Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureRendererTest	58	333	8	0.994169199.4%	Show methods

Class FeatureRendererTest

Class FeatureRendererTest	Line # 58	Total Statements 333	Complexity 8	TOTAL Coverage 0.994169199.4%
testFindAllFeatures() : void   testFindAllFeatures() : void	6161	61.061	1.01	1.0 1.0100%
testFindFeaturesAtColumn() : void   testFindFeaturesAtColumn() : void	175175	82.082	1.01	1.0 1.0100%
testFilterFeaturesForDisplay() : void   testFilterFeaturesForDisplay() : void	323323	46.046	1.01	1.0 1.0100%
testGetColour() : void   testGetColour() : void	397397	74.074	1.01	1.0 1.0100%
testIsVisible() : void   testIsVisible() : void	548548	37.037	1.01	1.0 1.0100%
testFindComplementFeaturesAtResidue() : void   testFindComplementFeaturesAtResidue() : void	615615	33.033	3.03	0.9459459 0.945945994.6%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2419825	jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn	1PASS
	0.2186589	jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour	1PASS
	0.18075801	jalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeaturesjalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeatures	1PASS
	0.13702624	jalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplayjalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplay	1PASS
	0.110787176	jalview.renderer.seqfeatures.FeatureRendererTest.testIsVisiblejalview.renderer.seqfeatures.FeatureRendererTest.testIsVisible	1PASS
	0.10495627	jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue	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.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
		99.4% Uncovered Elements: 2 (343) Complexity: 8 Complexity Density: 0.02
58		public class FeatureRendererTest
59		{
60
		100% Uncovered Elements: 0 (61) Complexity: 1 Complexity Density: 0.02 1PASS
61	1	@Test(groups = "Functional")...
62		public void testFindAllFeatures()
63		{
64	1	String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
65	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
66		DataSourceType.PASTE);
67	1	AlignViewportI av = af.getViewport();
68	1	FeatureRenderer fr = new FeatureRenderer(av);
69
70		/*
71		* with no features
72		*/
73	1	fr.findAllFeatures(true);
74	1	assertTrue(fr.getRenderOrder().isEmpty());
75	1	assertTrue(fr.getFeatureGroups().isEmpty());
76
77	1	List<SequenceI> seqs = av.getAlignment().getSequences();
78
79		// add a non-positional feature - should be ignored by FeatureRenderer
80	1	SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
81		"Group");
82	1	seqs.get(0).addSequenceFeature(sf1);
83	1	fr.findAllFeatures(true);
84		// ? bug - types and groups added for non-positional features
85	1	List<String> types = fr.getRenderOrder();
86	1	List<String> groups = fr.getFeatureGroups();
87	1	assertEquals(types.size(), 0);
88	1	assertFalse(types.contains("Type"));
89	1	assertEquals(groups.size(), 0);
90	1	assertFalse(groups.contains("Group"));
91
92		// add some positional features
93	1	seqs.get(1).addSequenceFeature(
94		new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
95	1	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	1	seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9,
99		Float.NaN, "RfamGroup"));
100		// existing feature type with null group
101	1	seqs.get(3).addSequenceFeature(
102		new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
103		// new feature type with null group
104	1	seqs.get(3).addSequenceFeature(
105		new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
106		// null value for type produces NullPointerException
107	1	fr.findAllFeatures(true);
108	1	types = fr.getRenderOrder();
109	1	groups = fr.getFeatureGroups();
110	1	assertEquals(types.size(), 3);
111	1	assertFalse(types.contains("Type"));
