Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EmblSourceTest	45	227	5	1.0100%	Show methods

Class EmblSourceTest

Class EmblSourceTest	Line # 45	Total Statements 227	Complexity 5	TOTAL Coverage 1.0100%
testGetCdsRanges() : void   testGetCdsRanges() : void	9898	5.05	1.01	1.0 1.0100%
testGetSequence() : void   testGetSequence() : void	114114	127.0127	1.01	1.0 1.0100%
testAdjustForProteinLength() : void   testAdjustForProteinLength() : void	310310	12.012	1.01	1.0 1.0100%
testGetEmblEntries() : void   testGetEmblEntries() : void	339339	82.082	1.01	1.0 1.0100%
getEmblEntries() : List<EntryType>   getEmblEntries() : List<EntryType>	458458	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5603448	jalview.ws.dbsources.EmblSourceTest.testGetSequencejalview.ws.dbsources.EmblSourceTest.testGetSequence	1PASS
	0.36637932	jalview.ws.dbsources.EmblSourceTest.testGetEmblEntriesjalview.ws.dbsources.EmblSourceTest.testGetEmblEntries	1PASS
	0.056034483	jalview.ws.dbsources.EmblSourceTest.testAdjustForProteinLengthjalview.ws.dbsources.EmblSourceTest.testAdjustForProteinLength	1PASS
	0.02586207	jalview.ws.dbsources.EmblSourceTest.testGetCdsRangesjalview.ws.dbsources.EmblSourceTest.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 jalview.datamodel.DBRefEntry;
30		import jalview.datamodel.DBRefSource;
31		import jalview.datamodel.SequenceI;
32		import jalview.util.MapList;
33		import jalview.xml.binding.embl.EntryType;
34		import jalview.xml.binding.embl.EntryType.Feature;
35		import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
36		import jalview.xml.binding.embl.XrefType;
37
38		import java.io.ByteArrayInputStream;
39		import java.util.ArrayList;
40		import java.util.Arrays;
41		import java.util.List;
42
43		import org.testng.annotations.Test;
44
		100% Uncovered Elements: 0 (232) Complexity: 5 Complexity Density: 0.02
45		public class EmblSourceTest
46		{
47
48		// adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
49		// dna and translations truncated for convenience
50		static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
51		+ "<ROOT>"
52		+ "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
53		+ " dataClass=\"STD\" taxonomicDivision=\"PRO\""
54		+ " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
55		+ " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
56		+ " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
57		+ "<secondaryAccession>X07574</secondaryAccession>"
58		+ "<description>C. trachomatis plasmid</description>"
59		+ "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
60		+ "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
61		+ "<xref db=\"MD5\" id=\"ac73317\" />"
62		/*
63		* first CDS (range and translation changed to keep test data manageable)
64		*/
65		+ "<feature name=\"CDS\" location=\"complement(46..57)\">"
66		// test the case of >1 cross-ref to the same database (JAL-2029)
67		+ "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
68		+ "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
69		+ "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value></qualifier>"
70		+ "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
71		+ "<qualifier name=\"translation\"><value>MLCF</value></qualifier>"
72		+ "</feature>"
73		/*
74		* second CDS (range and translation changed to keep test data manageable)
75		*/
76		+ "<feature name=\"CDS\" location=\"4..15\">"
77		+ "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
78		+ "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
79		+ "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
80		+ "</feature>"
81		/*
82		* third CDS is made up - has no xref - code should synthesize
83		* one to an assumed EMBLCDSPROTEIN accession
84		*/
85		+ "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
86		+ "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
87		+ "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
88		+ "</feature>"
89		/*
90		* sequence (modified for test purposes)
91		* emulates EMBL XML 1.2 which splits sequence data every 60 characters
92		* see EmblSequence.setSequence
93		*/
94		+ "<sequence>GGTATGTCCTCTAGTACAAAC\n"
95		+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
96		+ "</sequence></entry></ROOT>";
97
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
98	1	@Test(groups = "Functional")...
