Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureRendererTest	51	263	4	0	1.0100%	Show methods

Class FeatureRendererTest

Class FeatureRendererTest	Line # 51	Total Statements 263	Complexity 4	Uncovered Elements 0	TOTAL Coverage 1.0100%
testFindAllFeatures() : void   testFindAllFeatures() : void	5454	61.061	1.01	0.00	1.0 1.0100%
testFindFeaturesAtColumn() : void   testFindFeaturesAtColumn() : void	168168	82.082	1.01	0.00	1.0 1.0100%
testFilterFeaturesForDisplay() : void   testFilterFeaturesForDisplay() : void	316316	46.046	1.01	0.00	1.0 1.0100%
testGetColour() : void   testGetColour() : void	390390	74.074	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3108614	jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn	1PASS
	0.28089887	jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour	1PASS
	0.23220974	jalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeaturesjalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeatures	1PASS
	0.17602997	jalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplayjalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplay	1PASS

 

Source view

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.assertNull;
26		import static org.testng.Assert.assertTrue;
27
28		import jalview.api.AlignViewportI;
29		import jalview.api.FeatureColourI;
30		import jalview.datamodel.SequenceFeature;
31		import jalview.datamodel.SequenceI;
32		import jalview.datamodel.features.FeatureMatcher;
33		import jalview.datamodel.features.FeatureMatcherSet;
34		import jalview.datamodel.features.FeatureMatcherSetI;
35		import jalview.gui.AlignFrame;
36		import jalview.io.DataSourceType;
37		import jalview.io.FileLoader;
38		import jalview.schemes.FeatureColour;
39		import jalview.util.matcher.Condition;
40		import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
41
42		import java.awt.Color;
43		import java.util.ArrayList;
44		import java.util.Arrays;
45		import java.util.HashMap;
46		import java.util.List;
47		import java.util.Map;
48
49		import org.testng.annotations.Test;
50
		100% Uncovered Elements: 0 (267) Complexity: 4 Complexity Density: 0.02
51		public class FeatureRendererTest
52		{
53
		100% Uncovered Elements: 0 (61) Complexity: 1 Complexity Density: 0.02 1PASS
54	1	@Test(groups = "Functional")...
55		public void testFindAllFeatures()
56		{
57	1	String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
58	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
59		DataSourceType.PASTE);
60	1	AlignViewportI av = af.getViewport();
61	1	FeatureRenderer fr = new FeatureRenderer(av);
62
63		/*
64		* with no features
65		*/
66	1	fr.findAllFeatures(true);
67	1	assertTrue(fr.getRenderOrder().isEmpty());
68	1	assertTrue(fr.getFeatureGroups().isEmpty());
69
70	1	List<SequenceI> seqs = av.getAlignment().getSequences();
71
72		// add a non-positional feature - should be ignored by FeatureRenderer
73	1	SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
74		"Group");
75	1	seqs.get(0).addSequenceFeature(sf1);
76	1	fr.findAllFeatures(true);
77		// ? bug - types and groups added for non-positional features
78	1	List<String> types = fr.getRenderOrder();
79	1	List<String> groups = fr.getFeatureGroups();
80	1	assertEquals(types.size(), 0);
81	1	assertFalse(types.contains("Type"));
82	1	assertEquals(groups.size(), 0);
83	1	assertFalse(groups.contains("Group"));
84
85		// add some positional features
86	1	seqs.get(1).addSequenceFeature(
87		new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
88	1	seqs.get(2).addSequenceFeature(
89		new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
90		// bug in findAllFeatures - group not checked for a known feature type
91	1	seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9,
92		Float.NaN, "RfamGroup"));
93		// existing feature type with null group
94	1	seqs.get(3).addSequenceFeature(
95		new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
96		// new feature type with null group
97	1	seqs.get(3).addSequenceFeature(
98		new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
99		// null value for type produces NullPointerException
