2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.dbsources;
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;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.DBRefEntry;
31 import jalview.datamodel.DBRefSource;
32 import jalview.datamodel.SequenceI;
33 import jalview.util.MapList;
34 import jalview.xml.binding.embl.EntryType;
35 import jalview.xml.binding.embl.EntryType.Feature;
36 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
37 import jalview.xml.binding.embl.XrefType;
39 import java.io.ByteArrayInputStream;
40 import java.util.ArrayList;
41 import java.util.Arrays;
42 import java.util.List;
44 import org.testng.annotations.BeforeClass;
45 import org.testng.annotations.Test;
47 public class EmblXmlSourceTest
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\" ?>"
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\" />"
65 * first CDS (range and translation changed to keep test data manageable)
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>"
76 * second CDS (range and translation changed to keep test data manageable)
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>"
84 * third CDS is made up - has no xref - code should synthesize
85 * one to an assumed EMBLCDSPROTEIN accession
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>"
92 * sequence (modified for test purposes)
93 * emulates EMBL XML 1.2 which splits sequence data every 60 characters
94 * see EmblSequence.setSequence
96 + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
97 + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
98 + "</sequence></entry></ROOT>";
100 private EmblXmlSource testee;
102 @BeforeClass(alwaysRun = true)
105 testee = new EmblXmlSource()
109 public String getDbSource()
115 public String getDbName()
121 public String getTestQuery()
127 public AlignmentI getSequenceRecords(String queries) throws Exception
134 @Test(groups = "Functional")
135 public void testGetCdsRanges()
138 * Make a (CDS) Feature with 5 locations
140 Feature cds = new Feature();
142 "join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
144 int[] exons = testee.getCdsRanges("EMBL", cds);
145 assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
146 Arrays.toString(exons));
149 @Test(groups = "Functional")
150 public void testGetSequence()
152 // not the whole sequence but enough for this test...
153 List<SequenceI> peptides = new ArrayList<>();
154 List<EntryType> entries = getEmblEntries();
155 assertEquals(1, entries.size());
156 EntryType entry = entries.get(0);
157 String sourceDb = "EMBL";
158 SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
161 * newline has been removed from sequence
163 String seq = dna.getSequenceAsString();
165 "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
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
174 assertEquals(6, peptides.size());
175 assertEquals("CAA30420.1", peptides.get(0).getName());
176 assertEquals("MLCF", peptides.get(0).getSequenceAsString());
177 assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
178 assertEquals("MLCF", peptides.get(1).getSequenceAsString());
179 assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
180 assertEquals("MLCF", peptides.get(2).getSequenceAsString());
181 assertEquals("CAA30421.1", peptides.get(3).getName());
182 assertEquals("MSSS", peptides.get(3).getSequenceAsString());
183 assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
184 assertEquals("MSSS", peptides.get(4).getSequenceAsString());
185 assertEquals("CAA12345.6", peptides.get(5).getName());
186 assertEquals("MSS", peptides.get(5).getSequenceAsString());
189 * verify dna sequence has dbrefs
190 * - to 'self' (synthesized dbref)
192 * - to MD5 (with null version as "0")
193 * - with CDS mappings to the peptide 'products'
195 MapList mapToSelf = new MapList(new int[] { 1, 57 },
198 MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
200 MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
202 MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 },
206 DBRefEntry[] dbrefs = dna.getDBRefs();
207 assertEquals(7, dbrefs.length);
209 DBRefEntry dbRefEntry = dbrefs[0];
210 assertEquals("EMBL", dbRefEntry.getSource());
211 assertEquals("X07547", dbRefEntry.getAccessionId());
212 assertEquals("1", dbRefEntry.getVersion());
213 assertNotNull(dbRefEntry.getMap());
214 assertNull(dbRefEntry.getMap().getTo());
215 assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
217 dbRefEntry = dbrefs[1];
218 // DBRefEntry constructor puts dbSource in upper case
219 assertEquals("EUROPEPMC", dbRefEntry.getSource());
220 assertEquals("PMC107176", dbRefEntry.getAccessionId());
221 assertEquals("9573186", dbRefEntry.getVersion());
222 assertNull(dbRefEntry.getMap());
224 dbRefEntry = dbrefs[2];
225 assertEquals("MD5", dbRefEntry.getSource());
226 assertEquals("ac73317", dbRefEntry.getAccessionId());
227 assertEquals("0", dbRefEntry.getVersion());
228 assertNull(dbRefEntry.getMap());
230 dbRefEntry = dbrefs[3];
231 assertEquals("UNIPROT", dbRefEntry.getSource());
232 assertEquals("B0BCM4", dbRefEntry.getAccessionId());
233 assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
234 assertEquals(cds1Map, dbRefEntry.getMap().getMap());
236 dbRefEntry = dbrefs[4];
237 assertEquals("UNIPROT", dbRefEntry.getSource());
238 assertEquals("P0CE20", dbRefEntry.getAccessionId());
