Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureRendererTest	59	335	10	0.00%	Show methods

Class FeatureRendererTest

Class FeatureRendererTest	Line # 59	Total Statements 335	Complexity 10	TOTAL Coverage 0.00%
closeAll() : void   closeAll() : void	6161	2.02	2.02	0.0 0.00%
testFindAllFeatures() : void   testFindAllFeatures() : void	6969	61.061	1.01	0.0 0.00%
testFindFeaturesAtColumn() : void   testFindFeaturesAtColumn() : void	183183	82.082	1.01	0.0 0.00%
testFilterFeaturesForDisplay() : void   testFilterFeaturesForDisplay() : void	331331	46.046	1.01	0.0 0.00%
testGetColour() : void   testGetColour() : void	405405	74.074	1.01	0.0 0.00%
testIsVisible() : void   testIsVisible() : void	557557	37.037	1.01	0.0 0.00%
testFindComplementFeaturesAtResidue() : void   testFindComplementFeaturesAtResidue() : void	624624	33.033	3.03	0.0 0.00%

 

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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 java.awt.Color;
31		import java.util.ArrayList;
32		import java.util.Arrays;
33		import java.util.HashMap;
34		import java.util.List;
35		import java.util.Map;
36
37		import org.testng.annotations.BeforeMethod;
38		import org.testng.annotations.Test;
39
40		import jalview.analysis.GeneticCodes;
41		import jalview.api.AlignViewportI;
42		import jalview.api.FeatureColourI;
43		import jalview.bin.Jalview;
44		import jalview.datamodel.MappedFeatures;
45		import jalview.datamodel.SequenceFeature;
46		import jalview.datamodel.SequenceI;
47		import jalview.datamodel.features.FeatureMatcher;
48		import jalview.datamodel.features.FeatureMatcherSet;
49		import jalview.datamodel.features.FeatureMatcherSetI;
50		import jalview.gui.AlignFrame;
51		import jalview.gui.AlignViewport;
52		import jalview.gui.Desktop;
53		import jalview.io.DataSourceType;
54		import jalview.io.FileLoader;
55		import jalview.schemes.FeatureColour;
56		import jalview.util.matcher.Condition;
57		import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
58
		0% Uncovered Elements: 348 (348) Complexity: 10 Complexity Density: 0.03
59		public class FeatureRendererTest
60		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
61	0	@BeforeMethod(alwaysRun = true)...
62		public void closeAll()
63		{
64		// JAL-4107 - was @AfterMethod
65	0	if (Desktop.getInstance() != null)
66	0	Desktop.getInstance().closeAll_actionPerformed(null);
67		}
68
		0% Uncovered Elements: 61 (61) Complexity: 1 Complexity Density: 0.02 4-
69	0	@Test(groups = "Functional")...