100	1	fr.findAllFeatures(true);
101	1	types = fr.getRenderOrder();
102	1	groups = fr.getFeatureGroups();
103	1	assertEquals(types.size(), 3);
104	1	assertFalse(types.contains("Type"));
105	1	assertTrue(types.contains("Pfam"));
106	1	assertTrue(types.contains("Rfam"));
107	1	assertTrue(types.contains("Scop"));
108	1	assertEquals(groups.size(), 2);
109	1	assertFalse(groups.contains("Group"));
110	1	assertTrue(groups.contains("PfamGroup"));
111	1	assertTrue(groups.contains("RfamGroup"));
112	1	assertFalse(groups.contains(null)); // null group is ignored
113
114		/*
115		* check min-max values
116		*/
117	1	Map<String, float[][]> minMax = fr.getMinMax();
118	1	assertEquals(minMax.size(), 1); // non-positional and NaN not stored
119	1	assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
120	1	assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
121
122		// increase max for Pfam, add scores for Rfam
123	1	seqs.get(0).addSequenceFeature(
124		new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
125	1	seqs.get(1).addSequenceFeature(
126		new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
127	1	fr.findAllFeatures(true);
128		// note minMax is not a defensive copy, shouldn't expose this
129	1	assertEquals(minMax.size(), 2);
130	1	assertEquals(minMax.get("Pfam")[0][0], 1f);
131	1	assertEquals(minMax.get("Pfam")[0][1], 8f);
132	1	assertEquals(minMax.get("Rfam")[0][0], 6f);
133	1	assertEquals(minMax.get("Rfam")[0][1], 6f);
134
135		/*
136		* check render order (last is on top)
137		*/
138	1	List<String> renderOrder = fr.getRenderOrder();
139	1	assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
140
141		/*
142		* change render order (todo: an easier way)
143		* nb here last comes first in the data array
144		*/
145	1	FeatureSettingsBean[] data = new FeatureSettingsBean[3];
146	1	FeatureColourI colour = new FeatureColour(Color.RED);
147	1	data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
148	1	data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
149	1	data[2] = new FeatureSettingsBean("Scop", colour, null, false);
150	1	fr.setFeaturePriority(data);
151	1	assertEquals(fr.getRenderOrder(),
152		Arrays.asList("Scop", "Pfam", "Rfam"));
153	1	assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
154
155		/*
156		* add a new feature type: should go on top of render order as visible,
157		* other feature ordering and visibility should be unchanged
158		*/
159	1	seqs.get(2).addSequenceFeature(
160		new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
161	1	fr.findAllFeatures(true);
162	1	assertEquals(fr.getRenderOrder(),
163		Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
164	1	assertEquals(fr.getDisplayedFeatureTypes(),
165		Arrays.asList("Rfam", "Metal"));
166		}
167
		100% Uncovered Elements: 0 (82) Complexity: 1 Complexity Density: 0.01 1PASS
168	1	@Test(groups = "Functional")...
169		public void testFindFeaturesAtColumn()
170		{
171	1	String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
172	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
173		DataSourceType.PASTE);
174	1	AlignViewportI av = af.getViewport();
175	1	FeatureRenderer fr = new FeatureRenderer(av);
176	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
177
178		/*
179		* with no features
180		*/
181	1	List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
182	1	assertTrue(features.isEmpty());
183
184		/*
185		* add features
186		*/
187	1	SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
188		"Group"); // non-positional
189	1	seq.addSequenceFeature(sf1);
190	1	SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
191		"Group1");
192	1	seq.addSequenceFeature(sf2);
193	1	SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
194		"Group2");
195	1	seq.addSequenceFeature(sf3);
196	1	SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
197		null); // null group is always treated as visible
198	1	seq.addSequenceFeature(sf4);
199
200		/*
201		* add contact features
202		*/
203	1	SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
204		15, 1f, "Group1");
205	1	seq.addSequenceFeature(sf5);
206	1	SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