99		public void testGetCdsRanges()
100		{
101	1	EmblSource testee = new EmblSource();
102
103		/*
104		* Make a (CDS) Feature with 5 locations
105		*/
106	1	Feature cds = new Feature();
107	1	cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
108
109	1	int[] exons = testee.getCdsRanges("EMBL", cds);
110	1	assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
111		Arrays.toString(exons));
112		}
113
		100% Uncovered Elements: 0 (127) Complexity: 1 Complexity Density: 0.01 1PASS
114	1	@Test(groups = "Functional")...
115		public void testGetSequence()
116		{
117		// not the whole sequence but enough for this test...
118	1	List<SequenceI> peptides = new ArrayList<>();
119	1	List<EntryType> entries = EmblSourceTest.getEmblEntries();
120	1	assertEquals(1, entries.size());
121	1	EntryType entry = entries.get(0);
122	1	EmblSource testee = new EmblSource();
123	1	String sourceDb = "EMBL";
124	1	SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
125
126		/*
127		* newline has been removed from sequence
128		*/
129	1	String seq = dna.getSequenceAsString();
130	1	assertEquals(
131		"GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
132		seq);
133
134		/*
135		* peptides should now have five entries:
136		* EMBL product and two Uniprot accessions for the first CDS / translation
137		* EMBL product and one Uniprot accession for the second CDS / "
138		* EMBL product only for the third
139		*/
140	1	assertEquals(6, peptides.size());
141	1	assertEquals("CAA30420.1", peptides.get(0).getName());
142	1	assertEquals("MLCF", peptides.get(0).getSequenceAsString());
143	1	assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
144	1	assertEquals("MLCF", peptides.get(1).getSequenceAsString());
145	1	assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
146	1	assertEquals("MLCF", peptides.get(2).getSequenceAsString());
147	1	assertEquals("CAA30421.1", peptides.get(3).getName());
148	1	assertEquals("MSSS", peptides.get(3).getSequenceAsString());
149	1	assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
150	1	assertEquals("MSSS", peptides.get(4).getSequenceAsString());
151	1	assertEquals("CAA12345.6", peptides.get(5).getName());
152	1	assertEquals("MSS", peptides.get(5).getSequenceAsString());
153
154		/*
155		* verify dna sequence has dbrefs
156		* - to 'self' (synthesized dbref)
157		* - to EuropePMC
158		* - to MD5 (with null version as "0")
159		* - with CDS mappings to the peptide 'products'
160		*/
161	1	MapList mapToSelf = new MapList(new int[] { 1, 57 },
162		new int[]
163		{ 1, 57 }, 1, 1);
164	1	MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
165		3, 1);
166	1	MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
167		3, 1);
168	1	MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
169		1, 3 }, 3, 1);
170
171	1	List<DBRefEntry> dbrefs = dna.getDBRefs();
172	1	assertEquals(7, dbrefs.size());
173
174	1	DBRefEntry dbRefEntry = dbrefs.get(0);
175	1	assertEquals("EMBL", dbRefEntry.getSource());
176	1	assertEquals("X07547", dbRefEntry.getAccessionId());
177	1	assertEquals("1", dbRefEntry.getVersion());
178	1	assertNotNull(dbRefEntry.getMap());
179	1	assertNull(dbRefEntry.getMap().getTo());
180	1	assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
181
182	1	dbRefEntry = dbrefs.get(1);
183		// DBRefEntry constructor puts dbSource in upper case
184	1	assertEquals("EUROPEPMC", dbRefEntry.getSource());
185	1	assertEquals("PMC107176", dbRefEntry.getAccessionId());
186	1	assertEquals("9573186", dbRefEntry.getVersion());
187	1	assertNull(dbRefEntry.getMap());
188
189	1	dbRefEntry = dbrefs.get(2);
190	1	assertEquals("MD5", dbRefEntry.getSource());
191	1	assertEquals("ac73317", dbRefEntry.getAccessionId());
192	1	assertEquals("0", dbRefEntry.getVersion());
193	1	assertNull(dbRefEntry.getMap());
194
