Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceAnnotationReportTest	49	201	15	1.0100%	Show methods

Class SequenceAnnotationReportTest

Class SequenceAnnotationReportTest	Line # 49	Total Statements 201	Complexity 15	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5252	2.02	1.01	1.0 1.0100%
testAppendFeature_disulfideBond() : void   testAppendFeature_disulfideBond() : void	5959	10.010	1.01	1.0 1.0100%
testAppendFeatures_longText() : void   testAppendFeatures_longText() : void	8484	22.022	1.01	1.0 1.0100%
testAppendFeature_status() : void   testAppendFeature_status() : void	120120	6.06	1.01	1.0 1.0100%
testAppendFeature_withScore() : void   testAppendFeature_withScore() : void	133133	14.014	1.01	1.0 1.0100%
testAppendFeature_noScore() : void   testAppendFeature_noScore() : void	167167	5.05	1.01	1.0 1.0100%
testAppendFeature_colouredByAttribute() : void   testAppendFeature_colouredByAttribute() : void	182182	17.017	1.01	1.0 1.0100%
testAppendFeature_withScoreStatusAttribute() : void   testAppendFeature_withScoreStatusAttribute() : void	219219	13.013	1.01	1.0 1.0100%
testAppendFeature_DescEqualsType() : void   testAppendFeature_DescEqualsType() : void	243243	9.09	1.01	1.0 1.0100%
testAppendFeature_stripHtml() : void   testAppendFeature_stripHtml() : void	262262	9.09	1.01	1.0 1.0100%
testCreateSequenceAnnotationReport() : void   testCreateSequenceAnnotationReport() : void	282282	57.057	1.01	1.0 1.0100%
testCreateSequenceAnnotationReport_withEllipsis() : void   testCreateSequenceAnnotationReport_withEllipsis() : void	410410	13.013	3.03	1.0 1.0100%
testAppendFeature_virtualFeature() : void   testAppendFeature_virtualFeature() : void	443443	24.024	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.26605505	jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReportjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport	1PASS
	0.1146789	jalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeaturejalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeature	1PASS
	0.10550459	jalview.io.SequenceAnnotationReportTest.testAppendFeatures_longTextjalview.io.SequenceAnnotationReportTest.testAppendFeatures_longText	1PASS
	0.08256881	jalview.io.SequenceAnnotationReportTest.testAppendFeature_colouredByAttributejalview.io.SequenceAnnotationReportTest.testAppendFeature_colouredByAttribute	1PASS
	0.08256881	jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsisjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsis	1PASS
	0.06880734	jalview.io.SequenceAnnotationReportTest.testAppendFeature_withScorejalview.io.SequenceAnnotationReportTest.testAppendFeature_withScore	1PASS
	0.06422018	jalview.io.SequenceAnnotationReportTest.testAppendFeature_withScoreStatusAttributejalview.io.SequenceAnnotationReportTest.testAppendFeature_withScoreStatusAttribute	1PASS
	0.050458714	jalview.io.SequenceAnnotationReportTest.testAppendFeature_disulfideBondjalview.io.SequenceAnnotationReportTest.testAppendFeature_disulfideBond	1PASS
	0.04587156	jalview.io.SequenceAnnotationReportTest.testAppendFeature_DescEqualsTypejalview.io.SequenceAnnotationReportTest.testAppendFeature_DescEqualsType	1PASS
	0.04587156	jalview.io.SequenceAnnotationReportTest.testAppendFeature_stripHtmljalview.io.SequenceAnnotationReportTest.testAppendFeature_stripHtml	1PASS
	0.03211009	jalview.io.SequenceAnnotationReportTest.testAppendFeature_statusjalview.io.SequenceAnnotationReportTest.testAppendFeature_status	1PASS
	0.027522936	jalview.io.SequenceAnnotationReportTest.testAppendFeature_noScorejalview.io.SequenceAnnotationReportTest.testAppendFeature_noScore	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.io;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertTrue;
25
26		import java.awt.Color;
27		import java.util.ArrayList;
28		import java.util.List;
29		import java.util.Map;
30
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
34		import jalview.api.FeatureColourI;
35		import jalview.datamodel.DBRefEntry;
36		import jalview.datamodel.MappedFeatures;
37		import jalview.datamodel.Mapping;
38		import jalview.datamodel.Sequence;
39		import jalview.datamodel.SequenceFeature;
40		import jalview.datamodel.SequenceI;
41		import jalview.gui.JvOptionPane;
42		import jalview.io.gff.GffConstants;
43		import jalview.renderer.seqfeatures.FeatureRenderer;
44		import jalview.schemes.FeatureColour;
45		import jalview.util.MapList;
46		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
47		import junit.extensions.PA;
48
		100% Uncovered Elements: 0 (218) Complexity: 15 Complexity Density: 0.07
49		public class SequenceAnnotationReportTest
50		{
51
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
52	1	@BeforeClass(alwaysRun = true)...
