4, column 3, score 5 - at threshold
563 * should return Green (colour of Metal feature)
565 c = finder.findFeatureColour(Color.blue, seq, 3);
566 assertEquals(c, Color.green);
569 * position 7, column 9, score 10 - maximum colour in range
571 c = finder.findFeatureColour(Color.blue, seq, 9);
572 assertEquals(c, max);
575 * now colour below threshold of 5
577 fc.setBelowThreshold(true);
580 * position 2, column 1, score 0 - min colour
582 c = finder.findFeatureColour(Color.blue, seq, 1);
583 assertEquals(c, min);
586 * position 4, column 3, score 5 - at threshold
587 * should return Green (colour of Metal feature)
589 c = finder.findFeatureColour(Color.blue, seq, 3);
590 assertEquals(c, Color.green);
593 * position 7, column 9, score 10 - above threshold - default colour
595 c = finder.findFeatureColour(Color.blue, seq, 9);
596 assertEquals(c, Color.blue);