195	1	dbRefEntry = dbrefs.get(3);
196	1	assertEquals("UNIPROT", dbRefEntry.getSource());
197	1	assertEquals("B0BCM4", dbRefEntry.getAccessionId());
198	1	assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
199	1	assertEquals(cds1Map, dbRefEntry.getMap().getMap());
200
201	1	dbRefEntry = dbrefs.get(4);
202	1	assertEquals("UNIPROT", dbRefEntry.getSource());
203	1	assertEquals("P0CE20", dbRefEntry.getAccessionId());
204	1	assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
205	1	assertEquals(cds1Map, dbRefEntry.getMap().getMap());
206
207	1	dbRefEntry = dbrefs.get(5);
208	1	assertEquals("UNIPROT", dbRefEntry.getSource());
209	1	assertEquals("B0BCM3", dbRefEntry.getAccessionId());
210	1	assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
211	1	assertEquals(cds2Map, dbRefEntry.getMap().getMap());
212
213	1	dbRefEntry = dbrefs.get(6);
214	1	assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
215	1	assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
216	1	assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
217	1	assertEquals(cds3Map, dbRefEntry.getMap().getMap());
218
219		/*
220		* verify peptides have dbrefs
221		* - to EMBL sequence (with inverse 1:3 cds mapping)
222		* - to EMBLCDS (with 1:3 mapping)
223		* - direct (no mapping) to other protein accessions
224		*/
225	1	MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
226		1, 12 }, 1, 3);
227	1	MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
228		1, 9 }, 1, 3);
229
230		// dbrefs for first CDS EMBL product CAA30420.1
231	1	dbrefs = peptides.get(0).getDBRefs();
232	1	assertEquals(5, dbrefs.size());
233	1	assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
234	1	assertEquals("CAA30420.1", dbrefs.get(0).getAccessionId());
235		// TODO: verify getPrimaryDBRefs() for peptide products
236	1	assertEquals(cds1Map.getInverse(), dbrefs.get(0).getMap().getMap());
237	1	assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
238	1	assertEquals("CAA30420.1", dbrefs.get(1).getAccessionId());
239	1	assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
240	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
241	1	assertEquals("CAA30420.1", dbrefs.get(2).getAccessionId());
242	1	assertNull(dbrefs.get(2).getMap());
243	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
244		dbrefs.get(3));
245	1	assertNull(dbrefs.get(3).getMap());
246	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
247		dbrefs.get(4));
248	1	assertNull(dbrefs.get(4).getMap());
249
250		// dbrefs for first CDS first Uniprot xref
251	1	dbrefs = peptides.get(1).getDBRefs();
252	1	assertEquals(2, dbrefs.size());
253	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
254		dbrefs.get(0));
255	1	assertNull(dbrefs.get(0).getMap());
256	1	assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
257	1	assertEquals("X07547", dbrefs.get(1).getAccessionId());
258	1	assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
259
260		// dbrefs for first CDS second Uniprot xref
261	1	dbrefs = peptides.get(2).getDBRefs();
262	1	assertEquals(2, dbrefs.size());
263	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
264		dbrefs.get(0));
265	1	assertNull(dbrefs.get(0).getMap());
266	1	assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
267	1	assertEquals("X07547", dbrefs.get(1).getAccessionId());
268	1	assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
269
270		// dbrefs for second CDS EMBL product CAA30421.1
271	1	dbrefs = peptides.get(3).getDBRefs();
272	1	assertEquals(4, dbrefs.size());
273	1	assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
274	1	assertEquals("CAA30421.1", dbrefs.get(0).getAccessionId());
275	1	assertEquals(cds2Map.getInverse(), dbrefs.get(0).getMap().getMap());
276	1	assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
277	1	assertEquals("CAA30421.1", dbrefs.get(1).getAccessionId());
