Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EmblXmlSourceTest	47	231	10	0.96680596.7%	Show methods

Class EmblXmlSourceTest

Class EmblXmlSourceTest	Line # 47	Total Statements 231	Complexity 10	TOTAL Coverage 0.96680596.7%
getDbSource() : String   getDbSource() : String	108108	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	114114	1.01	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	120120	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	126126	1.01	1.01	0.0 0.00%
setUp() : void   setUp() : void	102102	1.01	1.01	1.0 1.0100%
testGetCdsRanges() : void   testGetCdsRanges() : void	134134	4.04	1.01	1.0 1.0100%
testGetSequence() : void   testGetSequence() : void	149149	126.0126	1.01	1.0 1.0100%
testAdjustForProteinLength() : void   testAdjustForProteinLength() : void	347347	13.013	1.01	1.0 1.0100%
testGetEmblEntries() : void   testGetEmblEntries() : void	377377	82.082	1.01	1.0 1.0100%
getEmblEntries() : List<EntryType>   getEmblEntries() : List<EntryType>	494494	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.53526974	jalview.ws.dbsources.EmblXmlSourceTest.testGetSequencejalview.ws.dbsources.EmblXmlSourceTest.testGetSequence	1PASS
	0.3526971	jalview.ws.dbsources.EmblXmlSourceTest.testGetEmblEntriesjalview.ws.dbsources.EmblXmlSourceTest.testGetEmblEntries	1PASS
	0.058091287	jalview.ws.dbsources.EmblXmlSourceTest.testAdjustForProteinLengthjalview.ws.dbsources.EmblXmlSourceTest.testAdjustForProteinLength	1PASS
	0.020746889	jalview.ws.dbsources.EmblXmlSourceTest.testGetCdsRangesjalview.ws.dbsources.EmblXmlSourceTest.testGetCdsRanges	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.ws.dbsources;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertNull;
26		import static org.testng.AssertJUnit.assertSame;
27		import static org.testng.AssertJUnit.assertTrue;
28
29		import java.io.ByteArrayInputStream;
30		import java.util.ArrayList;
31		import java.util.Arrays;
32		import java.util.List;
33
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
37		import jalview.datamodel.AlignmentI;
38		import jalview.datamodel.DBRefEntry;
39		import jalview.datamodel.DBRefSource;
40		import jalview.datamodel.SequenceI;
41		import jalview.util.MapList;
42		import jalview.xml.binding.embl.EntryType;
43		import jalview.xml.binding.embl.EntryType.Feature;
44		import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
45		import jalview.xml.binding.embl.XrefType;
46
		96.7% Uncovered Elements: 8 (241) Complexity: 10 Complexity Density: 0.04
47		public class EmblXmlSourceTest
48		{
49
50		// adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
51		// dna and translations truncated for convenience
52		static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
53		+ "<ROOT>"
54		+ "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
55		+ " dataClass=\"STD\" taxonomicDivision=\"PRO\""
56		+ " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
57		+ " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
58		+ " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
59		+ "<secondaryAccession>X07574</secondaryAccession>"
60		+ "<description>C. trachomatis plasmid</description>"
61		+ "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
62		+ "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
63		+ "<xref db=\"MD5\" id=\"ac73317\" />"
64		/*
65		* first CDS (range and translation changed to keep test data manageable)
66		*/
67		+ "<feature name=\"CDS\" location=\"complement(46..57)\">"
68		// test the case of >1 cross-ref to the same database (JAL-2029)
69		+ "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
70		+ "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
71		+ "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value></qualifier>"
72		+ "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
73		+ "<qualifier name=\"translation\"><value>MLCF</value></qualifier>"
74		+ "</feature>"
75		/*
76		* second CDS (range and translation changed to keep test data manageable)
77		*/
78		+ "<feature name=\"CDS\" location=\"4..15\">"
79		+ "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
80		+ "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
81		+ "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
82		+ "</feature>"
83		/*
84		* third CDS is made up - has no xref - code should synthesize
85		* one to an assumed EMBLCDSPROTEIN accession
86		*/
87		+ "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
88		+ "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
89		+ "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
90		+ "</feature>"
91		/*
92		* sequence (modified for test purposes)
93		* emulates EMBL XML 1.2 which splits sequence data every 60 characters
94		* see EmblSequence.setSequence
95		*/
96		+ "<sequence>GGTATGTCCTCTAGTACAAAC\n"
97		+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
98		+ "</sequence></entry></ROOT>";
99
100		private EmblXmlSource testee;
101
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
102	1	@BeforeClass(alwaysRun = true)...