70		public void testFindAllFeatures()
71		{
72	0	String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
73	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
74		DataSourceType.PASTE);
75	0	AlignViewportI av = af.getViewport();
76	0	FeatureRenderer fr = new FeatureRenderer(av);
77
78		/*
79		* with no features
80		*/
81	0	fr.findAllFeatures(true);
82	0	assertTrue(fr.getRenderOrder().isEmpty());
83	0	assertTrue(fr.getFeatureGroups().isEmpty());
84
85	0	List<SequenceI> seqs = av.getAlignment().getSequences();
86
87		// add a non-positional feature - should be ignored by FeatureRenderer
88	0	SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
89		"Group");
90	0	seqs.get(0).addSequenceFeature(sf1);
91	0	fr.findAllFeatures(true);
92		// ? bug - types and groups added for non-positional features
93	0	List<String> types = fr.getRenderOrder();
94	0	List<String> groups = fr.getFeatureGroups();
95	0	assertEquals(types.size(), 0);
96	0	assertFalse(types.contains("Type"));
97	0	assertEquals(groups.size(), 0);
98	0	assertFalse(groups.contains("Group"));
99
100		// add some positional features
101	0	seqs.get(1).addSequenceFeature(
102		new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
103	0	seqs.get(2).addSequenceFeature(
104		new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
105		// bug in findAllFeatures - group not checked for a known feature type
106	0	seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9,
107		Float.NaN, "RfamGroup"));
108		// existing feature type with null group
109	0	seqs.get(3).addSequenceFeature(
110		new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
111		// new feature type with null group
112	0	seqs.get(3).addSequenceFeature(
113		new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
114		// null value for type produces NullPointerException
115	0	fr.findAllFeatures(true);
116	0	types = fr.getRenderOrder();
117	0	groups = fr.getFeatureGroups();
118	0	assertEquals(types.size(), 3);
119	0	assertFalse(types.contains("Type"));
120	0	assertTrue(types.contains("Pfam"));
121	0	assertTrue(types.contains("Rfam"));
122	0	assertTrue(types.contains("Scop"));
123	0	assertEquals(groups.size(), 2);
124	0	assertFalse(groups.contains("Group"));
125	0	assertTrue(groups.contains("PfamGroup"));
126	0	assertTrue(groups.contains("RfamGroup"));
127	0	assertFalse(groups.contains(null)); // null group is ignored
128
129		/*
130		* check min-max values
131		*/
132	0	Map<String, float[][]> minMax = fr.getMinMax();
133	0	assertEquals(minMax.size(), 1); // non-positional and NaN not stored
134	0	assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
135	0	assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
136
137		// increase max for Pfam, add scores for Rfam
138	0	seqs.get(0).addSequenceFeature(
139		new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
140	0	seqs.get(1).addSequenceFeature(
141		new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
142	0	fr.findAllFeatures(true);
143		// note minMax is not a defensive copy, shouldn't expose this
144	0	assertEquals(minMax.size(), 2);
145	0	assertEquals(minMax.get("Pfam")[0][0], 1f);
146	0	assertEquals(minMax.get("Pfam")[0][1], 8f);
147	0	assertEquals(minMax.get("Rfam")[0][0], 6f);
148	0	assertEquals(minMax.get("Rfam")[0][1], 6f);
149
150		/*
151		* check render order (last is on top)
152		*/
153	0	List<String> renderOrder = fr.getRenderOrder();
154	0	assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
155
156		/*
157		* change render order (todo: an easier way)
158		* nb here last comes first in the data array
159		*/
160	0	FeatureSettingsBean[] data = new FeatureSettingsBean[3];
161	0	FeatureColourI colour = new FeatureColour(Color.RED);
162	0	data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
163	0	data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
164	0	data[2] = new FeatureSettingsBean("Scop", colour, null, false);
165	0	fr.setFeaturePriority(data);
166	0	assertEquals(fr.getRenderOrder(),
167		Arrays.asList("Scop", "Pfam", "Rfam"));
168	0	assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
169
170		/*
171		* add a new feature type: should go on top of render order as visible,
172		* other feature ordering and visibility should be unchanged
173		*/
174	0	seqs.get(2).addSequenceFeature(
175		new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
176	0	fr.findAllFeatures(true);
177	0	assertEquals(fr.getRenderOrder(),
178		Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
179	0	assertEquals(fr.getDisplayedFeatureTypes(),
180		Arrays.asList("Rfam", "Metal"));
181		}
182
		0% Uncovered Elements: 82 (82) Complexity: 1 Complexity Density: 0.01 4-
183	0	@Test(groups = "Functional")...