112	1	assertTrue(types.contains("Pfam"));
113	1	assertTrue(types.contains("Rfam"));
114	1	assertTrue(types.contains("Scop"));
115	1	assertEquals(groups.size(), 2);
116	1	assertFalse(groups.contains("Group"));
117	1	assertTrue(groups.contains("PfamGroup"));
118	1	assertTrue(groups.contains("RfamGroup"));
119	1	assertFalse(groups.contains(null)); // null group is ignored
120
121		/*
122		* check min-max values
123		*/
124	1	Map<String, float[][]> minMax = fr.getMinMax();
125	1	assertEquals(minMax.size(), 1); // non-positional and NaN not stored
126	1	assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
127	1	assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
128
129		// increase max for Pfam, add scores for Rfam
130	1	seqs.get(0).addSequenceFeature(
131		new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
132	1	seqs.get(1).addSequenceFeature(
133		new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
134	1	fr.findAllFeatures(true);
135		// note minMax is not a defensive copy, shouldn't expose this
136	1	assertEquals(minMax.size(), 2);
137	1	assertEquals(minMax.get("Pfam")[0][0], 1f);
138	1	assertEquals(minMax.get("Pfam")[0][1], 8f);
139	1	assertEquals(minMax.get("Rfam")[0][0], 6f);
140	1	assertEquals(minMax.get("Rfam")[0][1], 6f);
141
142		/*
143		* check render order (last is on top)
144		*/
145	1	List<String> renderOrder = fr.getRenderOrder();
146	1	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	1	FeatureSettingsBean[] data = new FeatureSettingsBean[3];
153	1	FeatureColourI colour = new FeatureColour(Color.RED);
154	1	data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
155	1	data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
156	1	data[2] = new FeatureSettingsBean("Scop", colour, null, false);
157	1	fr.setFeaturePriority(data);
158	1	assertEquals(fr.getRenderOrder(),
159		Arrays.asList("Scop", "Pfam", "Rfam"));
160	1	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	1	seqs.get(2).addSequenceFeature(
167		new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
168	1	fr.findAllFeatures(true);
169	1	assertEquals(fr.getRenderOrder(),
170		Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
171	1	assertEquals(fr.getDisplayedFeatureTypes(),
172		Arrays.asList("Rfam", "Metal"));
173		}
174
		100% Uncovered Elements: 0 (82) Complexity: 1 Complexity Density: 0.01 1PASS
175	1	@Test(groups = "Functional")...
176		public void testFindFeaturesAtColumn()
177		{
178	1	String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
179	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
180		DataSourceType.PASTE);
181	1	AlignViewportI av = af.getViewport();
182	1	FeatureRenderer fr = new FeatureRenderer(av);
183	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
184
185		/*
186		* with no features
187		*/
188	1	List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
189	1	assertTrue(features.isEmpty());
190
191		/*
192		* add features
193		*/
194	1	SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
195		"Group"); // non-positional
196	1	seq.addSequenceFeature(sf1);
197	1	SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
198		"Group1");
199	1	seq.addSequenceFeature(sf2);
200	1	SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
201		"Group2");
202	1	seq.addSequenceFeature(sf3);
203	1	SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
204		null); // null group is always treated as visible
205	1	seq.addSequenceFeature(sf4);
206
207		/*
208		* add contact features
209		*/
210	1	SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
211		15, 1f, "Group1");
212	1	seq.addSequenceFeature(sf5);
213	1	SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
214		15, 1f, "Group2");
215	1	seq.addSequenceFeature(sf6);
216	1	SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