103		public void setUp()
104		{
105	1	testee = new EmblXmlSource()
106		{
107
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
108	0	@Override...
109		public String getDbSource()
110		{
111	0	return null;
112		}
113
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
114	0	@Override...
115		public String getDbName()
116		{
117	0	return null;
118		}
119
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		public String getTestQuery()
122		{
123	0	return null;
124		}
125
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
126	0	@Override...
127		public AlignmentI getSequenceRecords(String queries) throws Exception
128		{
129	0	return null;
130		}
131		};
132		}
133
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25 1PASS
134	1	@Test(groups = "Functional")...
135		public void testGetCdsRanges()
136		{
137		/*
138		* Make a (CDS) Feature with 5 locations
139		*/
140	1	Feature cds = new Feature();
141	1	cds.setLocation(
142		"join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
143
144	1	int[] exons = testee.getCdsRanges("EMBL", cds);
145	1	assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
146		Arrays.toString(exons));
147		}
148
		100% Uncovered Elements: 0 (126) Complexity: 1 Complexity Density: 0.01 1PASS
149	1	@Test(groups = "Functional")...
150		public void testGetSequence()
151		{
152		// not the whole sequence but enough for this test...
153	1	List<SequenceI> peptides = new ArrayList<>();
154	1	List<EntryType> entries = getEmblEntries();
155	1	assertEquals(1, entries.size());
156	1	EntryType entry = entries.get(0);
157	1	String sourceDb = "EMBL";
158	1	SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
159
160		/*
161		* newline has been removed from sequence
162		*/
163	1	String seq = dna.getSequenceAsString();
164	1	assertEquals(
165		"GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
166		seq);
167
168		/*
169		* peptides should now have five entries:
170		* EMBL product and two Uniprot accessions for the first CDS / translation
171		* EMBL product and one Uniprot accession for the second CDS / "
172		* EMBL product only for the third
173		*/
174	1	assertEquals(6, peptides.size());
175	1	assertEquals("CAA30420.1", peptides.get(0).getName());
176	1	assertEquals("MLCF", peptides.get(0).getSequenceAsString());
177	1	assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
178	1	assertEquals("MLCF", peptides.get(1).getSequenceAsString());
179	1	assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
180	1	assertEquals("MLCF", peptides.get(2).getSequenceAsString());
181	1	assertEquals("CAA30421.1", peptides.get(3).getName());
182	1	assertEquals("MSSS", peptides.get(3).getSequenceAsString());
183	1	assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
184	1	assertEquals("MSSS", peptides.get(4).getSequenceAsString());
185	1	assertEquals("CAA12345.6", peptides.get(5).getName());
186	1	assertEquals("MSS", peptides.get(5).getSequenceAsString());
187
188		/*
189		* verify dna sequence has dbrefs
190		* - to 'self' (synthesized dbref)
191		* - to EuropePMC
192		* - to MD5 (with null version as "0")
193		* - with CDS mappings to the peptide 'products'
194		*/
195	1	MapList mapToSelf = new MapList(new int[] { 1, 57 },
196		new int[]
197		{ 1, 57 }, 1, 1);
198	1	MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
199		3, 1);
200	1	MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
201		3, 1);
202	1	MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 },
203		new int[]
204		{ 1, 3 }, 3, 1);
205
206	1	List<DBRefEntry> dbrefs = dna.getDBRefs();
207	1	assertEquals(7, dbrefs.size());
208
209	1	DBRefEntry dbRefEntry = dbrefs.get(0);
210	1	assertEquals("EMBL", dbRefEntry.getSource());
211	1	assertEquals("X07547", dbRefEntry.getAccessionId());