53		public void setUpJvOptionPane()
54		{
55	1	JvOptionPane.setInteractiveMode(false);
56	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57		}
58
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
59	1	@Test(groups = "Functional")...
60		public void testAppendFeature_disulfideBond()
61		{
62	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
63	1	StringBuilder sb = new StringBuilder();
64	1	sb.append("123456");
65	1	SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1, 3,
66		1.2f, "group");
67
68		// residuePos == 2 does not match start or end of feature, nothing done:
69	1	sar.appendFeature(sb, 2, null, sf, null, 0);
70	1	assertEquals("123456", sb.toString());
71
72		// residuePos == 1 matches start of feature, text appended (but no <br/>)
73		// feature score is not included
74	1	sar.appendFeature(sb, 1, null, sf, null, 0);
75	1	assertEquals("123456disulfide bond 1:3", sb.toString());
76
77		// residuePos == 3 matches end of feature, text appended
78		// <br/> is prefixed once sb.length() > 6
79	1	sar.appendFeature(sb, 3, null, sf, null, 0);
80	1	assertEquals("123456disulfide bond 1:3<br/>disulfide bond 1:3",
81		sb.toString());
82		}
83
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
84	1	@Test(groups = "Functional")...
85		public void testAppendFeatures_longText()
86		{
87	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
88	1	StringBuilder sb = new StringBuilder();
89	1	String longString = "Abcd".repeat(50);
90	1	SequenceFeature sf = new SequenceFeature("sequence", longString, 1, 3,
91		"group");
92
93	1	sar.appendFeature(sb, 1, null, sf, null, 0);
94	1	assertTrue(sb.length() < 100);
95
96	1	List<SequenceFeature> sfl = new ArrayList<>();
97	1	sb.setLength(0);
98	1	sfl.add(sf);
99	1	sfl.add(sf);
100	1	sfl.add(sf);
101	1	sfl.add(sf);
102	1	sfl.add(sf);
103	1	sfl.add(sf);
104	1	sfl.add(sf);
105	1	sfl.add(sf);
106	1	sfl.add(sf);
107	1	sfl.add(sf);
108	1	int n = sar.appendFeatures(sb, 1, sfl, new FeatureRenderer(null), 200); // text
109		// should
110		// terminate
111		// before
112		// 200
113		// characters
114	1	String s = sb.toString();
115	1	assertTrue(s.length() < 200);
116	1	assertEquals(n, 7); // should be 7 features left over
117
118		}
119
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
120	1	@Test(groups = "Functional")...
121		public void testAppendFeature_status()
122		{
123	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
124	1	StringBuilder sb = new StringBuilder();
125	1	SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
126		Float.NaN, "group");
127	1	sf.setStatus("Confirmed");
128
129	1	sar.appendFeature(sb, 1, null, sf, null, 0);
130	1	assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
131		}
132
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
133	1	@Test(groups = "Functional")...
134		public void testAppendFeature_withScore()
135		{
136	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
137	1	StringBuilder sb = new StringBuilder();
138	1	SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
139		"group");
140
141	1	FeatureRendererModel fr = new FeatureRenderer(null);
142	1	Map<String, float[][]> minmax = fr.getMinMax();
143	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
144		/*
145		* map has no entry for this feature type - score is not shown:
146		*/
147	1	assertEquals("METAL 1 3; Fe2-S", sb.toString());
148
149		/*
150		* map has entry for this feature type - score is shown:
151		*/
152	1	minmax.put("METAL", new float[][] { { 0f, 1f }, null });
153	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
154		// <br/> is appended to a buffer > 6 in length
155	1	assertEquals("METAL 1 3; Fe2-S<br/>METAL 1 3; Fe2-S Score=1.3",
156		sb.toString());
157
158		/*
159		* map has min == max for this feature type - score is not shown:
160		*/
161	1	minmax.put("METAL", new float[][] { { 2f, 2f }, null });
162	1	sb.setLength(0);
163	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
164	1	assertEquals("METAL 1 3; Fe2-S", sb.toString());
165		}
166
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
167	1	@Test(groups = "Functional")...