217		15, 1f, null);
218	1	seq.addSequenceFeature(sf7);
219
220		// feature spanning B--C
221	1	SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
222		"Group");
223	1	seq.addSequenceFeature(sf8);
224		// contact feature B/C
225	1	SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
226		6, 1f, "Group");
227	1	seq.addSequenceFeature(sf9);
228
229		/*
230		* let feature renderer discover features (and make visible)
231		*/
232	1	fr.findAllFeatures(true);
233	1	features = fr.findFeaturesAtColumn(seq, 15); // all positional
234	1	assertEquals(features.size(), 6);
235	1	assertTrue(features.contains(sf2));
236	1	assertTrue(features.contains(sf3));
237	1	assertTrue(features.contains(sf4));
238	1	assertTrue(features.contains(sf5));
239	1	assertTrue(features.contains(sf6));
240	1	assertTrue(features.contains(sf7));
241
242		/*
243		* at a non-contact position
244		*/
245	1	features = fr.findFeaturesAtColumn(seq, 14);
246	1	assertEquals(features.size(), 3);
247	1	assertTrue(features.contains(sf2));
248	1	assertTrue(features.contains(sf3));
249	1	assertTrue(features.contains(sf4));
250
251		/*
252		* make "Type2" not displayed
253		*/
254	1	FeatureColourI colour = new FeatureColour(Color.RED);
255	1	FeatureSettingsBean[] data = new FeatureSettingsBean[4];
256	1	data[0] = new FeatureSettingsBean("Type1", colour, null, true);
257	1	data[1] = new FeatureSettingsBean("Type2", colour, null, false);
258	1	data[2] = new FeatureSettingsBean("Type3", colour, null, true);
259	1	data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
260		true);
261	1	fr.setFeaturePriority(data);
262
263	1	features = fr.findFeaturesAtColumn(seq, 15);
264	1	assertEquals(features.size(), 5); // no sf2
265	1	assertTrue(features.contains(sf3));
266	1	assertTrue(features.contains(sf4));
267	1	assertTrue(features.contains(sf5));
268	1	assertTrue(features.contains(sf6));
269	1	assertTrue(features.contains(sf7));
270
271		/*
272		* make "Group2" not displayed
273		*/
274	1	fr.setGroupVisibility("Group2", false);
275
276	1	features = fr.findFeaturesAtColumn(seq, 15);
277	1	assertEquals(features.size(), 3); // no sf2, sf3, sf6
278	1	assertTrue(features.contains(sf4));
279	1	assertTrue(features.contains(sf5));
280	1	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	1	features = fr.findFeaturesAtColumn(seq, 4);
285	1	assertEquals(features.size(), 1);
286	1	assertTrue(features.contains(sf8));
287	1	features = fr.findFeaturesAtColumn(seq, 5);
288	1	assertEquals(features.size(), 1);
289	1	assertTrue(features.contains(sf8));
290
291		/*
292		* give "Type3" features a graduated colour scheme
293		* - first with no threshold
294		*/
295	1	FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
296		Color.red, null, 0f, 10f);
297	1	fr.getFeatureColours().put("Type3", gc);
298	1	features = fr.findFeaturesAtColumn(seq, 8);
299	1	assertTrue(features.contains(sf4));
300		// now with threshold > 2f - feature score of 1f is excluded
301	1	gc.setAboveThreshold(true);
302	1	gc.setThreshold(2f);
303	1	features = fr.findFeaturesAtColumn(seq, 8);
304	1	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	1	gc.setAttributeName("AF");
311	1	features = fr.findFeaturesAtColumn(seq, 8);
312	1	assertFalse(features.contains(sf4));
313		// now with the attribute above threshold - should be included
314	1	sf4.setValue("AF", "2.4");
315	1	features = fr.findFeaturesAtColumn(seq, 8);
316	1	assertTrue(features.contains(sf4));
317		// now with the attribute below threshold - should be excluded
318	1	sf4.setValue("AF", "1.4");
319	1	features = fr.findFeaturesAtColumn(seq, 8);
320	1	assertFalse(features.contains(sf4));
321		}
322
		100% Uncovered Elements: 0 (46) Complexity: 1 Complexity Density: 0.02 1PASS
323	1	@Test(groups = "Functional")...