184		public void testFindFeaturesAtColumn()
185		{
186	0	String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
187	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
188		DataSourceType.PASTE);
189	0	AlignViewportI av = af.getViewport();
190	0	FeatureRenderer fr = new FeatureRenderer(av);
191	0	SequenceI seq = av.getAlignment().getSequenceAt(0);
192
193		/*
194		* with no features
195		*/
196	0	List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
197	0	assertTrue(features.isEmpty());
198
199		/*
200		* add features
201		*/
202	0	SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
203		"Group"); // non-positional
204	0	seq.addSequenceFeature(sf1);
205	0	SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
206		"Group1");
207	0	seq.addSequenceFeature(sf2);
208	0	SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
209		"Group2");
210	0	seq.addSequenceFeature(sf3);
211	0	SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
212		null); // null group is always treated as visible
213	0	seq.addSequenceFeature(sf4);
214
215		/*
216		* add contact features
217		*/
218	0	SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
219		15, 1f, "Group1");
220	0	seq.addSequenceFeature(sf5);
221	0	SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
222		15, 1f, "Group2");
223	0	seq.addSequenceFeature(sf6);
224	0	SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
225		15, 1f, null);
226	0	seq.addSequenceFeature(sf7);
227
228		// feature spanning B--C
229	0	SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
230		"Group");
231	0	seq.addSequenceFeature(sf8);
232		// contact feature B/C
233	0	SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
234		6, 1f, "Group");
235	0	seq.addSequenceFeature(sf9);
236
237		/*
238		* let feature renderer discover features (and make visible)
239		*/
240	0	fr.findAllFeatures(true);
241	0	features = fr.findFeaturesAtColumn(seq, 15); // all positional
242	0	assertEquals(features.size(), 6);
243	0	assertTrue(features.contains(sf2));
244	0	assertTrue(features.contains(sf3));
245	0	assertTrue(features.contains(sf4));
246	0	assertTrue(features.contains(sf5));
247	0	assertTrue(features.contains(sf6));
248	0	assertTrue(features.contains(sf7));
249
250		/*
251		* at a non-contact position
252		*/
253	0	features = fr.findFeaturesAtColumn(seq, 14);
254	0	assertEquals(features.size(), 3);
255	0	assertTrue(features.contains(sf2));
256	0	assertTrue(features.contains(sf3));
257	0	assertTrue(features.contains(sf4));
258
259		/*
260		* make "Type2" not displayed
261		*/
262	0	FeatureColourI colour = new FeatureColour(Color.RED);
263	0	FeatureSettingsBean[] data = new FeatureSettingsBean[4];
264	0	data[0] = new FeatureSettingsBean("Type1", colour, null, true);
265	0	data[1] = new FeatureSettingsBean("Type2", colour, null, false);
266	0	data[2] = new FeatureSettingsBean("Type3", colour, null, true);
267	0	data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
268		true);
269	0	fr.setFeaturePriority(data);
270
271	0	features = fr.findFeaturesAtColumn(seq, 15);
272	0	assertEquals(features.size(), 5); // no sf2
273	0	assertTrue(features.contains(sf3));
274	0	assertTrue(features.contains(sf4));
275	0	assertTrue(features.contains(sf5));
276	0	assertTrue(features.contains(sf6));
277	0	assertTrue(features.contains(sf7));
278
279		/*
280		* make "Group2" not displayed
281		*/
282	0	fr.setGroupVisibility("Group2", false);
283
284	0	features = fr.findFeaturesAtColumn(seq, 15);
285	0	assertEquals(features.size(), 3); // no sf2, sf3, sf6
286	0	assertTrue(features.contains(sf4));
287	0	assertTrue(features.contains(sf5));
288	0	assertTrue(features.contains(sf7));
289
290		// features 'at' a gap between b and c
291		// - returns enclosing feature BC but not contact feature B/C
292	0	features = fr.findFeaturesAtColumn(seq, 4);
293	0	assertEquals(features.size(), 1);
294	0	assertTrue(features.contains(sf8));
295	0	features = fr.findFeaturesAtColumn(seq, 5);
296	0	assertEquals(features.size(), 1);
297	0	assertTrue(features.contains(sf8));
298
299		/*
300		* give "Type3" features a graduated colour scheme
