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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ws.dbsources

File EmblSourceTest.java

 

Code metrics

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Classes

Class Line # Actions
EmblSourceTest 45 227 5
1.0100%
 

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This file is covered by 4 tests. .

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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   
 
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   
 
98  1 toggle @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   
 
114  1 toggle @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   
 
310  1 toggle @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   
 
339  1 toggle @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   
 
458  2 toggle static List<EntryType> getEmblEntries()
459    {
460  2 return new EmblSource()
461    .getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
462    }
463    }