207		15, 1f, "Group2");
208	1	seq.addSequenceFeature(sf6);
209	1	SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
210		15, 1f, null);
211	1	seq.addSequenceFeature(sf7);
212
213		// feature spanning B--C
214	1	SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
215		"Group");
216	1	seq.addSequenceFeature(sf8);
217		// contact feature B/C
218	1	SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
219		6, 1f, "Group");
220	1	seq.addSequenceFeature(sf9);
221
222		/*
223		* let feature renderer discover features (and make visible)
224		*/
225	1	fr.findAllFeatures(true);
226	1	features = fr.findFeaturesAtColumn(seq, 15); // all positional
227	1	assertEquals(features.size(), 6);
228	1	assertTrue(features.contains(sf2));
229	1	assertTrue(features.contains(sf3));
230	1	assertTrue(features.contains(sf4));
231	1	assertTrue(features.contains(sf5));
232	1	assertTrue(features.contains(sf6));
233	1	assertTrue(features.contains(sf7));
234
235		/*
236		* at a non-contact position
237		*/
238	1	features = fr.findFeaturesAtColumn(seq, 14);
239	1	assertEquals(features.size(), 3);
240	1	assertTrue(features.contains(sf2));
241	1	assertTrue(features.contains(sf3));
242	1	assertTrue(features.contains(sf4));
243
244		/*
245		* make "Type2" not displayed
246		*/
247	1	FeatureColourI colour = new FeatureColour(Color.RED);
248	1	FeatureSettingsBean[] data = new FeatureSettingsBean[4];
249	1	data[0] = new FeatureSettingsBean("Type1", colour, null, true);
250	1	data[1] = new FeatureSettingsBean("Type2", colour, null, false);
251	1	data[2] = new FeatureSettingsBean("Type3", colour, null, true);
252	1	data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
253		true);
254	1	fr.setFeaturePriority(data);
255
256	1	features = fr.findFeaturesAtColumn(seq, 15);
257	1	assertEquals(features.size(), 5); // no sf2
258	1	assertTrue(features.contains(sf3));
259	1	assertTrue(features.contains(sf4));
260	1	assertTrue(features.contains(sf5));
261	1	assertTrue(features.contains(sf6));
262	1	assertTrue(features.contains(sf7));
263
264		/*
265		* make "Group2" not displayed
266		*/
267	1	fr.setGroupVisibility("Group2", false);
268
269	1	features = fr.findFeaturesAtColumn(seq, 15);
270	1	assertEquals(features.size(), 3); // no sf2, sf3, sf6
271	1	assertTrue(features.contains(sf4));
272	1	assertTrue(features.contains(sf5));
273	1	assertTrue(features.contains(sf7));
274
275		// features 'at' a gap between b and c
276		// - returns enclosing feature BC but not contact feature B/C
277	1	features = fr.findFeaturesAtColumn(seq, 4);
278	1	assertEquals(features.size(), 1);
279	1	assertTrue(features.contains(sf8));
280	1	features = fr.findFeaturesAtColumn(seq, 5);
281	1	assertEquals(features.size(), 1);
282	1	assertTrue(features.contains(sf8));
283
284		/*
285		* give "Type3" features a graduated colour scheme
286		* - first with no threshold
287		*/
288	1	FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f,
289		10f);
290	1	fr.getFeatureColours().put("Type3", gc);
291	1	features = fr.findFeaturesAtColumn(seq, 8);
292	1	assertTrue(features.contains(sf4));
293		// now with threshold > 2f - feature score of 1f is excluded
294	1	gc.setAboveThreshold(true);
295	1	gc.setThreshold(2f);
296	1	features = fr.findFeaturesAtColumn(seq, 8);
297	1	assertFalse(features.contains(sf4));
298
299		/*
300		* make "Type3" graduated colour by attribute "AF"
301		* - first with no attribute held - feature should be excluded
302		*/
303	1	gc.setAttributeName("AF");
304	1	features = fr.findFeaturesAtColumn(seq, 8);
305	1	assertFalse(features.contains(sf4));
306		// now with the attribute above threshold - should be included
307	1	sf4.setValue("AF", "2.4");
308	1	features = fr.findFeaturesAtColumn(seq, 8);
309	1	assertTrue(features.contains(sf4));
310		// now with the attribute below threshold - should be excluded
311	1	sf4.setValue("AF", "1.4");
312	1	features = fr.findFeaturesAtColumn(seq, 8);
313	1	assertFalse(features.contains(sf4));
314		}
315
		100% Uncovered Elements: 0 (46) Complexity: 1 Complexity Density: 0.02 1PASS
316	1	@Test(groups = "Functional")...