278	1	assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
279	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
280	1	assertEquals("CAA30421.1", dbrefs.get(2).getAccessionId());
281	1	assertNull(dbrefs.get(2).getMap());
282	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
283		dbrefs.get(3));
284	1	assertNull(dbrefs.get(3).getMap());
285
286		// dbrefs for second CDS second Uniprot xref
287	1	dbrefs = peptides.get(4).getDBRefs();
288	1	assertEquals(2, dbrefs.size());
289	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
290		dbrefs.get(0));
291	1	assertNull(dbrefs.get(0).getMap());
292	1	assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
293	1	assertEquals("X07547", dbrefs.get(1).getAccessionId());
294	1	assertEquals(cds2Map.getInverse(), dbrefs.get(1).getMap().getMap());
295
296		// dbrefs for third CDS inferred EMBL product CAA12345.6
297	1	dbrefs = peptides.get(5).getDBRefs();
298	1	assertEquals(3, dbrefs.size());
299	1	assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
300	1	assertEquals("CAA12345.6", dbrefs.get(0).getAccessionId());
301	1	assertEquals(cds3Map.getInverse(), dbrefs.get(0).getMap().getMap());
302	1	assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
303	1	assertEquals("CAA12345.6", dbrefs.get(1).getAccessionId());
304	1	assertEquals(proteinToCdsMap2, dbrefs.get(1).getMap().getMap());
305	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
306	1	assertEquals("CAA12345.6", dbrefs.get(2).getAccessionId());
307	1	assertNull(dbrefs.get(2).getMap());
308		}
309
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
310	1	@Test(groups = "Functional")...
311		public void testAdjustForProteinLength()
312		{
313	1	int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
314
315		// exact length match:
316	1	assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
317
318		// match if we assume exons include stop codon not in protein:
319	1	assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
320
321		// truncate last exon by 6bp
322	1	int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
323	1	assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
324
325		// remove last exon and truncate preceding by 1bp
326	1	truncated = EmblXmlSource.adjustForProteinLength(3, exons);
327	1	assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
328
329		// exact removal of exon case:
330	1	exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
331	1	truncated = EmblXmlSource.adjustForProteinLength(4, exons);
332	1	assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
333
334		// what if exons are too short for protein?
335	1	truncated = EmblXmlSource.adjustForProteinLength(7, exons);
336	1	assertSame(exons, truncated);
337		}
338
		100% Uncovered Elements: 0 (82) Complexity: 1 Complexity Density: 0.01 1PASS
339	1	@Test(groups = { "Functional" })...
340		public void testGetEmblEntries()
341		{
342	1	List<EntryType> entries = EmblSourceTest.getEmblEntries();
343	1	assertEquals(1, entries.size());
344	1	EntryType entry = entries.get(0);
345
346	1	assertEquals("X07547", entry.getAccession());
347	1	assertEquals("C. trachomatis plasmid", entry.getDescription());
348	1	assertEquals("STD", entry.getDataClass());
349	1	assertEquals("PRO", entry.getTaxonomicDivision());
350	1	assertEquals("1999-02-10", entry.getLastUpdated().toString());
351	1	assertEquals(58, entry.getLastUpdatedRelease().intValue());
352	1	assertEquals("1988-11-10", entry.getFirstPublic().toString());
353	1	assertEquals(18, entry.getFirstPublicRelease().intValue());
354	1	assertEquals("genomic DNA", entry.getMoleculeType());
355	1	assertEquals(1, entry.getVersion().intValue());
356	1	assertEquals(8, entry.getEntryVersion().intValue());
357	1	assertEquals("linear", entry.getTopology());