301		* - first with no threshold
302		*/
303	0	FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
304		Color.red, null, 0f, 10f);
305	0	fr.getFeatureColours().put("Type3", gc);
306	0	features = fr.findFeaturesAtColumn(seq, 8);
307	0	assertTrue(features.contains(sf4));
308		// now with threshold > 2f - feature score of 1f is excluded
309	0	gc.setAboveThreshold(true);
310	0	gc.setThreshold(2f);
311	0	features = fr.findFeaturesAtColumn(seq, 8);
312	0	assertFalse(features.contains(sf4));
313
314		/*
315		* make "Type3" graduated colour by attribute "AF"
316		* - first with no attribute held - feature should be excluded
317		*/
318	0	gc.setAttributeName("AF");
319	0	features = fr.findFeaturesAtColumn(seq, 8);
320	0	assertFalse(features.contains(sf4));
321		// now with the attribute above threshold - should be included
322	0	sf4.setValue("AF", "2.4");
323	0	features = fr.findFeaturesAtColumn(seq, 8);
324	0	assertTrue(features.contains(sf4));
325		// now with the attribute below threshold - should be excluded
326	0	sf4.setValue("AF", "1.4");
327	0	features = fr.findFeaturesAtColumn(seq, 8);
328	0	assertFalse(features.contains(sf4));
329		}
330
		0% Uncovered Elements: 46 (46) Complexity: 1 Complexity Density: 0.02 4-
331	0	@Test(groups = "Functional")...
332		public void testFilterFeaturesForDisplay()
333		{
334	0	String seqData = ">s1\nabcdef\n";
335	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
336		DataSourceType.PASTE);
337	0	AlignViewportI av = af.getViewport();
338	0	FeatureRenderer fr = new FeatureRenderer(av);
339
340	0	List<SequenceFeature> features = new ArrayList<>();
341	0	fr.filterFeaturesForDisplay(features); // empty list, does nothing
342
343	0	SequenceI seq = av.getAlignment().getSequenceAt(0);
344	0	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
345		"group1");
346	0	SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
347		"group2");
348	0	SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
349		"group3");
350	0	SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
351		"group4");
352	0	SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
353		"group4");
354	0	seq.addSequenceFeature(sf1);
355	0	seq.addSequenceFeature(sf2);
356	0	seq.addSequenceFeature(sf3);
357	0	seq.addSequenceFeature(sf4);
358	0	seq.addSequenceFeature(sf5);
359
360	0	fr.findAllFeatures(true);
361
362	0	features = seq.getSequenceFeatures();
363	0	assertEquals(features.size(), 5);
364	0	assertTrue(features.contains(sf1));
365	0	assertTrue(features.contains(sf2));
366	0	assertTrue(features.contains(sf3));
367	0	assertTrue(features.contains(sf4));
368	0	assertTrue(features.contains(sf5));
369
370		/*
371		* filter out duplicate (co-located) features
372		* note: which gets removed is not guaranteed
373		*/
374	0	fr.filterFeaturesForDisplay(features);
375	0	assertEquals(features.size(), 3);
376	0	assertTrue(features.contains(sf1) || features.contains(sf4));
377	0	assertFalse(features.contains(sf1) && features.contains(sf4));
378	0	assertTrue(features.contains(sf2) || features.contains(sf3));
379	0	assertFalse(features.contains(sf2) && features.contains(sf3));
380	0	assertTrue(features.contains(sf5));
381
382		/*
383		* features in hidden groups are removed
384		*/
385	0	fr.setGroupVisibility("group2", false);
386	0	fr.setGroupVisibility("group3", false);
387	0	features = seq.getSequenceFeatures();
388	0	fr.filterFeaturesForDisplay(features);
389	0	assertEquals(features.size(), 2);
390	0	assertTrue(features.contains(sf1) || features.contains(sf4));
391	0	assertFalse(features.contains(sf1) && features.contains(sf4));
392	0	assertFalse(features.contains(sf2));
393	0	assertFalse(features.contains(sf3));
394	0	assertTrue(features.contains(sf5));
395
396		/*
397		* no filtering if transparency is applied
398		*/
399	0	fr.setTransparency(0.5f);
400	0	features = seq.getSequenceFeatures();
401	0	fr.filterFeaturesForDisplay(features);
402	0	assertEquals(features.size(), 5);
403		}
404
		0% Uncovered Elements: 74 (74) Complexity: 1 Complexity Density: 0.01 4-
405	0	@Test(groups = "Functional")...
