Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureRendererTest	59	335	10	0.991379399.1%	Show methods

Class FeatureRendererTest

Class FeatureRendererTest	Line # 59	Total Statements 335	Complexity 10	TOTAL Coverage 0.991379399.1%
closeAll() : void   closeAll() : void	6161	2.02	2.02	0.75 0.7575%
testFindAllFeatures() : void   testFindAllFeatures() : void	6868	61.061	1.01	1.0 1.0100%
testFindFeaturesAtColumn() : void   testFindFeaturesAtColumn() : void	182182	82.082	1.01	1.0 1.0100%
testFilterFeaturesForDisplay() : void   testFilterFeaturesForDisplay() : void	330330	46.046	1.01	1.0 1.0100%
testGetColour() : void   testGetColour() : void	404404	74.074	1.01	1.0 1.0100%
testIsVisible() : void   testIsVisible() : void	556556	37.037	1.01	1.0 1.0100%
testFindComplementFeaturesAtResidue() : void   testFindComplementFeaturesAtResidue() : void	623623	33.033	3.03	0.9459459 0.945945994.6%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.23850575	jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn	1PASS
	0.21551724	jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour	1PASS
	0.17816092	jalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeaturesjalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeatures	1PASS
	0.13505746	jalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplayjalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplay	1PASS
	0.109195404	jalview.renderer.seqfeatures.FeatureRendererTest.testIsVisiblejalview.renderer.seqfeatures.FeatureRendererTest.testIsVisible	1PASS
	0.10344828	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 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
		99.1% Uncovered Elements: 3 (348) Complexity: 10 Complexity Density: 0.03
59		public class FeatureRendererTest
60		{
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
61	6	@BeforeMethod(alwaysRun = true)...
62		public void closeAll()
63		{
64	6	if (Desktop.instance != null)
65	6	Desktop.instance.closeAll_actionPerformed(null);
66		}
67
		100% Uncovered Elements: 0 (61) Complexity: 1 Complexity Density: 0.02 1PASS
68	1	@Test(groups = "Functional")...
69		public void testFindAllFeatures()
70		{
71	1	String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
72	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
73		DataSourceType.PASTE);
74	1	AlignViewportI av = af.getViewport();
75	1	FeatureRenderer fr = new FeatureRenderer(av);
76
77		/*
78		* with no features
79		*/
80	1	fr.findAllFeatures(true);
81	1	assertTrue(fr.getRenderOrder().isEmpty());
82	1	assertTrue(fr.getFeatureGroups().isEmpty());
83
84	1	List<SequenceI> seqs = av.getAlignment().getSequences();
85
86		// add a non-positional feature - should be ignored by FeatureRenderer
87	1	SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
88		"Group");
89	1	seqs.get(0).addSequenceFeature(sf1);
90	1	fr.findAllFeatures(true);
91		// ? bug - types and groups added for non-positional features
92	1	List<String> types = fr.getRenderOrder();
93	1	List<String> groups = fr.getFeatureGroups();
94	1	assertEquals(types.size(), 0);
95	1	assertFalse(types.contains("Type"));
96	1	assertEquals(groups.size(), 0);
97	1	assertFalse(groups.contains("Group"));
98
99		// add some positional features
100	1	seqs.get(1).addSequenceFeature(
101		new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
102	1	seqs.get(2).addSequenceFeature(
103		new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
104		// bug in findAllFeatures - group not checked for a known feature type
105	1	seqs.get(2).addSequenceFeature(new SequenceFeature("Rfam", "Desc", 5, 9,
106		Float.NaN, "RfamGroup"));
107		// existing feature type with null group
108	1	seqs.get(3).addSequenceFeature(
109		new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
110		// new feature type with null group
111	1	seqs.get(3).addSequenceFeature(
112		new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
113		// null value for type produces NullPointerException
114	1	fr.findAllFeatures(true);
115	1	types = fr.getRenderOrder();
116	1	groups = fr.getFeatureGroups();