168		public void testAppendFeature_noScore()
169		{
170	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
171	1	StringBuilder sb = new StringBuilder();
172	1	SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
173		Float.NaN, "group");
174
175	1	sar.appendFeature(sb, 1, null, sf, null, 0);
176	1	assertEquals("METAL 1 3; Fe2-S", sb.toString());
177		}
178
179		/**
180		* A specific attribute value is included if it is used to colour the feature
181		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
182	1	@Test(groups = "Functional")...
183		public void testAppendFeature_colouredByAttribute()
184		{
185	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
186	1	StringBuilder sb = new StringBuilder();
187	1	SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
188		Float.NaN, "group");
189	1	sf.setValue("clinical_significance", "Benign");
190
191		/*
192		* first with no colour by attribute
193		*/
194	1	FeatureRendererModel fr = new FeatureRenderer(null);
195	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
196	1	assertEquals("METAL 1 3; Fe2-S", sb.toString());
197
198		/*
199		* then with colour by an attribute the feature lacks
200		*/
201	1	FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
202		null, 5, 10);
203	1	fc.setAttributeName("Pfam");
204	1	fr.setColour("METAL", fc);
205	1	sb.setLength(0);
206	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
207	1	assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
208
209		/*
210		* then with colour by an attribute the feature has
211		*/
212	1	fc.setAttributeName("clinical_significance");
213	1	sb.setLength(0);
214	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
215	1	assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
216		sb.toString());
217		}
218
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
219	1	@Test(groups = "Functional")...
220		public void testAppendFeature_withScoreStatusAttribute()
221		{
222	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
223	1	StringBuilder sb = new StringBuilder();
224	1	SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f,
225		"group");
226	1	sf.setStatus("Confirmed");
227	1	sf.setValue("clinical_significance", "Benign");
228
229	1	FeatureRendererModel fr = new FeatureRenderer(null);
230	1	Map<String, float[][]> minmax = fr.getMinMax();
231	1	FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
232		null, 12, 22);
233	1	fc.setAttributeName("clinical_significance");
234	1	fr.setColour("METAL", fc);
235	1	minmax.put("METAL", new float[][] { { 0f, 1f }, null });
236	1	sar.appendFeature(sb, 1, fr, sf, null, 0);
237
238	1	assertEquals(
239		"METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
240		sb.toString());
241		}
242
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
243	1	@Test(groups = "Functional")...
244		public void testAppendFeature_DescEqualsType()
245		{
246	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
247	1	StringBuilder sb = new StringBuilder();
248	1	SequenceFeature sf = new SequenceFeature("METAL", "METAL", 1, 3,
249		Float.NaN, "group");
250
251		// description is not included if it duplicates type:
252	1	sar.appendFeature(sb, 1, null, sf, null, 0);
253	1	assertEquals("METAL 1 3", sb.toString());
254
255	1	sb.setLength(0);
256	1	sf.setDescription("Metal");
257		// test is case-sensitive:
258	1	sar.appendFeature(sb, 1, null, sf, null, 0);
259	1	assertEquals("METAL 1 3; Metal", sb.toString());
260		}
261
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
262	1	@Test(groups = "Functional")...
263		public void testAppendFeature_stripHtml()
264		{
265	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
266	1	StringBuilder sb = new StringBuilder();
267	1	SequenceFeature sf = new SequenceFeature("METAL",
268		"<html><body>hello<em>world</em></body></html>", 1, 3,
269		Float.NaN, "group");
270
271	1	sar.appendFeature(sb, 1, null, sf, null, 0);
272		// !! strips off </body> but not <body> ??
273	1	assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
274
275	1	sb.setLength(0);
276	1	sf.setDescription("<br>&kHD>6");
277	1	sar.appendFeature(sb, 1, null, sf, null, 0);
278		// if no <html> tag, html-encodes > and < (only):
279	1	assertEquals("METAL 1 3; &lt;br&gt;&kHD&gt;6", sb.toString());
280		}
281
		100% Uncovered Elements: 0 (57) Complexity: 1 Complexity Density: 0.02 1PASS
282	1	@Test(groups = "Functional")...