239 assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
240 assertEquals(cds1Map, dbRefEntry.getMap().getMap());
242 dbRefEntry = dbrefs[5];
243 assertEquals("UNIPROT", dbRefEntry.getSource());
244 assertEquals("B0BCM3", dbRefEntry.getAccessionId());
245 assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
246 assertEquals(cds2Map, dbRefEntry.getMap().getMap());
248 dbRefEntry = dbrefs[6];
249 assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
250 assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
251 assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
252 assertEquals(cds3Map, dbRefEntry.getMap().getMap());
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
260 MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 },
263 MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 },
267 // dbrefs for first CDS EMBL product CAA30420.1
268 dbrefs = peptides.get(0).getDBRefs();
269 assertEquals(5, dbrefs.length);
270 assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
271 assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
272 // TODO: verify getPrimaryDBRefs() for peptide products
273 assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
274 assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
275 assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
276 assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
277 assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
278 assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
279 assertNull(dbrefs[2].getMap());
280 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
282 assertNull(dbrefs[3].getMap());
283 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
285 assertNull(dbrefs[4].getMap());
287 // dbrefs for first CDS first Uniprot xref
288 dbrefs = peptides.get(1).getDBRefs();
289 assertEquals(2, dbrefs.length);
290 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
292 assertNull(dbrefs[0].getMap());
293 assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
294 assertEquals("X07547", dbrefs[1].getAccessionId());
295 assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
297 // dbrefs for first CDS second Uniprot xref
298 dbrefs = peptides.get(2).getDBRefs();
299 assertEquals(2, dbrefs.length);
300 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
302 assertNull(dbrefs[0].getMap());
303 assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
304 assertEquals("X07547", dbrefs[1].getAccessionId());
305 assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
307 // dbrefs for second CDS EMBL product CAA30421.1
308 dbrefs = peptides.get(3).getDBRefs();
309 assertEquals(4, dbrefs.length);
310 assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
311 assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
312 assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
313 assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
314 assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
315 assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
316 assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
317 assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
318 assertNull(dbrefs[2].getMap());
319 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
321 assertNull(dbrefs[3].getMap());
323 // dbrefs for second CDS second Uniprot xref
324 dbrefs = peptides.get(4).getDBRefs();
325 assertEquals(2, dbrefs.length);
326 assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
328 assertNull(dbrefs[0].getMap());
329 assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
330 assertEquals("X07547", dbrefs[1].getAccessionId());
331 assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
333 // dbrefs for third CDS inferred EMBL product CAA12345.6
334 dbrefs = peptides.get(5).getDBRefs();
335 assertEquals(3, dbrefs.length);
336 assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
337 assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
338 assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
339 assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
340 assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
341 assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
342 assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
343 assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
344 assertNull(dbrefs[2].getMap());
347 @Test(groups = "Functional")
348 public void testAdjustForProteinLength()
350 int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
352 // exact length match:
353 assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
355 // match if we assume exons include stop codon not in protein:
356 assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
358 // truncate last exon by 6bp
359 int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
360 assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
362 // remove last exon and truncate preceding by 1bp
363 truncated = EmblXmlSource.adjustForProteinLength(3, exons);
364 assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
366 // exact removal of exon case:
367 exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
368 truncated = EmblXmlSource.adjustForProteinLength(4, exons);
369 assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
371 // what if exons are too short for protein?