117	1	assertEquals(types.size(), 3);
118	1	assertFalse(types.contains("Type"));
119	1	assertTrue(types.contains("Pfam"));
120	1	assertTrue(types.contains("Rfam"));
121	1	assertTrue(types.contains("Scop"));
122	1	assertEquals(groups.size(), 2);
123	1	assertFalse(groups.contains("Group"));
124	1	assertTrue(groups.contains("PfamGroup"));
125	1	assertTrue(groups.contains("RfamGroup"));
126	1	assertFalse(groups.contains(null)); // null group is ignored
127
128		/*
129		* check min-max values
130		*/
131	1	Map<String, float[][]> minMax = fr.getMinMax();
132	1	assertEquals(minMax.size(), 1); // non-positional and NaN not stored
133	1	assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
134	1	assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
135
136		// increase max for Pfam, add scores for Rfam
137	1	seqs.get(0).addSequenceFeature(
138		new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
139	1	seqs.get(1).addSequenceFeature(
140		new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
141	1	fr.findAllFeatures(true);
142		// note minMax is not a defensive copy, shouldn't expose this
143	1	assertEquals(minMax.size(), 2);
144	1	assertEquals(minMax.get("Pfam")[0][0], 1f);
145	1	assertEquals(minMax.get("Pfam")[0][1], 8f);
146	1	assertEquals(minMax.get("Rfam")[0][0], 6f);
147	1	assertEquals(minMax.get("Rfam")[0][1], 6f);
148
149		/*
150		* check render order (last is on top)
151		*/
152	1	List<String> renderOrder = fr.getRenderOrder();
153	1	assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
154
155		/*
156		* change render order (todo: an easier way)
157		* nb here last comes first in the data array
158		*/
159	1	FeatureSettingsBean[] data = new FeatureSettingsBean[3];
160	1	FeatureColourI colour = new FeatureColour(Color.RED);
161	1	data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
162	1	data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
163	1	data[2] = new FeatureSettingsBean("Scop", colour, null, false);
164	1	fr.setFeaturePriority(data);
165	1	assertEquals(fr.getRenderOrder(),
166		Arrays.asList("Scop", "Pfam", "Rfam"));
167	1	assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
168
169		/*
170		* add a new feature type: should go on top of render order as visible,
171		* other feature ordering and visibility should be unchanged
172		*/
173	1	seqs.get(2).addSequenceFeature(
174		new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
175	1	fr.findAllFeatures(true);
176	1	assertEquals(fr.getRenderOrder(),
177		Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
178	1	assertEquals(fr.getDisplayedFeatureTypes(),
179		Arrays.asList("Rfam", "Metal"));
180		}
181
		100% Uncovered Elements: 0 (82) Complexity: 1 Complexity Density: 0.01 1PASS
182	1	@Test(groups = "Functional")...
183		public void testFindFeaturesAtColumn()
184		{
185	1	String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
186	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
187		DataSourceType.PASTE);
188	1	AlignViewportI av = af.getViewport();
189	1	FeatureRenderer fr = new FeatureRenderer(av);
190	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
191
192		/*
193		* with no features
194		*/
195	1	List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
196	1	assertTrue(features.isEmpty());
197
198		/*
199		* add features
200		*/
201	1	SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
202		"Group"); // non-positional
203	1	seq.addSequenceFeature(sf1);
204	1	SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
205		"Group1");
206	1	seq.addSequenceFeature(sf2);
207	1	SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
208		"Group2");
209	1	seq.addSequenceFeature(sf3);
210	1	SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
211		null); // null group is always treated as visible
212	1	seq.addSequenceFeature(sf4);
213
214		/*
215		* add contact features
216		*/
217	1	SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
218		15, 1f, "Group1");
219	1	seq.addSequenceFeature(sf5);
220	1	SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
221		15, 1f, "Group2");
