1 package jalview.renderer.seqfeatures;
3 import static org.testng.Assert.assertEquals;
4 import static org.testng.Assert.assertFalse;
5 import static org.testng.Assert.assertNull;
6 import static org.testng.Assert.assertTrue;
8 import jalview.api.FeatureColourI;
9 import jalview.datamodel.SequenceFeature;
10 import jalview.datamodel.SequenceI;
11 import jalview.gui.AlignFrame;
12 import jalview.gui.AlignViewport;
13 import jalview.gui.FeatureRenderer;
14 import jalview.io.DataSourceType;
15 import jalview.io.FileLoader;
16 import jalview.schemes.FeatureColour;
18 import java.awt.Color;
20 import org.testng.annotations.BeforeMethod;
21 import org.testng.annotations.BeforeTest;
22 import org.testng.annotations.Test;
25 * Unit tests for feature colour determination, including but not limited to
27 * <li>gap position</li>
28 * <li>no features present</li>
29 * <li>features present but show features turned off</li>
30 * <li>features displayed but selected feature turned off</li>
31 * <li>features displayed but feature group turned off</li>
32 * <li>feature displayed but none at the specified position</li>
33 * <li>multiple features at position, with no transparency</li>
34 * <li>multiple features at position, with transparency</li>
35 * <li>score graduated feature colour</li>
36 * <li>contact feature start at the selected position</li>
37 * <li>contact feature end at the selected position</li>
38 * <li>contact feature straddling the selected position (not shown)</li>
41 public class FeatureColourFinderTest
43 private AlignViewport av;
45 private SequenceI seq;
47 private FeatureColourFinder finder;
49 private AlignFrame af;
51 private FeatureRenderer fr;
53 @BeforeTest(alwaysRun = true)
56 // aligned column 8 is sequence position 6
57 String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
58 af = new FileLoader().LoadFileWaitTillLoaded(s,
59 DataSourceType.PASTE);
60 av = af.getViewport();
61 seq = av.getAlignment().getSequenceAt(0);
62 fr = af.getFeatureRenderer();
63 finder = new FeatureColourFinder(fr);
67 * Clear down any sequence features before each test (not as easy as it
70 @BeforeMethod(alwaysRun = true)
71 public void setUpBeforeTest()
73 SequenceFeature[] sfs = seq.getSequenceFeatures();
76 for (SequenceFeature sf : sfs)
78 seq.deleteFeature(sf);
81 fr.findAllFeatures(true);
84 * reset all feature groups to visible
86 for (String group : fr.getGroups(false))
88 fr.setGroupVisibility(group, true);
91 fr.clearRenderOrder();
92 av.setShowSequenceFeatures(true);
95 @Test(groups = "Functional")
96 public void testFindFeatureColour_noFeatures()
98 av.setShowSequenceFeatures(false);
99 Color c = finder.findFeatureColour(Color.blue, seq, 10);
100 assertEquals(c, Color.blue);
102 av.setShowSequenceFeatures(true);
103 c = finder.findFeatureColour(Color.blue, seq, 10);
104 assertEquals(c, Color.blue);
107 @Test(groups = "Functional")
108 public void testFindFeatureColour_noFeaturesShown()
110 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
111 Float.NaN, "MetalGroup"));
113 av.setShowSequenceFeatures(false);
114 Color c = finder.findFeatureColour(Color.blue, seq, 10);
115 assertEquals(c, Color.blue);
118 @Test(groups = "Functional")
119 public void testFindFeatureColour_singleFeatureAtPosition()
121 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
122 Float.NaN, "MetalGroup"));
123 fr.setColour("Metal", new FeatureColour(Color.red));
125 av.setShowSequenceFeatures(true);
126 Color c = finder.findFeatureColour(Color.blue, seq, 10);
127 assertEquals(c, Color.red);
131 * feature colour at a gap is null (not white) - a user defined colour scheme
132 * can then provide a bespoke gap colour if configured to do so
134 @Test(groups = "Functional")
135 public void testFindFeatureColour_gapPosition()
137 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
139 fr.setColour("Metal", new FeatureColour(Color.red));
141 av.setShowSequenceFeatures(true);