212	1	assertEquals("1", dbRefEntry.getVersion());
213	1	assertNotNull(dbRefEntry.getMap());
214	1	assertNull(dbRefEntry.getMap().getTo());
215	1	assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
216
217	1	dbRefEntry = dbrefs.get(1);
218		// DBRefEntry constructor puts dbSource in upper case
219	1	assertEquals("EUROPEPMC", dbRefEntry.getSource());
220	1	assertEquals("PMC107176", dbRefEntry.getAccessionId());
221	1	assertEquals("9573186", dbRefEntry.getVersion());
222	1	assertNull(dbRefEntry.getMap());
223
224	1	dbRefEntry = dbrefs.get(2);
225	1	assertEquals("MD5", dbRefEntry.getSource());
226	1	assertEquals("ac73317", dbRefEntry.getAccessionId());
227	1	assertEquals("0", dbRefEntry.getVersion());
228	1	assertNull(dbRefEntry.getMap());
229
230	1	dbRefEntry = dbrefs.get(3);
231	1	assertEquals("UNIPROT", dbRefEntry.getSource());
232	1	assertEquals("B0BCM4", dbRefEntry.getAccessionId());
233	1	assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
234	1	assertEquals(cds1Map, dbRefEntry.getMap().getMap());
235
236	1	dbRefEntry = dbrefs.get(4);
237	1	assertEquals("UNIPROT", dbRefEntry.getSource());
238	1	assertEquals("P0CE20", dbRefEntry.getAccessionId());
239	1	assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
240	1	assertEquals(cds1Map, dbRefEntry.getMap().getMap());
241
242	1	dbRefEntry = dbrefs.get(5);
243	1	assertEquals("UNIPROT", dbRefEntry.getSource());
244	1	assertEquals("B0BCM3", dbRefEntry.getAccessionId());
245	1	assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
246	1	assertEquals(cds2Map, dbRefEntry.getMap().getMap());
247
248	1	dbRefEntry = dbrefs.get(6);
249	1	assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
250	1	assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
251	1	assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
252	1	assertEquals(cds3Map, dbRefEntry.getMap().getMap());
253
254		/*
255		* verify peptides have dbrefs
256		* - to EMBL sequence (with inverse 1:3 cds mapping)
257		* - to EMBLCDS (with 1:3 mapping)
258		* - direct (no mapping) to other protein accessions
259		*/
260	1	MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 },
261		new int[]
262		{ 1, 12 }, 1, 3);
263	1	MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 },
264		new int[]
265		{ 1, 9 }, 1, 3);
266
267		// dbrefs for first CDS EMBL product CAA30420.1
268	1	dbrefs = peptides.get(0).getDBRefs();
269	1	assertEquals(5, dbrefs.size());
270	1	assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
271	1	assertEquals("CAA30420.1", dbrefs.get(0).getAccessionId());
272		// TODO: verify getPrimaryDBRefs() for peptide products
273	1	assertEquals(cds1Map.getInverse(), dbrefs.get(0).getMap().getMap());
274	1	assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
275	1	assertEquals("CAA30420.1", dbrefs.get(1).getAccessionId());
276	1	assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
277	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
278	1	assertEquals("CAA30420.1", dbrefs.get(2).getAccessionId());
279	1	assertNull(dbrefs.get(2).getMap());
280	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
281		dbrefs.get(3));
282	1	assertNull(dbrefs.get(3).getMap());
283	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
284		dbrefs.get(4));
285	1	assertNull(dbrefs.get(4).getMap());
286
287		// dbrefs for first CDS first Uniprot xref
288	1	dbrefs = peptides.get(1).getDBRefs();
289	1	assertEquals(2, dbrefs.size());
290	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
291		dbrefs.get(0));
292	1	assertNull(dbrefs.get(0).getMap());
293	1	assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
294	1	assertEquals("X07547", dbrefs.get(1).getAccessionId());
295	1	assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
296
297		// dbrefs for first CDS second Uniprot xref