222	1	seq.addSequenceFeature(sf6);
223	1	SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
224		15, 1f, null);
225	1	seq.addSequenceFeature(sf7);
226
227		// feature spanning B--C
228	1	SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
229		"Group");
230	1	seq.addSequenceFeature(sf8);
231		// contact feature B/C
232	1	SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
233		6, 1f, "Group");
234	1	seq.addSequenceFeature(sf9);
235
236		/*
237		* let feature renderer discover features (and make visible)
238		*/
239	1	fr.findAllFeatures(true);
240	1	features = fr.findFeaturesAtColumn(seq, 15); // all positional
241	1	assertEquals(features.size(), 6);
242	1	assertTrue(features.contains(sf2));
243	1	assertTrue(features.contains(sf3));
244	1	assertTrue(features.contains(sf4));
245	1	assertTrue(features.contains(sf5));
246	1	assertTrue(features.contains(sf6));
247	1	assertTrue(features.contains(sf7));
248
249		/*
250		* at a non-contact position
251		*/
252	1	features = fr.findFeaturesAtColumn(seq, 14);
253	1	assertEquals(features.size(), 3);
254	1	assertTrue(features.contains(sf2));
255	1	assertTrue(features.contains(sf3));
256	1	assertTrue(features.contains(sf4));
257
258		/*
259		* make "Type2" not displayed
260		*/
261	1	FeatureColourI colour = new FeatureColour(Color.RED);
262	1	FeatureSettingsBean[] data = new FeatureSettingsBean[4];
263	1	data[0] = new FeatureSettingsBean("Type1", colour, null, true);
264	1	data[1] = new FeatureSettingsBean("Type2", colour, null, false);
265	1	data[2] = new FeatureSettingsBean("Type3", colour, null, true);
266	1	data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
267		true);
268	1	fr.setFeaturePriority(data);
269
270	1	features = fr.findFeaturesAtColumn(seq, 15);
271	1	assertEquals(features.size(), 5); // no sf2
272	1	assertTrue(features.contains(sf3));
273	1	assertTrue(features.contains(sf4));
274	1	assertTrue(features.contains(sf5));
275	1	assertTrue(features.contains(sf6));
276	1	assertTrue(features.contains(sf7));
277
278		/*
279		* make "Group2" not displayed
280		*/
281	1	fr.setGroupVisibility("Group2", false);
282
283	1	features = fr.findFeaturesAtColumn(seq, 15);
284	1	assertEquals(features.size(), 3); // no sf2, sf3, sf6
285	1	assertTrue(features.contains(sf4));
286	1	assertTrue(features.contains(sf5));
287	1	assertTrue(features.contains(sf7));
288
289		// features 'at' a gap between b and c
290		// - returns enclosing feature BC but not contact feature B/C
291	1	features = fr.findFeaturesAtColumn(seq, 4);
292	1	assertEquals(features.size(), 1);
293	1	assertTrue(features.contains(sf8));
294	1	features = fr.findFeaturesAtColumn(seq, 5);
295	1	assertEquals(features.size(), 1);
296	1	assertTrue(features.contains(sf8));
297
298		/*
299		* give "Type3" features a graduated colour scheme
300		* - first with no threshold
301		*/
302	1	FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
303		Color.red, null, 0f, 10f);
304	1	fr.getFeatureColours().put("Type3", gc);
305	1	features = fr.findFeaturesAtColumn(seq, 8);
306	1	assertTrue(features.contains(sf4));
307		// now with threshold > 2f - feature score of 1f is excluded
308	1	gc.setAboveThreshold(true);
309	1	gc.setThreshold(2f);
310	1	features = fr.findFeaturesAtColumn(seq, 8);
311	1	assertFalse(features.contains(sf4));
312
313		/*
314		* make "Type3" graduated colour by attribute "AF"
315		* - first with no attribute held - feature should be excluded
316		*/
317	1	gc.setAttributeName("AF");
318	1	features = fr.findFeaturesAtColumn(seq, 8);
319	1	assertFalse(features.contains(sf4));
320		// now with the attribute above threshold - should be included
321	1	sf4.setValue("AF", "2.4");
322	1	features = fr.findFeaturesAtColumn(seq, 8);
323	1	assertTrue(features.contains(sf4));
324		// now with the attribute below threshold - should be excluded
325	1	sf4.setValue("AF", "1.4");
326	1	features = fr.findFeaturesAtColumn(seq, 8);
327	1	assertFalse(features.contains(sf4));
328		}
329
		100% Uncovered Elements: 0 (46) Complexity: 1 Complexity Density: 0.02 1PASS
330	1	@Test(groups = "Functional")...