406		public void testGetColour()
407		{
408	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n",
409		DataSourceType.PASTE);
410	0	AlignViewportI av = af.getViewport();
411	0	FeatureRenderer fr = new FeatureRenderer(av);
412
413		/*
414		* simple colour, feature type and group displayed
415		*/
416	0	FeatureColourI fc = new FeatureColour(Color.red);
417	0	fr.getFeatureColours().put("Cath", fc);
418	0	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
419		"group1");
420	0	assertEquals(fr.getColour(sf1), Color.red);
421
422		/*
423		* hide feature type, then unhide
424		* - feature type visibility should not affect the result
425		*/
426	0	FeatureSettingsBean[] data = new FeatureSettingsBean[1];
427	0	data[0] = new FeatureSettingsBean("Cath", fc, null, false);
428	0	fr.setFeaturePriority(data);
429	0	assertEquals(fr.getColour(sf1), Color.red);
430	0	data[0] = new FeatureSettingsBean("Cath", fc, null, true);
431	0	fr.setFeaturePriority(data);
432	0	assertEquals(fr.getColour(sf1), Color.red);
433
434		/*
435		* hide feature group, then unhide
436		*/
437	0	fr.setGroupVisibility("group1", false);
438	0	assertNull(fr.getColour(sf1));
439	0	fr.setGroupVisibility("group1", true);
440	0	assertEquals(fr.getColour(sf1), Color.red);
441
442		/*
443		* graduated colour by score, no threshold, no score
444		*
445		*/
446	0	FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
447		Color.red, Color.green, 1f, 11f);
448	0	fr.getFeatureColours().put("Cath", gc);
449	0	assertEquals(fr.getColour(sf1), Color.green);
450
451		/*
452		* graduated colour by score, no threshold, with score value
453		*/
454	0	SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
455		"group1");
456		// score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
457	0	Color expected = new Color(255, 128, 0);
458	0	assertEquals(fr.getColour(sf2), expected);
459
460		/*
461		* above threshold, score is above threshold - no change
462		*/
463	0	gc.setAboveThreshold(true);
464	0	gc.setThreshold(5f);
465	0	assertEquals(fr.getColour(sf2), expected);
466
467		/*
468		* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
469		* or from yellow(255, 255, 0) to red(255, 0, 0)
470		*/
471	0	gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
472		5f, 11f);
473	0	fr.getFeatureColours().put("Cath", gc);
474	0	gc.setAutoScaled(false); // this does little other than save a checkbox
475		// setting!