283		public void testCreateSequenceAnnotationReport()
284		{
285	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
286	1	StringBuilder sb = new StringBuilder();
287
288	1	SequenceI seq = new Sequence("s1", "MAKLKRFQSSTLL");
289	1	seq.setDescription("SeqDesc");
290
291		/*
292		* positional features are ignored
293		*/
294	1	seq.addSequenceFeature(
295		new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null));
296	1	sar.createSequenceAnnotationReport(sb, seq, true, true, null);
297	1	assertEquals("<i>SeqDesc\n" + "\n" + "</i>", sb.toString());
298
299		/*
300		* non-positional feature
301		*/
302	1	seq.addSequenceFeature(
303		new SequenceFeature("Type1", "Nonpos", 0, 0, 1f, null));
304	1	sb.setLength(0);
305	1	sar.createSequenceAnnotationReport(sb, seq, true, true, null);
306	1	String expected = "<i>SeqDesc\n" + "\n"
307		+ "<br/>Type1 ; Nonpos Score=1.0</i>";
308	1	assertEquals(expected, sb.toString());
309
310		/*
311		* non-positional features not wanted
312		*/
313	1	sb.setLength(0);
314	1	sar.createSequenceAnnotationReport(sb, seq, true, false, null);
315	1	assertEquals("<i>SeqDesc\n\n</i>", sb.toString());
316
317		/*
318		* add non-pos feature with score inside min-max range for feature type
319		* minmax holds { [positionalMin, positionalMax], [nonPosMin, nonPosMax] }
320		* score is only appended for positional features so ignored here!
321		* minMax are not recorded for non-positional features
322		*/
323	1	seq.addSequenceFeature(
324		new SequenceFeature("Metal", "Desc", 0, 0, 5f, null));
325
326	1	FeatureRendererModel fr = new FeatureRenderer(null);
327	1	Map<String, float[][]> minmax = fr.getMinMax();
328	1	minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } });
329
330	1	sb.setLength(0);
331	1	sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
332	1	expected = "<i>SeqDesc\n" + "\n"
333		+ "<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
334	1	assertEquals(expected, sb.toString());
335
336		/*
337		* 'linkonly' features are ignored; this is obsolete, as linkonly
338		* is only set by DasSequenceFetcher, and DAS is history
339		*/
340	1	SequenceFeature sf = new SequenceFeature("Metal", "Desc", 0, 0, 5f,
341		null);
342	1	sf.setValue("linkonly", Boolean.TRUE);
343	1	seq.addSequenceFeature(sf);
344	1	sb.setLength(0);
345	1	sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
346	1	assertEquals(expected, sb.toString()); // unchanged!
347
348		/*
349		* 'clinical_significance' attribute is only included in description
350		* when used for feature colouring
351		*/
352	1	SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0, 5f,
353		null);
354	1	sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign");
355	1	seq.addSequenceFeature(sf2);
356	1	sb.setLength(0);
357	1	sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
358	1	expected = "<i>SeqDesc\n" + "\n"
359		+ "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana</i>";
360	1	assertEquals(expected, sb.toString());
361
362		/*
363		* add dbrefs
364		*/
365	1	seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1"));
366	1	seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419"));
367
368		// with showDbRefs = false
369	1	sb.setLength(0);
370	1	sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
371	1	assertEquals(expected, sb.toString()); // unchanged
372
373		// with showDbRefs = true, colour Variant features by clinical_significance
374	1	sb.setLength(0);
375	1	FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
376		null, 2, 3);
377	1	fc.setAttributeName("clinical_significance");
378	1	fr.setColour("Variant", fc);
379	1	sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
380	1	expected = "<i>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
381		+ "PDB 3iu1\n"
382		+ "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; Havana; clinical_significance=benign</i>";
383	1	assertEquals(expected, sb.toString());
384		// with showNonPositionalFeatures = false
385	1	sb.setLength(0);
386	1	sar.createSequenceAnnotationReport(sb, seq, true, false, fr);
387	1	expected = "<i>SeqDesc\n" + "<br/>\n" + "UNIPROT P30419<br/>\n"
388		+ "PDB 3iu1\n" + "</i>";
389	1	assertEquals(expected, sb.toString());
390
391		/*
392		* long feature description is truncated with ellipsis
393		*/
394	1	sb.setLength(0);
395	1	sf2.setDescription(
396		"This is a very long description which should be truncated");
397	1	sar.createSequenceAnnotationReport(sb, seq, false, true, fr);
398	1	expected = "<i>SeqDesc\n" + "\n"
399		+ "<br/>Metal ; Desc<br/>Type1 ; Nonpos<br/>Variant ; This is a very long description which sh...; clinical_significance=benign</i>";
400	1	assertEquals(expected, sb.toString());
401
402		// see other tests for treatment of status and html
403		}
404
405		/**
406		* Test that exercises an abbreviated sequence details report, with ellipsis
407		* where there are more than 40 different sources, or more than 4 dbrefs for a
408		* single source
409		*/
		100% Uncovered Elements: 0 (17) Complexity: 3 Complexity Density: 0.23 1PASS
410	1	@Test(groups = "Functional")...