358	1	assertEquals(7499, entry.getSequenceLength().intValue());
359	1	assertEquals(2, entry.getKeyword().size());
360	1	assertEquals("plasmid", entry.getKeyword().get(0));
361	1	assertEquals("unidentified reading frame", entry.getKeyword().get(1));
362
363		/*
364		* dbrefs
365		*/
366	1	assertEquals(2, entry.getXref().size());
367	1	XrefType dbref = entry.getXref().get(0);
368	1	assertEquals("EuropePMC", dbref.getDb());
369	1	assertEquals("PMC107176", dbref.getId());
370	1	assertEquals("9573186", dbref.getSecondaryId());
371	1	dbref = entry.getXref().get(1);
372	1	assertEquals("MD5", dbref.getDb());
373	1	assertEquals("ac73317", dbref.getId());
374	1	assertNull(dbref.getSecondaryId());
375
376		/*
377		* three sequence features for CDS
378		*/
379	1	assertEquals(3, entry.getFeature().size());
380		/*
381		* first CDS
382		*/
383	1	Feature ef = entry.getFeature().get(0);
384	1	assertEquals("CDS", ef.getName());
385	1	assertEquals("complement(46..57)", ef.getLocation());
386	1	assertEquals(2, ef.getXref().size());
387	1	dbref = ef.getXref().get(0);
388	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
389	1	assertEquals("B0BCM4", dbref.getId());
390	1	assertEquals("2.1", dbref.getSecondaryId());
391	1	dbref = ef.getXref().get(1);
392	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
393	1	assertEquals("P0CE20", dbref.getId());
394	1	assertNull(dbref.getSecondaryId());
395		// CDS feature qualifiers
396	1	assertEquals(3, ef.getQualifier().size());
397	1	Qualifier q = ef.getQualifier().get(0);
398	1	assertEquals("note", q.getName());
399	1	assertEquals("ORF 8 (AA 1-330)", q.getValue());
400	1	q = ef.getQualifier().get(1);
401	1	assertEquals("protein_id", q.getName());
402	1	assertEquals("CAA30420.1", q.getValue());
403	1	q = ef.getQualifier().get(2);
404	1	assertEquals("translation", q.getName());
405	1	assertEquals("MLCF", q.getValue());
406
407		/*
408		* second CDS
409		*/
410	1	ef = entry.getFeature().get(1);
411	1	assertEquals("CDS", ef.getName());
412	1	assertEquals("4..15", ef.getLocation());
413	1	assertEquals(1, ef.getXref().size());
414	1	dbref = ef.getXref().get(0);
415	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
416	1	assertEquals("B0BCM3", dbref.getId());
417	1	assertNull(dbref.getSecondaryId());
418	1	assertEquals(2, ef.getQualifier().size());
419	1	q = ef.getQualifier().get(0);
420	1	assertEquals("protein_id", q.getName());
421	1	assertEquals("CAA30421.1", q.getValue());
422	1	q = ef.getQualifier().get(1);
423	1	assertEquals("translation", q.getName());
424	1	assertEquals("MSSS", q.getValue());
425
426		/*
427		* third CDS
428		*/
429	1	ef = entry.getFeature().get(2);
430	1	assertEquals("CDS", ef.getName());
431	1	assertEquals("join(4..6,10..15)", ef.getLocation());
432	1	assertNotNull(ef.getXref());
433	1	assertTrue(ef.getXref().isEmpty());
434	1	assertEquals(2, ef.getQualifier().size());
435	1	q = ef.getQualifier().get(0);
436	1	assertEquals("protein_id", q.getName());
437	1	assertEquals("CAA12345.6", q.getValue());
438	1	q = ef.getQualifier().get(1);
439	1	assertEquals("translation", q.getName());
440	1	assertEquals("MSS", q.getValue());
441
442		/*
443		* Sequence - raw data before removal of newlines
444		*/
445	1	String seq = entry.getSequence();
446	1	assertEquals(
447		"GGTATGTCCTCTAGTACAAAC\n"
448		+ "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
449		seq);
450
451		/*
452		* getSequence() converts empty DBRefEntry.version to "0"
453		*/
454	1	assertNull(entry.getXref().get(1).getSecondaryId());
455	1	assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
456		}
457
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
458	2	static List<EntryType> getEmblEntries()...
459		{
460	2	return new EmblSource()
461		.getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
462		}
463		}