142 Color c = finder.findFeatureColour(null, seq, 6);
146 @Test(groups = "Functional")
147 public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
150 * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
151 * new features 'on top' (but reverses the order of any added features)
153 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
154 Float.NaN, "MetalGroup"));
155 FeatureColour red = new FeatureColour(Color.red);
156 fr.setColour("Metal", red);
158 seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
159 Float.NaN, "DomainGroup"));
160 FeatureColour green = new FeatureColour(Color.green);
161 fr.setColour("Domain", green);
163 av.setShowSequenceFeatures(true);
166 * expect Domain (green) to be rendered above Metal (red)
168 Color c = finder.findFeatureColour(Color.blue, seq, 10);
169 assertEquals(c, Color.green);
172 * now promote Metal above Domain
173 * - currently no way other than mimicking reordering of
174 * table in Feature Settings
176 Object[][] data = new Object[2][];
177 data[0] = new Object[] { "Metal", red, true };
178 data[1] = new Object[] { "Domain", green, true };
179 fr.setFeaturePriority(data);
180 c = finder.findFeatureColour(Color.blue, seq, 10);
181 assertEquals(c, Color.red);
184 * ..and turn off display of Metal
187 fr.setFeaturePriority(data);
188 c = finder.findFeatureColour(Color.blue, seq, 10);
189 assertEquals(c, Color.green);
192 @Test(groups = "Functional")
193 public void testFindFeatureColour_singleFeatureNotAtPosition()
195 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
196 Float.NaN, "MetalGroup"));
197 fr.setColour("Metal", new FeatureColour(Color.red));
199 av.setShowSequenceFeatures(true);
200 // column 2 = sequence position 3
201 Color c = finder.findFeatureColour(Color.blue, seq, 2);
202 assertEquals(c, Color.blue);
205 @Test(groups = "Functional")
206 public void testFindFeatureColour_featureTypeNotDisplayed()
208 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
209 Float.NaN, "MetalGroup"));
210 FeatureColour red = new FeatureColour(Color.red);
211 fr.setColour("Metal", red);
213 av.setShowSequenceFeatures(true);
214 Color c = finder.findFeatureColour(Color.blue, seq, 10);
215 assertEquals(c, Color.red);
218 * turn off display of Metal - is this the easiest way to do it??
220 Object[][] data = new Object[1][];
221 data[0] = new Object[] { "Metal", red, false };
222 fr.setFeaturePriority(data);
223 c = finder.findFeatureColour(Color.blue, seq, 10);
224 assertEquals(c, Color.blue);
227 * turn display of Metal back on
229 data[0] = new Object[] { "Metal", red, true };
230 fr.setFeaturePriority(data);
231 c = finder.findFeatureColour(Color.blue, seq, 10);
232 assertEquals(c, Color.red);
235 @Test(groups = "Functional")
236 public void testFindFeatureColour_featureGroupNotDisplayed()
238 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
239 Float.NaN, "MetalGroup"));
240 FeatureColour red = new FeatureColour(Color.red);
241 fr.setColour("Metal", red);
243 av.setShowSequenceFeatures(true);
244 Color c = finder.findFeatureColour(Color.blue, seq, 10);
245 assertEquals(c, Color.red);
248 * turn off display of MetalGroup
250 fr.setGroupVisibility("MetalGroup", false);
251 c = finder.findFeatureColour(Color.blue, seq, 10);
252 assertEquals(c, Color.blue);
255 * turn display of MetalGroup back on
257 fr.setGroupVisibility("MetalGroup", true);
258 c = finder.findFeatureColour(Color.blue, seq, 10);
259 assertEquals(c, Color.red);
262 @Test(groups = "Functional")
263 public void testFindFeatureColour_contactFeature()
266 * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
268 seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
269 "Contact", 2, 12, Float.NaN, "Disulphide"));
270 fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
272 av.setShowSequenceFeatures(true);
275 * Contact positions are residues 2 and 12
276 * which are columns 1 and 14
277 * positions in between don't count for a contact feature!