331		public void testFilterFeaturesForDisplay()
332		{
333	1	String seqData = ">s1\nabcdef\n";
334	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
335		DataSourceType.PASTE);
336	1	AlignViewportI av = af.getViewport();
337	1	FeatureRenderer fr = new FeatureRenderer(av);
338
339	1	List<SequenceFeature> features = new ArrayList<>();
340	1	fr.filterFeaturesForDisplay(features); // empty list, does nothing
341
342	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
343	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
344		"group1");
345	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
346		"group2");
347	1	SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
348		"group3");
349	1	SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
350		"group4");
351	1	SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
352		"group4");
353	1	seq.addSequenceFeature(sf1);
354	1	seq.addSequenceFeature(sf2);
355	1	seq.addSequenceFeature(sf3);
356	1	seq.addSequenceFeature(sf4);
357	1	seq.addSequenceFeature(sf5);
358
359	1	fr.findAllFeatures(true);
360
361	1	features = seq.getSequenceFeatures();
362	1	assertEquals(features.size(), 5);
363	1	assertTrue(features.contains(sf1));
364	1	assertTrue(features.contains(sf2));
365	1	assertTrue(features.contains(sf3));
366	1	assertTrue(features.contains(sf4));
367	1	assertTrue(features.contains(sf5));
368
369		/*
370		* filter out duplicate (co-located) features
371		* note: which gets removed is not guaranteed
372		*/
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		* features in hidden groups are removed
383		*/
384	1	fr.setGroupVisibility("group2", false);
385	1	fr.setGroupVisibility("group3", false);
386	1	features = seq.getSequenceFeatures();
387	1	fr.filterFeaturesForDisplay(features);
388	1	assertEquals(features.size(), 2);
389	1	assertTrue(features.contains(sf1) || features.contains(sf4));
390	1	assertFalse(features.contains(sf1) && features.contains(sf4));
391	1	assertFalse(features.contains(sf2));
392	1	assertFalse(features.contains(sf3));
393	1	assertTrue(features.contains(sf5));
394
395		/*
396		* no filtering if transparency is applied
397		*/
398	1	fr.setTransparency(0.5f);
399	1	features = seq.getSequenceFeatures();
400	1	fr.filterFeaturesForDisplay(features);
401	1	assertEquals(features.size(), 5);
402		}
403
		100% Uncovered Elements: 0 (74) Complexity: 1 Complexity Density: 0.01 1PASS
404	1	@Test(groups = "Functional")...
405		public void testGetColour()
406		{
407	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(">s1\nABCD\n",
408		DataSourceType.PASTE);
409	1	AlignViewportI av = af.getViewport();
410	1	FeatureRenderer fr = new FeatureRenderer(av);
411
412		/*
413		* simple colour, feature type and group displayed
414		*/
415	1	FeatureColourI fc = new FeatureColour(Color.red);
416	1	fr.getFeatureColours().put("Cath", fc);
417	1	SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
418		"group1");
419	1	assertEquals(fr.getColour(sf1), Color.red);
420
421		/*
422		* hide feature type, then unhide
423		* - feature type visibility should not affect the result
424		*/
425	1	FeatureSettingsBean[] data = new FeatureSettingsBean[1];
426	1	data[0] = new FeatureSettingsBean("Cath", fc, null, false);
427	1	fr.setFeaturePriority(data);
428	1	assertEquals(fr.getColour(sf1), Color.red);
429	1	data[0] = new FeatureSettingsBean("Cath", fc, null, true);
430	1	fr.setFeaturePriority(data);
431	1	assertEquals(fr.getColour(sf1), Color.red);
432
433		/*
434		* hide feature group, then unhide
435		*/
436	1	fr.setGroupVisibility("group1", false);
437	1	assertNull(fr.getColour(sf1));
438	1	fr.setGroupVisibility("group1", true);
439	1	assertEquals(fr.getColour(sf1), Color.red);
440
441		/*
442		* graduated colour by score, no threshold, no score
443		*
444		*/
445	1	FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
446		Color.red, Color.green, 1f, 11f);
447	1	fr.getFeatureColours().put("Cath", gc);
448	1	assertEquals(fr.getColour(sf1), Color.green);
449
450		/*
451		* graduated colour by score, no threshold, with score value
452		*/
453	1	SequenceFeature sf2 = new SequenceFeature("Cath", "", 6, 8, 6f,
454		"group1");
455		// score 6 is half way from yellow(255, 255, 0) to red(255, 0, 0)
456	1	Color expected = new Color(255, 128, 0);
457	1	assertEquals(fr.getColour(sf2), expected);
458
459		/*
460		* above threshold, score is above threshold - no change
461		*/
462	1	gc.setAboveThreshold(true);
463	1	gc.setThreshold(5f);
464	1	assertEquals(fr.getColour(sf2), expected);
465
466		/*
467		* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
468		* or from yellow(255, 255, 0) to red(255, 0, 0)
469		*/
470	1	gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
471		5f, 11f);
472	1	fr.getFeatureColours().put("Cath", gc);
473	1	gc.setAutoScaled(false); // this does little other than save a checkbox
474		// setting!