411		public void testCreateSequenceAnnotationReport_withEllipsis()
412		{
413	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
414	1	StringBuilder sb = new StringBuilder();
415
416	1	SequenceI seq = new Sequence("s1", "ABC");
417
418	1	int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
419	7	for (int i = 0; i <= maxSources; i++)
420		{
421	6	seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1"));
422		}
423
424	1	int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE");
425	6	for (int i = 0; i <= maxRefs; i++)
426		{
427	5	seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i));
428		}
429
430	1	sar.createSequenceAnnotationReport(sb, seq, true, true, null, true);
431	1	String report = sb.toString();
432	1	assertTrue(report.startsWith("<i>\n" + "<br/>\n" + "UNIPROT P30410,\n"
433		+ " P30411,\n" + " P30412,\n" + " P30413,...<br/>\n"
434		+ "PDB0 3iu1<br/>\n" + "PDB1 3iu1<br/>"));
435	1	assertTrue(report.endsWith("PDB3 3iu1<br/>\n" + "PDB4,...<br/>\n"
436		+ "(Output Sequence Details to list all database references)\n"
437		+ "</i>"));
438		}
439
440		/**
441		* Test adding a linked feature to the tooltip
442		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
443	1	@Test(groups = "Functional")...
444		public void testAppendFeature_virtualFeature()
445		{
446		/*
447		* map CDS to peptide sequence
448		*/
449	1	SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
450	1	SequenceI peptide = new Sequence("Peptide/8-14", "PLRFQMD");
451	1	MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
452		3, 1);
453	1	Mapping mapping = new Mapping(peptide, map);
454
455		/*
456		* assume variant feature found at CDS position 106 G>C
457		*/
458	1	List<SequenceFeature> features = new ArrayList<>();
459		// vary ttg (Leu) to ttc (Phe)
460	1	SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
461		Float.NaN, null);
462	1	features.add(sf);
463	1	MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
464
465	1	StringBuilder sb = new StringBuilder();
466	1	SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
467	1	sar.appendFeature(sb, 1, null, sf, mf, 0);
468
469		/*
470		* linked feature shown in tooltip in protein coordinates
471		*/
472	1	assertEquals("variant 9; G,C", sb.toString());
473
474		/*
475		* adding "alleles" attribute to variant allows peptide consequence
476		* to be calculated and added to the tooltip
477		*/
478	1	sf.setValue("alleles", "G,C");
479	1	sb = new StringBuilder();
480	1	sar.appendFeature(sb, 1, null, sf, mf, 0);
481	1	assertEquals("variant 9; G,C p.Leu9Phe", sb.toString());
482
483		/*
484		* now a virtual peptide feature on CDS
485		* feature at 11-12 on peptide maps to 110-115 on CDS
486		* here we test for tooltip at 113 (t)
487		*/
488	1	SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, 2.3f,
489		"Uniprot");
490	1	features.clear();
491	1	features.add(sf2);
492	1	mapping = new Mapping(peptide, map);
493	1	mf = new MappedFeatures(mapping, peptide, 113, 't', features);
494	1	sb = new StringBuilder();
495	1	sar.appendFeature(sb, 1, null, sf2, mf, 0);
496	1	assertEquals("metal 110 115; Fe Score=2.3", sb.toString());
497		}
498		}