324		public void testFilterFeaturesForDisplay()
325		{
326	1	String seqData = ">s1\nabcdef\n";
327	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
328		DataSourceType.PASTE);
329	1	AlignViewportI av = af.getViewport();
330	1	FeatureRenderer fr = new FeatureRenderer(av);
331
332	1	List<SequenceFeature> features = new ArrayList<>();
333	1	fr.filterFeaturesForDisplay(features); // empty list, does nothing
334
335	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
336	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
337		"group1");
338	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
339		"group2");
340	1	SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
341		"group3");
342	1	SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
343		"group4");
344	1	SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
345		"group4");
346	1	seq.addSequenceFeature(sf1);
347	1	seq.addSequenceFeature(sf2);
348	1	seq.addSequenceFeature(sf3);
349	1	seq.addSequenceFeature(sf4);
350	1	seq.addSequenceFeature(sf5);
351
352	1	fr.findAllFeatures(true);
353
354	1	features = seq.getSequenceFeatures();
355	1	assertEquals(features.size(), 5);
356	1	assertTrue(features.contains(sf1));
357	1	assertTrue(features.contains(sf2));
358	1	assertTrue(features.contains(sf3));
359	1	assertTrue(features.contains(sf4));
360	1	assertTrue(features.contains(sf5));
361
362		/*
363		* filter out duplicate (co-located) features
364		* note: which gets removed is not guaranteed
365		*/
366	1	fr.filterFeaturesForDisplay(features);
367	1	assertEquals(features.size(), 3);
368	1	assertTrue(features.contains(sf1) || features.contains(sf4));
369	1	assertFalse(features.contains(sf1) && features.contains(sf4));
370	1	assertTrue(features.contains(sf2) || features.contains(sf3));
371	1	assertFalse(features.contains(sf2) && features.contains(sf3));
372	1	assertTrue(features.contains(sf5));
373
374		/*
375		* features in hidden groups are removed
376		*/
377	1	fr.setGroupVisibility("group2", false);
378	1	fr.setGroupVisibility("group3", false);
379	1	features = seq.getSequenceFeatures();
380	1	fr.filterFeaturesForDisplay(features);
381	1	assertEquals(features.size(), 2);
382	1	assertTrue(features.contains(sf1) || features.contains(sf4));
383	1	assertFalse(features.contains(sf1) && features.contains(sf4));
384	1	assertFalse(features.contains(sf2));
385	1	assertFalse(features.contains(sf3));
386	1	assertTrue(features.contains(sf5));
387
388		/*
389		* no filtering if transparency is applied
390		*/
391	1	fr.setTransparency(0.5f);
392	1	features = seq.getSequenceFeatures();
393	1	fr.filterFeaturesForDisplay(features);
394	1	assertEquals(features.size(), 5);
395		}
396
		100% Uncovered Elements: 0 (74) Complexity: 1 Complexity Density: 0.01 1PASS
397	1	@Test(groups = "Functional")...
398		public void testGetColour()
399		{
400	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n",
401		DataSourceType.PASTE);
402	1	AlignViewportI av = af.getViewport();
403	1	FeatureRenderer fr = new FeatureRenderer(av);
404
405		/*
406		* simple colour, feature type and group displayed
407		*/
408	1	FeatureColourI fc = new FeatureColour(Color.red);
409	1	fr.getFeatureColours().put("Cath", fc);
410	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
411		"group1");
412	1	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	1	FeatureSettingsBean[] data = new FeatureSettingsBean[1];
419	1	data[0] = new FeatureSettingsBean("Cath", fc, null, false);
420	1	fr.setFeaturePriority(data);
421	1	assertEquals(fr.getColour(sf1), Color.red);
422	1	data[0] = new FeatureSettingsBean("Cath", fc, null, true);
423	1	fr.setFeaturePriority(data);
424	1	assertEquals(fr.getColour(sf1), Color.red);
425
426		/*
427		* hide feature group, then unhide
428		*/
429	1	fr.setGroupVisibility("group1", false);
430	1	assertNull(fr.getColour(sf1));
431	1	fr.setGroupVisibility("group1", true);
432	1	assertEquals(fr.getColour(sf1), Color.red);
433
434		/*
435		* graduated colour by score, no threshold, no score
436		*
437		*/
438	1	FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
439		Color.red, Color.green, 1f, 11f);
440	1	fr.getFeatureColours().put("Cath", gc);
441	1	assertEquals(fr.getColour(sf1), Color.green);
442
443		/*
444		* graduated colour by score, no threshold, with score value
445		*/
446	1	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	1	Color expected = new Color(255, 128, 0);
450	1	assertEquals(fr.getColour(sf2), expected);
451
452		/*
453		* above threshold, score is above threshold - no change
454		*/
455	1	gc.setAboveThreshold(true);
456	1	gc.setThreshold(5f);
457	1	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	1	gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
464		5f, 11f);
465	1	fr.getFeatureColours().put("Cath", gc);
466	1	gc.setAutoScaled(false); // this does little other than save a checkbox setting!