298	1	dbrefs = peptides.get(2).getDBRefs();
299	1	assertEquals(2, dbrefs.size());
300	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
301		dbrefs.get(0));
302	1	assertNull(dbrefs.get(0).getMap());
303	1	assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
304	1	assertEquals("X07547", dbrefs.get(1).getAccessionId());
305	1	assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
306
307		// dbrefs for second CDS EMBL product CAA30421.1
308	1	dbrefs = peptides.get(3).getDBRefs();
309	1	assertEquals(4, dbrefs.size());
310	1	assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
311	1	assertEquals("CAA30421.1", dbrefs.get(0).getAccessionId());
312	1	assertEquals(cds2Map.getInverse(), dbrefs.get(0).getMap().getMap());
313	1	assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
314	1	assertEquals("CAA30421.1", dbrefs.get(1).getAccessionId());
315	1	assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
316	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
317	1	assertEquals("CAA30421.1", dbrefs.get(2).getAccessionId());
318	1	assertNull(dbrefs.get(2).getMap());
319	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
320		dbrefs.get(3));
321	1	assertNull(dbrefs.get(3).getMap());
322
323		// dbrefs for second CDS second Uniprot xref
324	1	dbrefs = peptides.get(4).getDBRefs();
325	1	assertEquals(2, dbrefs.size());
326	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
327		dbrefs.get(0));
328	1	assertNull(dbrefs.get(0).getMap());
329	1	assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
330	1	assertEquals("X07547", dbrefs.get(1).getAccessionId());
331	1	assertEquals(cds2Map.getInverse(), dbrefs.get(1).getMap().getMap());
332
333		// dbrefs for third CDS inferred EMBL product CAA12345.6
334	1	dbrefs = peptides.get(5).getDBRefs();
335	1	assertEquals(3, dbrefs.size());
336	1	assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
337	1	assertEquals("CAA12345.6", dbrefs.get(0).getAccessionId());
338	1	assertEquals(cds3Map.getInverse(), dbrefs.get(0).getMap().getMap());
339	1	assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
340	1	assertEquals("CAA12345.6", dbrefs.get(1).getAccessionId());
341	1	assertEquals(proteinToCdsMap2, dbrefs.get(1).getMap().getMap());
342	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
343	1	assertEquals("CAA12345.6", dbrefs.get(2).getAccessionId());
344	1	assertNull(dbrefs.get(2).getMap());
345		}
346
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
347	1	@Test(groups = "Functional")...
348		public void testAdjustForProteinLength()
349		{
350	1	int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
351
352		// exact length match:
353	1	assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
354
355		// truncate last exon by 3bp (e.g. stop codon)
356	1	int[] truncated = EmblXmlSource.adjustForProteinLength(5, exons);
357	1	assertEquals("[11, 15, 21, 25, 31, 35]", Arrays.toString(truncated));
358
359		// truncate last exon by 6bp
360	1	truncated = EmblXmlSource.adjustForProteinLength(4, exons);
361	1	assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
362
363		// remove last exon and truncate preceding by 1bp
364	1	truncated = EmblXmlSource.adjustForProteinLength(3, exons);
365	1	assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
366
367		// exact removal of exon case:
368	1	exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
369	1	truncated = EmblXmlSource.adjustForProteinLength(4, exons);
370	1	assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
371
372		// what if exons are too short for protein?
373	1	truncated = EmblXmlSource.adjustForProteinLength(7, exons);
374	1	assertSame(exons, truncated);
375		}
376
		100% Uncovered Elements: 0 (82) Complexity: 1 Complexity Density: 0.01 1PASS
377	1	@Test(groups = { "Functional" })...