317		public void testFilterFeaturesForDisplay()
318		{
319	1	String seqData = ">s1\nabcdef\n";
320	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
321		DataSourceType.PASTE);
322	1	AlignViewportI av = af.getViewport();
323	1	FeatureRenderer fr = new FeatureRenderer(av);
324
325	1	List<SequenceFeature> features = new ArrayList<>();
326	1	fr.filterFeaturesForDisplay(features); // empty list, does nothing
327
328	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
329	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
330		"group1");
331	1	seq.addSequenceFeature(sf1);
332	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
333		"group2");
334	1	seq.addSequenceFeature(sf2);
335	1	SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
336		"group3");
337	1	seq.addSequenceFeature(sf3);
338	1	SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
339		"group4");
340	1	seq.addSequenceFeature(sf4);
341	1	SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
342		"group4");
343	1	seq.addSequenceFeature(sf5);
344
345	1	fr.findAllFeatures(true);
346
347	1	features = seq.getSequenceFeatures();
348	1	assertEquals(features.size(), 5);
349	1	assertTrue(features.contains(sf1));
350	1	assertTrue(features.contains(sf2));
351	1	assertTrue(features.contains(sf3));
352	1	assertTrue(features.contains(sf4));
353	1	assertTrue(features.contains(sf5));
354
355		/*
356		* filter out duplicate (co-located) features
357		* note: which gets removed is not guaranteed
358		*/
359	1	fr.filterFeaturesForDisplay(features);
360	1	assertEquals(features.size(), 3);
361	1	assertTrue(features.contains(sf1) || features.contains(sf4));
362	1	assertFalse(features.contains(sf1) && features.contains(sf4));
363	1	assertTrue(features.contains(sf2) || features.contains(sf3));
364	1	assertFalse(features.contains(sf2) && features.contains(sf3));
365	1	assertTrue(features.contains(sf5));
366
367		/*
368		* hide groups 2 and 3 makes no difference to this method
369		*/
370	1	fr.setGroupVisibility("group2", false);
371	1	fr.setGroupVisibility("group3", false);
372	1	features = seq.getSequenceFeatures();
373	1	fr.filterFeaturesForDisplay(features);
374	1	assertEquals(features.size(), 3);
375	1	assertTrue(features.contains(sf1) || features.contains(sf4));
376	1	assertFalse(features.contains(sf1) && features.contains(sf4));
377	1	assertTrue(features.contains(sf2) || features.contains(sf3));
378	1	assertFalse(features.contains(sf2) && features.contains(sf3));
379	1	assertTrue(features.contains(sf5));
380
381		/*
382		* no filtering if transparency is applied
383		*/
384	1	fr.setTransparency(0.5f);
385	1	features = seq.getSequenceFeatures();
386	1	fr.filterFeaturesForDisplay(features);
387	1	assertEquals(features.size(), 5);
388		}
389
		100% Uncovered Elements: 0 (74) Complexity: 1 Complexity Density: 0.01 1PASS
390	1	@Test(groups = "Functional")...
391		public void testGetColour()
392		{
393	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n",
394		DataSourceType.PASTE);
395	1	AlignViewportI av = af.getViewport();
396	1	FeatureRenderer fr = new FeatureRenderer(av);
397
398		/*
399		* simple colour, feature type and group displayed
400		*/
401	1	FeatureColourI fc = new FeatureColour(Color.red);
402	1	fr.getFeatureColours().put("Cath", fc);
403	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
404		"group1");
405	1	assertEquals(fr.getColour(sf1), Color.red);
406
407		/*
408		* hide feature type, then unhide
409		* - feature type visibility should not affect the result
410		*/
411	1	FeatureSettingsBean[] data = new FeatureSettingsBean[1];
412	1	data[0] = new FeatureSettingsBean("Cath", fc, null, false);
413	1	fr.setFeaturePriority(data);
414	1	assertEquals(fr.getColour(sf1), Color.red);
415	1	data[0] = new FeatureSettingsBean("Cath", fc, null, true);
416	1	fr.setFeaturePriority(data);
417	1	assertEquals(fr.getColour(sf1), Color.red);
418
419		/*
420		* hide feature group, then unhide
421		*/
422	1	fr.setGroupVisibility("group1", false);
423	1	assertNull(fr.getColour(sf1));
424	1	fr.setGroupVisibility("group1", true);
425	1	assertEquals(fr.getColour(sf1), Color.red);
426
427		/*
428		* graduated colour by score, no threshold, no score
429		*
430		*/
431	1	FeatureColourI gc = new FeatureColour(Color.yellow, Color.red,
432		Color.green, 1f, 11f);
433	1	fr.getFeatureColours().put("Cath", gc);
434	1	assertEquals(fr.getColour(sf1), Color.green);
435
436		/*
437		* graduated colour by score, no threshold, with score value
438		*/
439	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
440		"group1");
441		// score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
442	1	Color expected = new Color(255, 128, 0);
443	1	assertEquals(fr.getColour(sf2), expected);
444
445		/*
446		* above threshold, score is above threshold - no change
447		*/
448	1	gc.setAboveThreshold(true);
449	1	gc.setThreshold(5f);
450	1	assertEquals(fr.getColour(sf2), expected);
451
452		/*
453		* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
454		* or from yellow(255, 255, 0) to red(255, 0, 0)
455		*/
456	1	gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f);
457	1	fr.getFeatureColours().put("Cath", gc);
458	1	gc.setAutoScaled(false); // this does little other than save a checkbox setting!