467	1	assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
468
469		/*
470		* feature score is below threshold - no colour
471		*/
472	1	gc.setAboveThreshold(true);
473	1	gc.setThreshold(7f);
474	1	assertNull(fr.getColour(sf2));
475
476		/*
477		* feature score is above threshold - no colour
478		*/
479	1	gc.setBelowThreshold(true);
480	1	gc.setThreshold(3f);
481	1	assertNull(fr.getColour(sf2));
482
483		/*
484		* colour by feature attribute value
485		* first with no value held
486		*/
487	1	gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
488		1f, 11f);
489	1	fr.getFeatureColours().put("Cath", gc);
490	1	gc.setAttributeName("AF");
491	1	assertEquals(fr.getColour(sf2), Color.green);
492
493		// with non-numeric attribute value
494	1	sf2.setValue("AF", "Five");
495	1	assertEquals(fr.getColour(sf2), Color.green);
496
497		// with numeric attribute value
498	1	sf2.setValue("AF", "6");
499	1	assertEquals(fr.getColour(sf2), expected);
500
501		// with numeric value outwith threshold
502	1	gc.setAboveThreshold(true);
503	1	gc.setThreshold(10f);
504	1	assertNull(fr.getColour(sf2));
505
506		// with filter on AF < 4
507	1	gc.setAboveThreshold(false);
508	1	assertEquals(fr.getColour(sf2), expected);
509	1	FeatureMatcherSetI filter = new FeatureMatcherSet();
510	1	filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
511	1	fr.setFeatureFilter("Cath", filter);
512	1	assertNull(fr.getColour(sf2));
513
514		// with filter on 'Consequence contains missense'
515	1	filter = new FeatureMatcherSet();
516	1	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
517		"Consequence"));
518	1	fr.setFeatureFilter("Cath", filter);
519		// if feature has no Consequence attribute, no colour
520	1	assertNull(fr.getColour(sf2));
521		// if attribute does not match filter, no colour
522	1	sf2.setValue("Consequence", "Synonymous");
523	1	assertNull(fr.getColour(sf2));
524		// attribute matches filter
525	1	sf2.setValue("Consequence", "Missense variant");
526	1	assertEquals(fr.getColour(sf2), expected);
527
528		// with filter on CSQ:Feature contains "ENST01234"
529	1	filter = new FeatureMatcherSet();
530	1	filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
531		"CSQ", "Feature"));
532	1	fr.setFeatureFilter("Cath", filter);
533		// if feature has no CSQ data, no colour
534	1	assertNull(fr.getColour(sf2));
535		// if CSQ data does not include Feature, no colour
536	1	Map<String, String> csqData = new HashMap<>();
537	1	csqData.put("BIOTYPE", "Transcript");
538	1	sf2.setValue("CSQ", csqData);
539	1	assertNull(fr.getColour(sf2));
540		// if attribute does not match filter, no colour
541	1	csqData.put("Feature", "ENST9876");
542	1	assertNull(fr.getColour(sf2));
543		// attribute matches filter
544	1	csqData.put("Feature", "ENST01234");
545	1	assertEquals(fr.getColour(sf2), expected);
546		}
547
		100% Uncovered Elements: 0 (37) Complexity: 1 Complexity Density: 0.03 1PASS
548	1	@Test(groups = "Functional")...