378		public void testGetEmblEntries()
379		{
380	1	List<EntryType> entries = getEmblEntries();
381	1	assertEquals(1, entries.size());
382	1	EntryType entry = entries.get(0);
383
384	1	assertEquals("X07547", entry.getAccession());
385	1	assertEquals("C. trachomatis plasmid", entry.getDescription());
386	1	assertEquals("STD", entry.getDataClass());
387	1	assertEquals("PRO", entry.getTaxonomicDivision());
388	1	assertEquals("1999-02-10", entry.getLastUpdated().toString());
389	1	assertEquals(58, entry.getLastUpdatedRelease().intValue());
390	1	assertEquals("1988-11-10", entry.getFirstPublic().toString());
391	1	assertEquals(18, entry.getFirstPublicRelease().intValue());
392	1	assertEquals("genomic DNA", entry.getMoleculeType());
393	1	assertEquals(1, entry.getVersion().intValue());
394	1	assertEquals(8, entry.getEntryVersion().intValue());
395	1	assertEquals("linear", entry.getTopology());
396	1	assertEquals(7499, entry.getSequenceLength().intValue());
397	1	assertEquals(2, entry.getKeyword().size());
398	1	assertEquals("plasmid", entry.getKeyword().get(0));
399	1	assertEquals("unidentified reading frame", entry.getKeyword().get(1));
400
401		/*
402		* dbrefs
403		*/
404	1	assertEquals(2, entry.getXref().size());
405	1	XrefType dbref = entry.getXref().get(0);
406	1	assertEquals("EuropePMC", dbref.getDb());
407	1	assertEquals("PMC107176", dbref.getId());
408	1	assertEquals("9573186", dbref.getSecondaryId());
409	1	dbref = entry.getXref().get(1);
410	1	assertEquals("MD5", dbref.getDb());
411	1	assertEquals("ac73317", dbref.getId());
412	1	assertNull(dbref.getSecondaryId());
413
414		/*
415		* three sequence features for CDS
416		*/
417	1	assertEquals(3, entry.getFeature().size());
418		/*
419		* first CDS
420		*/
421	1	Feature ef = entry.getFeature().get(0);
422	1	assertEquals("CDS", ef.getName());
423	1	assertEquals("complement(46..57)", ef.getLocation());
424	1	assertEquals(2, ef.getXref().size());
425	1	dbref = ef.getXref().get(0);
426	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
427	1	assertEquals("B0BCM4", dbref.getId());
428	1	assertEquals("2.1", dbref.getSecondaryId());
429	1	dbref = ef.getXref().get(1);
430	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
431	1	assertEquals("P0CE20", dbref.getId());
432	1	assertNull(dbref.getSecondaryId());
433		// CDS feature qualifiers
434	1	assertEquals(3, ef.getQualifier().size());
435	1	Qualifier q = ef.getQualifier().get(0);
436	1	assertEquals("note", q.getName());
437	1	assertEquals("ORF 8 (AA 1-330)", q.getValue());
438	1	q = ef.getQualifier().get(1);
439	1	assertEquals("protein_id", q.getName());
440	1	assertEquals("CAA30420.1", q.getValue());
441	1	q = ef.getQualifier().get(2);
442	1	assertEquals("translation", q.getName());
443	1	assertEquals("MLCF", q.getValue());
444
445		/*
446		* second CDS
447		*/
448	1	ef = entry.getFeature().get(1);
449	1	assertEquals("CDS", ef.getName());
450	1	assertEquals("4..15", ef.getLocation());
451	1	assertEquals(1, ef.getXref().size());
452	1	dbref = ef.getXref().get(0);
453	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
454	1	assertEquals("B0BCM3", dbref.getId());
455	1	assertNull(dbref.getSecondaryId());
456	1	assertEquals(2, ef.getQualifier().size());
457	1	q = ef.getQualifier().get(0);
458	1	assertEquals("protein_id", q.getName());
459	1	assertEquals("CAA30421.1", q.getValue());
460	1	q = ef.getQualifier().get(1);
461	1	assertEquals("translation", q.getName());
462	1	assertEquals("MSSS", q.getValue());
463
464		/*
465		* third CDS
466		*/
467	1	ef = entry.getFeature().get(2);
468	1	assertEquals("CDS", ef.getName());
469	1	assertEquals("join(4..6,10..15)", ef.getLocation());
470	1	assertNotNull(ef.getXref());
471	1	assertTrue(ef.getXref().isEmpty());
472	1	assertEquals(2, ef.getQualifier().size());
473	1	q = ef.getQualifier().get(0);
474	1	assertEquals("protein_id", q.getName());
475	1	assertEquals("CAA12345.6", q.getValue());
476	1	q = ef.getQualifier().get(1);
477	1	assertEquals("translation", q.getName());
478	1	assertEquals("MSS", q.getValue());
479
480		/*
481		* Sequence - raw data before removal of newlines
482		*/
483	1	String seq = entry.getSequence();
484	1	assertEquals("GGTATGTCCTCTAGTACAAAC\n"
485		+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT", seq);
486
487		/*
488		* getSequence() converts empty DBRefEntry.version to "0"
489		*/
490	1	assertNull(entry.getXref().get(1).getSecondaryId());
491	1	assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
492		}
493
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
494	2	List<EntryType> getEmblEntries()...
495		{
496	2	return testee
497		.getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
498		}
499		}