475	1	assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
476
477		/*
478		* feature score is below threshold - no colour
479		*/
480	1	gc.setAboveThreshold(true);
481	1	gc.setThreshold(7f);
482	1	assertNull(fr.getColour(sf2));
483
484		/*
485		* feature score is above threshold - no colour
486		*/
487	1	gc.setBelowThreshold(true);
488	1	gc.setThreshold(3f);
489	1	assertNull(fr.getColour(sf2));
490
491		/*
492		* colour by feature attribute value
493		* first with no value held
494		*/
495	1	gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
496		1f, 11f);
497	1	fr.getFeatureColours().put("Cath", gc);
498	1	gc.setAttributeName("AF");
499	1	assertEquals(fr.getColour(sf2), Color.green);
500
501		// with non-numeric attribute value
502	1	sf2.setValue("AF", "Five");
503	1	assertEquals(fr.getColour(sf2), Color.green);
504
505		// with numeric attribute value
506	1	sf2.setValue("AF", "6");
507	1	assertEquals(fr.getColour(sf2), expected);
508
509		// with numeric value outwith threshold
510	1	gc.setAboveThreshold(true);
511	1	gc.setThreshold(10f);
512	1	assertNull(fr.getColour(sf2));
513
514		// with filter on AF < 4
515	1	gc.setAboveThreshold(false);
516	1	assertEquals(fr.getColour(sf2), expected);
517	1	FeatureMatcherSetI filter = new FeatureMatcherSet();
518	1	filter.and(FeatureMatcher.byAttribute(Condition.LT, "4.0", "AF"));
519	1	fr.setFeatureFilter("Cath", filter);
520	1	assertNull(fr.getColour(sf2));
521
522		// with filter on 'Consequence contains missense'
523	1	filter = new FeatureMatcherSet();
524	1	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "missense",
525		"Consequence"));
526	1	fr.setFeatureFilter("Cath", filter);
527		// if feature has no Consequence attribute, no colour
528	1	assertNull(fr.getColour(sf2));
529		// if attribute does not match filter, no colour
530	1	sf2.setValue("Consequence", "Synonymous");
531	1	assertNull(fr.getColour(sf2));
532		// attribute matches filter
533	1	sf2.setValue("Consequence", "Missense variant");
534	1	assertEquals(fr.getColour(sf2), expected);
535
536		// with filter on CSQ:Feature contains "ENST01234"
537	1	filter = new FeatureMatcherSet();
538	1	filter.and(FeatureMatcher.byAttribute(Condition.Matches, "ENST01234",
539		"CSQ", "Feature"));
540	1	fr.setFeatureFilter("Cath", filter);
541		// if feature has no CSQ data, no colour
542	1	assertNull(fr.getColour(sf2));
543		// if CSQ data does not include Feature, no colour
544	1	Map<String, String> csqData = new HashMap<>();
545	1	csqData.put("BIOTYPE", "Transcript");
546	1	sf2.setValue("CSQ", csqData);
547	1	assertNull(fr.getColour(sf2));
548		// if attribute does not match filter, no colour
549	1	csqData.put("Feature", "ENST9876");
550	1	assertNull(fr.getColour(sf2));
551		// attribute matches filter
552	1	csqData.put("Feature", "ENST01234");
553	1	assertEquals(fr.getColour(sf2), expected);
554		}
555
		100% Uncovered Elements: 0 (37) Complexity: 1 Complexity Density: 0.03 1PASS
556	1	@Test(groups = "Functional")...