279 Color c = finder.findFeatureColour(Color.blue, seq, 10);
280 assertEquals(c, Color.blue);
281 c = finder.findFeatureColour(Color.blue, seq, 8);
282 assertEquals(c, Color.blue);
283 c = finder.findFeatureColour(Color.blue, seq, 1);
284 assertEquals(c, Color.red);
285 c = finder.findFeatureColour(Color.blue, seq, 14);
286 assertEquals(c, Color.red);
289 @Test(groups = "Functional")
290 public void testFindFeatureColour_graduatedFeatureColour()
292 seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
294 seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
296 seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
300 * graduated colour from 0 to 10
302 Color min = new Color(100, 50, 150);
303 Color max = new Color(200, 0, 100);
304 FeatureColourI fc = new FeatureColour(min, max, 0, 10);
305 fr.setColour("kd", fc);
307 av.setShowSequenceFeatures(true);
310 * position 2, column 1, score 0 - minimum colour in range
312 Color c = finder.findFeatureColour(Color.blue, seq, 1);
313 assertEquals(c, min);
316 * position 7, column 9, score 10 - maximum colour in range
318 c = finder.findFeatureColour(Color.blue, seq, 9);
319 assertEquals(c, max);
322 * position 4, column 3, score 5 - half way from min to max
324 c = finder.findFeatureColour(Color.blue, seq, 3);
325 assertEquals(c, new Color(150, 25, 125));
328 @Test(groups = "Functional")
329 public void testFindFeatureColour_transparencySingleFeature()
331 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
332 Float.NaN, "MetalGroup"));
333 FeatureColour red = new FeatureColour(Color.red);
334 fr.setColour("Metal", red);
336 av.setShowSequenceFeatures(true);
339 * the FeatureSettings transparency slider has range 0-70 which
340 * corresponds to a transparency value of 1 - 0.3
341 * A value of 0.4 gives a combination of
342 * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
344 fr.setTransparency(0.4f);
345 Color c = finder.findFeatureColour(Color.cyan, seq, 10);
346 assertEquals(c, new Color(102, 153, 153));
349 @Test(groups = "Functional")
350 public void testFindFeatureColour_transparencyTwoFeatures()
352 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
353 Float.NaN, "MetalGroup"));
354 FeatureColour red = new FeatureColour(Color.red);
355 fr.setColour("Metal", red);
357 seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
358 Float.NaN, "DomainGroup"));
359 FeatureColour green = new FeatureColour(Color.green);
360 fr.setColour("Domain", green);
362 av.setShowSequenceFeatures(true);
365 * Domain (green) rendered above Metal (red) above background (cyan)
366 * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
367 * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
369 fr.setTransparency(0.6f);
370 Color c = finder.findFeatureColour(Color.cyan, seq, 10);
371 assertEquals(c, new Color(61, 194, 41));
374 * now promote Metal above Domain
375 * - currently no way other than mimicking reordering of
376 * table in Feature Settings
377 * Metal (red) rendered above Domain (green) above background (cyan)
378 * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
379 * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
381 Object[][] data = new Object[2][];
382 data[0] = new Object[] { "Metal", red, true };
383 data[1] = new Object[] { "Domain", green, true };
384 fr.setFeaturePriority(data);
385 c = finder.findFeatureColour(Color.cyan, seq, 10);
386 assertEquals(c, new Color(153, 102, 41));
389 * ..and turn off display of Metal
390 * Domain (green) above background (pink)
391 * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
394 fr.setFeaturePriority(data);
395 c = finder.findFeatureColour(Color.pink, seq, 10);
396 assertEquals(c, new Color(102, 223, 70));
399 @Test(groups = "Functional")
400 public void testNoFeaturesDisplayed()
403 * no features on alignment to render
405 assertTrue(finder.noFeaturesDisplayed());
409 * it will be automatically set visible but we leave
410 * the viewport configured not to show features
412 av.setShowSequenceFeatures(false);
413 seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
414 Float.NaN, "MetalGroup"));
415 FeatureColour red = new FeatureColour(Color.red);
416 fr.setColour("Metal", red);
418 assertTrue(finder.noFeaturesDisplayed());
421 * turn on feature display
423 av.setShowSequenceFeatures(true);
424 assertFalse(finder.noFeaturesDisplayed());
427 * turn off display of Metal
429 Object[][] data = new Object[1][];
430 data[0] = new Object[] { "Metal", red, false };
431 fr.setFeaturePriority(data);
432 assertTrue(finder.noFeaturesDisplayed());
435 * turn display of Metal back on
437 fr.setVisible("Metal");
438 assertFalse(finder.noFeaturesDisplayed());
441 * turn off MetalGroup - has no effect here since the group of a
442 * sequence feature instance is independent of its type
444 fr.setGroupVisibility("MetalGroup", false);
445 assertFalse(finder.noFeaturesDisplayed());
448 * a finder with no feature renderer
450 FeatureColourFinder finder2 = new FeatureColourFinder(null);
451 assertTrue(finder2.noFeaturesDisplayed());