372 truncated = EmblXmlSource.adjustForProteinLength(7, exons);
373 assertSame(exons, truncated);
376 @Test(groups = { "Functional" })
377 public void testGetEmblEntries()
379 List<EntryType> entries = getEmblEntries();
380 assertEquals(1, entries.size());
381 EntryType entry = entries.get(0);
383 assertEquals("X07547", entry.getAccession());
384 assertEquals("C. trachomatis plasmid", entry.getDescription());
385 assertEquals("STD", entry.getDataClass());
386 assertEquals("PRO", entry.getTaxonomicDivision());
387 assertEquals("1999-02-10", entry.getLastUpdated().toString());
388 assertEquals(58, entry.getLastUpdatedRelease().intValue());
389 assertEquals("1988-11-10", entry.getFirstPublic().toString());
390 assertEquals(18, entry.getFirstPublicRelease().intValue());
391 assertEquals("genomic DNA", entry.getMoleculeType());
392 assertEquals(1, entry.getVersion().intValue());
393 assertEquals(8, entry.getEntryVersion().intValue());
394 assertEquals("linear", entry.getTopology());
395 assertEquals(7499, entry.getSequenceLength().intValue());
396 assertEquals(2, entry.getKeyword().size());
397 assertEquals("plasmid", entry.getKeyword().get(0));
398 assertEquals("unidentified reading frame", entry.getKeyword().get(1));
403 assertEquals(2, entry.getXref().size());
404 XrefType dbref = entry.getXref().get(0);
405 assertEquals("EuropePMC", dbref.getDb());
406 assertEquals("PMC107176", dbref.getId());
407 assertEquals("9573186", dbref.getSecondaryId());
408 dbref = entry.getXref().get(1);
409 assertEquals("MD5", dbref.getDb());
410 assertEquals("ac73317", dbref.getId());
411 assertNull(dbref.getSecondaryId());
414 * three sequence features for CDS
416 assertEquals(3, entry.getFeature().size());
420 Feature ef = entry.getFeature().get(0);
421 assertEquals("CDS", ef.getName());
422 assertEquals("complement(46..57)", ef.getLocation());
423 assertEquals(2, ef.getXref().size());
424 dbref = ef.getXref().get(0);
425 assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
426 assertEquals("B0BCM4", dbref.getId());
427 assertEquals("2.1", dbref.getSecondaryId());
428 dbref = ef.getXref().get(1);
429 assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
430 assertEquals("P0CE20", dbref.getId());
431 assertNull(dbref.getSecondaryId());
432 // CDS feature qualifiers
433 assertEquals(3, ef.getQualifier().size());
434 Qualifier q = ef.getQualifier().get(0);
435 assertEquals("note", q.getName());
436 assertEquals("ORF 8 (AA 1-330)", q.getValue());
437 q = ef.getQualifier().get(1);
438 assertEquals("protein_id", q.getName());
439 assertEquals("CAA30420.1", q.getValue());
440 q = ef.getQualifier().get(2);
441 assertEquals("translation", q.getName());
442 assertEquals("MLCF", q.getValue());
447 ef = entry.getFeature().get(1);
448 assertEquals("CDS", ef.getName());
449 assertEquals("4..15", ef.getLocation());
450 assertEquals(1, ef.getXref().size());
451 dbref = ef.getXref().get(0);
452 assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
453 assertEquals("B0BCM3", dbref.getId());
454 assertNull(dbref.getSecondaryId());
455 assertEquals(2, ef.getQualifier().size());
456 q = ef.getQualifier().get(0);
457 assertEquals("protein_id", q.getName());
458 assertEquals("CAA30421.1", q.getValue());
459 q = ef.getQualifier().get(1);
460 assertEquals("translation", q.getName());
461 assertEquals("MSSS", q.getValue());
466 ef = entry.getFeature().get(2);
467 assertEquals("CDS", ef.getName());
468 assertEquals("join(4..6,10..15)", ef.getLocation());
469 assertNotNull(ef.getXref());
470 assertTrue(ef.getXref().isEmpty());
471 assertEquals(2, ef.getQualifier().size());
472 q = ef.getQualifier().get(0);
473 assertEquals("protein_id", q.getName());
474 assertEquals("CAA12345.6", q.getValue());
475 q = ef.getQualifier().get(1);
476 assertEquals("translation", q.getName());
477 assertEquals("MSS", q.getValue());
480 * Sequence - raw data before removal of newlines
482 String seq = entry.getSequence();
483 assertEquals("GGTATGTCCTCTAGTACAAAC\n"
484 + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT", seq);
487 * getSequence() converts empty DBRefEntry.version to "0"
489 assertNull(entry.getXref().get(1).getSecondaryId());
490 assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
493 List<EntryType> getEmblEntries()
496 .getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));