459	1	assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
460
461		/*
462		* feature score is below threshold - no colour
463		*/
464	1	gc.setAboveThreshold(true);
465	1	gc.setThreshold(7f);
466	1	assertNull(fr.getColour(sf2));
467
468		/*
469		* feature score is above threshold - no colour
470		*/
471	1	gc.setBelowThreshold(true);
472	1	gc.setThreshold(3f);
473	1	assertNull(fr.getColour(sf2));
474
475		/*
476		* colour by feature attribute value
477		* first with no value held
478		*/
479	1	gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f);
480	1	fr.getFeatureColours().put("Cath", gc);
481	1	gc.setAttributeName("AF");
482	1	assertEquals(fr.getColour(sf2), Color.green);
483
484		// with non-numeric attribute value
485	1	sf2.setValue("AF", "Five");
486	1	assertEquals(fr.getColour(sf2), Color.green);
487
488		// with numeric attribute value
489	1	sf2.setValue("AF", "6");
490	1	assertEquals(fr.getColour(sf2), expected);
491
492		// with numeric value outwith threshold
493	1	gc.setAboveThreshold(true);
494	1	gc.setThreshold(10f);
495	1	assertNull(fr.getColour(sf2));
496
497		// with filter on AF < 4
498	1	gc.setAboveThreshold(false);
499	1	assertEquals(fr.getColour(sf2), expected);
500	1	FeatureMatcherSetI filter = new FeatureMatcherSet();
501	1	filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
502	1	fr.setFeatureFilter("Cath", filter);
503	1	assertNull(fr.getColour(sf2));
504
505		// with filter on 'Consequence contains missense'
506	1	filter = new FeatureMatcherSet();
507	1	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
508		"Consequence"));
509	1	fr.setFeatureFilter("Cath", filter);
510		// if feature has no Consequence attribute, no colour
511	1	assertNull(fr.getColour(sf2));
512		// if attribute does not match filter, no colour
513	1	sf2.setValue("Consequence", "Synonymous");
514	1	assertNull(fr.getColour(sf2));
515		// attribute matches filter
516	1	sf2.setValue("Consequence", "Missense variant");
517	1	assertEquals(fr.getColour(sf2), expected);
518
519		// with filter on CSQ:Feature contains "ENST01234"
520	1	filter = new FeatureMatcherSet();
521	1	filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
522		"CSQ", "Feature"));
523	1	fr.setFeatureFilter("Cath", filter);
524		// if feature has no CSQ data, no colour
525	1	assertNull(fr.getColour(sf2));
526		// if CSQ data does not include Feature, no colour
527	1	Map<String, String> csqData = new HashMap<>();
528	1	csqData.put("BIOTYPE", "Transcript");
529	1	sf2.setValue("CSQ", csqData);
530	1	assertNull(fr.getColour(sf2));
531		// if attribute does not match filter, no colour
532	1	csqData.put("Feature", "ENST9876");
533	1	assertNull(fr.getColour(sf2));
534		// attribute matches filter
535	1	csqData.put("Feature", "ENST01234");
536	1	assertEquals(fr.getColour(sf2), expected);
537		}
538		}