476	0	assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
477
478		/*
479		* feature score is below threshold - no colour
480		*/
481	0	gc.setAboveThreshold(true);
482	0	gc.setThreshold(7f);
483	0	assertNull(fr.getColour(sf2));
484
485		/*
486		* feature score is above threshold - no colour
487		*/
488	0	gc.setBelowThreshold(true);
489	0	gc.setThreshold(3f);
490	0	assertNull(fr.getColour(sf2));
491
492		/*
493		* colour by feature attribute value
494		* first with no value held
495		*/
496	0	gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
497		1f, 11f);
498	0	fr.getFeatureColours().put("Cath", gc);
499	0	gc.setAttributeName("AF");
500	0	assertEquals(fr.getColour(sf2), Color.green);
501
502		// with non-numeric attribute value
503	0	sf2.setValue("AF", "Five");
504	0	assertEquals(fr.getColour(sf2), Color.green);
505
506		// with numeric attribute value
507	0	sf2.setValue("AF", "6");
508	0	assertEquals(fr.getColour(sf2), expected);
509
510		// with numeric value outwith threshold
511	0	gc.setAboveThreshold(true);
512	0	gc.setThreshold(10f);
513	0	assertNull(fr.getColour(sf2));
514
515		// with filter on AF < 4
516	0	gc.setAboveThreshold(false);
517	0	assertEquals(fr.getColour(sf2), expected);
518	0	FeatureMatcherSetI filter = new FeatureMatcherSet();
519	0	filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
520	0	fr.setFeatureFilter("Cath", filter);
521	0	assertNull(fr.getColour(sf2));
522
523		// with filter on 'Consequence contains missense'
524	0	filter = new FeatureMatcherSet();
525	0	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
526		"Consequence"));
527	0	fr.setFeatureFilter("Cath", filter);
528		// if feature has no Consequence attribute, no colour
529	0	assertNull(fr.getColour(sf2));
530		// if attribute does not match filter, no colour
531	0	sf2.setValue("Consequence", "Synonymous");
532	0	assertNull(fr.getColour(sf2));
533		// attribute matches filter
534	0	sf2.setValue("Consequence", "Missense variant");
535	0	assertEquals(fr.getColour(sf2), expected);
536
537		// with filter on CSQ:Feature contains "ENST01234"
538	0	filter = new FeatureMatcherSet();
539	0	filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
540		"CSQ", "Feature"));
541	0	fr.setFeatureFilter("Cath", filter);
542		// if feature has no CSQ data, no colour
543	0	assertNull(fr.getColour(sf2));
544		// if CSQ data does not include Feature, no colour
545	0	Map<String, String> csqData = new HashMap<>();
546	0	csqData.put("BIOTYPE", "Transcript");
547	0	sf2.setValue("CSQ", csqData);
548	0	assertNull(fr.getColour(sf2));
549		// if attribute does not match filter, no colour
550	0	csqData.put("Feature", "ENST9876");
551	0	assertNull(fr.getColour(sf2));
552		// attribute matches filter
553	0	csqData.put("Feature", "ENST01234");
554	0	assertEquals(fr.getColour(sf2), expected);
555		}
556
		0% Uncovered Elements: 37 (37) Complexity: 1 Complexity Density: 0.03 4-
557	0	@Test(groups = "Functional")...
558		public void testIsVisible()
559		{
560	0	String seqData = ">s1\nMLQGIFPRS\n";
561	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
562		DataSourceType.PASTE);
563	0	AlignViewportI av = af.getViewport();
564	0	FeatureRenderer fr = new FeatureRenderer(av);
565	0	SequenceI seq = av.getAlignment().getSequenceAt(0);
566	0	SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
567		"Group");
568	0	sf.setValue("AC", "11");
569	0	sf.setValue("CLIN_SIG", "Likely Pathogenic");
570	0	seq.addSequenceFeature(sf);
571
572	0	assertFalse(fr.isVisible(null));
573
574		/*
575		* initial state FeatureRenderer hasn't 'found' feature
576		* and so its feature type has not yet been set visible
577		*/
578	0	assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
579	0	assertFalse(fr.isVisible(sf));
580
581	0	fr.findAllFeatures(true);
582	0	assertTrue(fr.isVisible(sf));
583
584		/*
585		* feature group not visible
586		*/
587	0	fr.setGroupVisibility("Group", false);
588	0	assertFalse(fr.isVisible(sf));
589	0	fr.setGroupVisibility("Group", true);
590	0	assertTrue(fr.isVisible(sf));
591
592		/*
593		* feature score outwith colour threshold (score > 2)
594		*/
595	0	FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
596		Color.white, 0, 10);
597	0	fc.setAboveThreshold(true);
598	0	fc.setThreshold(2f);
599	0	fr.setColour("METAL", fc);
600	0	assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
601	0	fc.setBelowThreshold(true);
602	0	assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
603
604		/*
605		* colour with threshold on attribute AC (value is 11)
606		*/
607	0	fc.setAttributeName("AC");
608	0	assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
609	0	fc.setAboveThreshold(true);
610	0	assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
611
612	0	fc.setAttributeName("AF"); // attribute AF is absent in sf
613	0	assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
614
615	0	FeatureMatcherSetI filter = new FeatureMatcherSet();
616	0	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
617		"CLIN_SIG"));
618	0	fr.setFeatureFilter("METAL", filter);
619	0	assertTrue(fr.isVisible(sf)); // feature matches filter
620	0	filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
621	0	assertFalse(fr.isVisible(sf)); // feature doesn't match filter
622		}
623
		0% Uncovered Elements: 37 (37) Complexity: 3 Complexity Density: 0.09 4-
624	0	@Test(groups = "Functional")...