549		public void testIsVisible()
550		{
551	1	String seqData = ">s1\nMLQGIFPRS\n";
552	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
553		DataSourceType.PASTE);
554	1	AlignViewportI av = af.getViewport();
555	1	FeatureRenderer fr = new FeatureRenderer(av);
556	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
557	1	SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
558		"Group");
559	1	sf.setValue("AC", "11");
560	1	sf.setValue("CLIN_SIG", "Likely Pathogenic");
561	1	seq.addSequenceFeature(sf);
562
563	1	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	1	assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
570	1	assertFalse(fr.isVisible(sf));
571
572	1	fr.findAllFeatures(true);
573	1	assertTrue(fr.isVisible(sf));
574
575		/*
576		* feature group not visible
577		*/
578	1	fr.setGroupVisibility("Group", false);
579	1	assertFalse(fr.isVisible(sf));
580	1	fr.setGroupVisibility("Group", true);
581	1	assertTrue(fr.isVisible(sf));
582
583		/*
584		* feature score outwith colour threshold (score > 2)
585		*/
586	1	FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
587		Color.white, 0, 10);
588	1	fc.setAboveThreshold(true);
589	1	fc.setThreshold(2f);
590	1	fr.setColour("METAL", fc);
591	1	assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
592	1	fc.setBelowThreshold(true);
593	1	assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
594
595		/*
596		* colour with threshold on attribute AC (value is 11)
597		*/
598	1	fc.setAttributeName("AC");
599	1	assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
600	1	fc.setAboveThreshold(true);
601	1	assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
602
603	1	fc.setAttributeName("AF"); // attribute AF is absent in sf
604	1	assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
605
606	1	FeatureMatcherSetI filter = new FeatureMatcherSet();
607	1	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
608		"CLIN_SIG"));
609	1	fr.setFeatureFilter("METAL", filter);
610	1	assertTrue(fr.isVisible(sf)); // feature matches filter
611	1	filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
612	1	assertFalse(fr.isVisible(sf)); // feature doesn't match filter
613		}
614
		94.6% Uncovered Elements: 2 (37) Complexity: 3 Complexity Density: 0.09 1PASS
615	1	@Test(groups = "Functional")...
616		public void testFindComplementFeaturesAtResidue()
617		{
618	1	Jalview.main(
619		new String[]
620		{ "-nonews", "-props", "test/jalview/testProps.jvprops" });
621
622		// codons for MCWHSE
623	1	String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";
624	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(cdsSeq,
625		DataSourceType.PASTE);
626	1	af.showTranslation_actionPerformed(
627		GeneticCodes.getInstance().getStandardCodeTable());
628	1	af.closeMenuItem_actionPerformed(true);
629
630		/*
631		* find the complement frames (ugly)
632		*/
633	1	AlignFrame[] frames = Desktop.getAlignFrames();
634	1	assertEquals(frames.length, 2);
635	1	AlignViewport av1 = frames[0].getViewport();
636	1	AlignViewport av2 = frames[1].getViewport();
637	1	AlignViewport cds = av1.getAlignment().isNucleotide() ? av1 : av2;
638	1	AlignViewport peptide = cds == av1 ? av2 : av1;
639	1	assertNotNull(cds);
640	1	assertNotNull(peptide);
641
642		/*
643		* add features to CDS at first codon, positions 2-3
644		*/
645	1	SequenceI seq1 = cds.getAlignment().getSequenceAt(0);
646	1	SequenceFeature sf1 = new SequenceFeature("sequence_variant", "G,GT", 2,
647		2, "ensembl");
648	1	seq1.addSequenceFeature(sf1);
649	1	SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA",
650		3, 3, "ensembl");
651	1	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	1	SequenceI seq2 = peptide.getAlignment().getSequenceAt(0);
658	1	FeatureRenderer frC = new FeatureRenderer(cds);
659	1	frC.featuresAdded();
660	1	MappedFeatures mf = frC.findComplementFeaturesAtResidue(seq2, 1);
661	1	assertNotNull(mf);
662	1	assertEquals(mf.features.size(), 2);
663	1	assertSame(mf.features.get(0), sf1);
664	1	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	1	SequenceFeature sf3 = new SequenceFeature("exon", "exon1", 4, 12,
671		"ensembl");
672	1	seq1.addSequenceFeature(sf3);
673	1	frC.featuresAdded();
674	1	mf = frC.findComplementFeaturesAtResidue(seq2, 3);
675	1	assertNotNull(mf);
676	1	assertEquals(mf.features.size(), 1);
677	1	assertSame(mf.features.get(0), sf3);
678		}
679		}