557		public void testIsVisible()
558		{
559	1	String seqData = ">s1\nMLQGIFPRS\n";
560	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
561		DataSourceType.PASTE);
562	1	AlignViewportI av = af.getViewport();
563	1	FeatureRenderer fr = new FeatureRenderer(av);
564	1	SequenceI seq = av.getAlignment().getSequenceAt(0);
565	1	SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
566		"Group");
567	1	sf.setValue("AC", "11");
568	1	sf.setValue("CLIN_SIG", "Likely Pathogenic");
569	1	seq.addSequenceFeature(sf);
570
571	1	assertFalse(fr.isVisible(null));
572
573		/*
574		* initial state FeatureRenderer hasn't 'found' feature
575		* and so its feature type has not yet been set visible
576		*/
577	1	assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
578	1	assertFalse(fr.isVisible(sf));
579
580	1	fr.findAllFeatures(true);
581	1	assertTrue(fr.isVisible(sf));
582
583		/*
584		* feature group not visible
585		*/
586	1	fr.setGroupVisibility("Group", false);
587	1	assertFalse(fr.isVisible(sf));
588	1	fr.setGroupVisibility("Group", true);
589	1	assertTrue(fr.isVisible(sf));
590
591		/*
592		* feature score outwith colour threshold (score > 2)
593		*/
594	1	FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
595		Color.white, 0, 10);
596	1	fc.setAboveThreshold(true);
597	1	fc.setThreshold(2f);
598	1	fr.setColour("METAL", fc);
599	1	assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
600	1	fc.setBelowThreshold(true);
601	1	assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
602
603		/*
604		* colour with threshold on attribute AC (value is 11)
605		*/
606	1	fc.setAttributeName("AC");
607	1	assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
608	1	fc.setAboveThreshold(true);
609	1	assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
610
611	1	fc.setAttributeName("AF"); // attribute AF is absent in sf
612	1	assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
613
614	1	FeatureMatcherSetI filter = new FeatureMatcherSet();
615	1	filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
616		"CLIN_SIG"));
617	1	fr.setFeatureFilter("METAL", filter);
618	1	assertTrue(fr.isVisible(sf)); // feature matches filter
619	1	filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
620	1	assertFalse(fr.isVisible(sf)); // feature doesn't match filter
621		}
622
		94.6% Uncovered Elements: 2 (37) Complexity: 3 Complexity Density: 0.09 1PASS
623	1	@Test(groups = "Functional")...
624		public void testFindComplementFeaturesAtResidue()
625		{
626	1	Jalview.main(
627		new String[]
628		{ "--nonews", "--props", "test/jalview/testProps.jvprops" });
629
630		// codons for MCWHSE
631	1	String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";
632	1	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(cdsSeq,
633		DataSourceType.PASTE);
634	1	af.showTranslation_actionPerformed(
635		GeneticCodes.getInstance().getStandardCodeTable());
636	1	af.closeMenuItem_actionPerformed(true);
637
638		/*
639		* find the complement frames (ugly)
640		*/
641	1	AlignFrame[] frames = Desktop.getDesktopAlignFrames();
642	1	assertEquals(frames.length, 2);
643	1	AlignViewport av1 = frames[0].getViewport();
644	1	AlignViewport av2 = frames[1].getViewport();
645	1	AlignViewport cds = av1.getAlignment().isNucleotide() ? av1 : av2;
646	1	AlignViewport peptide = cds == av1 ? av2 : av1;
647	1	assertNotNull(cds);
648	1	assertNotNull(peptide);
649
650		/*
651		* add features to CDS at first codon, positions 2-3
652		*/
653	1	SequenceI seq1 = cds.getAlignment().getSequenceAt(0);
654	1	SequenceFeature sf1 = new SequenceFeature("sequence_variant", "G,GT", 2,
655		2, "ensembl");
656	1	seq1.addSequenceFeature(sf1);
657	1	SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA",
658		3, 3, "ensembl");
659	1	seq1.addSequenceFeature(sf2);
660
661		/*
662		* 'find' mapped features from the peptide position
663		* - first with CDS features _not_ shown on peptide alignment
664		*/
665	1	SequenceI seq2 = peptide.getAlignment().getSequenceAt(0);
666	1	FeatureRenderer frC = new FeatureRenderer(cds);
667	1	frC.featuresAdded();
668	1	MappedFeatures mf = frC.findComplementFeaturesAtResidue(seq2, 1);
669	1	assertNotNull(mf);
670	1	assertEquals(mf.features.size(), 2);
671	1	assertSame(mf.features.get(0), sf1);
672	1	assertSame(mf.features.get(1), sf2);
673
674		/*
675		* add exon feature and verify it is only returned once for a
676		* peptide position, even though it is on all 3 codon positions
677		*/
678	1	SequenceFeature sf3 = new SequenceFeature("exon", "exon1", 4, 12,
679		"ensembl");
680	1	seq1.addSequenceFeature(sf3);
681	1	frC.featuresAdded();
682	1	mf = frC.findComplementFeaturesAtResidue(seq2, 3);
683	1	assertNotNull(mf);
684	1	assertEquals(mf.features.size(), 1);
685	1	assertSame(mf.features.get(0), sf3);
686		}
687		}