625		public void testFindComplementFeaturesAtResidue()
626		{
627	0	Jalview.main(
628		new String[]
629		{ "--nonews", "--props", "test/jalview/testProps.jvprops" });
630
631		// codons for MCWHSE
632	0	String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";
633	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(cdsSeq,
634		DataSourceType.PASTE);
635	0	af.showTranslation_actionPerformed(
636		GeneticCodes.getInstance().getStandardCodeTable());
637	0	af.closeMenuItem_actionPerformed(true);
638
639		/*
640		* find the complement frames (ugly)
641		*/
642	0	AlignFrame[] frames = Desktop.getDesktopAlignFrames();
643	0	assertEquals(frames.length, 2);
644	0	AlignViewport av1 = frames[0].getViewport();
645	0	AlignViewport av2 = frames[1].getViewport();
646	0	AlignViewport cds = av1.getAlignment().isNucleotide() ? av1 : av2;
647	0	AlignViewport peptide = cds == av1 ? av2 : av1;
648	0	assertNotNull(cds);
649	0	assertNotNull(peptide);
650
651		/*
652		* add features to CDS at first codon, positions 2-3
653		*/
654	0	SequenceI seq1 = cds.getAlignment().getSequenceAt(0);
655	0	SequenceFeature sf1 = new SequenceFeature("sequence_variant", "G,GT", 2,
656		2, "ensembl");
657	0	seq1.addSequenceFeature(sf1);
658	0	SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA",
659		3, 3, "ensembl");
660	0	seq1.addSequenceFeature(sf2);
661
662		/*
663		* 'find' mapped features from the peptide position
664		* - first with CDS features _not_ shown on peptide alignment
665		*/
666	0	SequenceI seq2 = peptide.getAlignment().getSequenceAt(0);
667	0	FeatureRenderer frC = new FeatureRenderer(cds);
668	0	frC.featuresAdded();
669	0	MappedFeatures mf = frC.findComplementFeaturesAtResidue(seq2, 1);
670	0	assertNotNull(mf);
671	0	assertEquals(mf.features.size(), 2);
672	0	assertSame(mf.features.get(0), sf1);
673	0	assertSame(mf.features.get(1), sf2);
674
675		/*
676		* add exon feature and verify it is only returned once for a
677		* peptide position, even though it is on all 3 codon positions
678		*/
679	0	SequenceFeature sf3 = new SequenceFeature("exon", "exon1", 4, 12,
680		"ensembl");
681	0	seq1.addSequenceFeature(sf3);
682	0	frC.featuresAdded();
683	0	mf = frC.findComplementFeaturesAtResidue(seq2, 3);
684	0	assertNotNull(mf);
685	0	assertEquals(mf.features.size(), 1);
686	0	assertSame(mf.features.get(0), sf3);
687		}
688		}