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.datamodel.xdb.embl;
23 import jalview.analysis.SequenceIdMatcher;
24 import jalview.bin.Cache;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.datamodel.DBRefSource;
27 import jalview.datamodel.FeatureProperties;
28 import jalview.datamodel.Mapping;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceI;
32 import jalview.util.DBRefUtils;
33 import jalview.util.DnaUtils;
34 import jalview.util.MapList;
35 import jalview.util.MappingUtils;
36 import jalview.util.StringUtils;
38 import java.text.ParseException;
39 import java.util.Arrays;
40 import java.util.Hashtable;
41 import java.util.List;
43 import java.util.Map.Entry;
44 import java.util.Vector;
45 import java.util.regex.Pattern;
48 * Data model for one entry returned from an EMBL query, as marshalled by a
51 * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
53 * @see embl_mapping.xml
55 public class EmblEntry
57 private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
63 String sequenceVersion;
71 String sequenceLength;
73 String taxonomicDivision;
77 String firstPublicDate;
79 String firstPublicRelease;
81 String lastUpdatedDate;
83 String lastUpdatedRelease;
85 Vector<String> keywords;
87 Vector<DBRefEntry> dbRefs;
89 Vector<EmblFeature> features;
91 EmblSequence sequence;
94 * @return the accession
96 public String getAccession()
103 * the accession to set
105 public void setAccession(String accession)
107 this.accession = accession;
113 public Vector<DBRefEntry> getDbRefs()
122 public void setDbRefs(Vector<DBRefEntry> dbRefs)
124 this.dbRefs = dbRefs;
128 * @return the features
130 public Vector<EmblFeature> getFeatures()
137 * the features to set
139 public void setFeatures(Vector<EmblFeature> features)
141 this.features = features;
145 * @return the keywords
147 public Vector<String> getKeywords()
154 * the keywords to set
156 public void setKeywords(Vector<String> keywords)
158 this.keywords = keywords;
162 * @return the sequence
164 public EmblSequence getSequence()
171 * the sequence to set
173 public void setSequence(EmblSequence sequence)
175 this.sequence = sequence;
179 * Recover annotated sequences from EMBL file
183 * a list of protein products found so far (to add to)
184 * @return dna dataset sequence with DBRefs and features
186 public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
188 SequenceI dna = makeSequence(sourceDb);
193 dna.setDescription(description);
194 DBRefEntry retrievedref = new DBRefEntry(sourceDb,
195 getSequenceVersion(), accession);
196 dna.addDBRef(retrievedref);
197 // add map to indicate the sequence is a valid coordinate frame for the
199 retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
200 new int[] { 1, dna.getLength() }, 1, 1));
203 * transform EMBL Database refs to canonical form
207 for (DBRefEntry dbref : dbRefs)
209 dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
214 SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
217 for (EmblFeature feature : features)
219 if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
221 parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
224 } catch (Exception e)
226 System.err.println("EMBL Record Features parsing error!");
228 .println("Please report the following to help@jalview.org :");
229 System.err.println("EMBL Record " + accession);
230 System.err.println("Resulted in exception: " + e.getMessage());
231 e.printStackTrace(System.err);
241 SequenceI makeSequence(String sourceDb)
243 if (sequence == null)
245 System.err.println("No sequence was returned for ENA accession "
249 SequenceI dna = new Sequence(sourceDb + "|" + accession,
250 sequence.getSequence());
255 * Extracts coding region and product from a CDS feature and properly decorate
256 * it with annotations.
261 * source database for the EMBLXML
263 * parent dna sequence for this record
265 * list of protein product sequences for Embl entry
267 * helper to match xrefs in already retrieved sequences
269 void parseCodingFeature(EmblFeature feature, String sourceDb,
270 SequenceI dna, List<SequenceI> peptides, SequenceIdMatcher matcher)
272 boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
274 int[] exons = getCdsRanges(feature);
276 String translation = null;
277 String proteinName = "";
278 String proteinId = null;
279 Map<String, String> vals = new Hashtable<String, String>();
282 * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
283 * (phase is required for CDS features in GFF3 format)
288 * parse qualifiers, saving protein translation, protein id,
289 * codon start position, product (name), and 'other values'
291 if (feature.getQualifiers() != null)
293 for (Qualifier q : feature.getQualifiers())
295 String qname = q.getName();
296 if (qname.equals("translation"))
298 // remove all spaces (precompiled String.replaceAll(" ", ""))
299 translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll(
302 else if (qname.equals("protein_id"))
304 proteinId = q.getValues()[0].trim();
306 else if (qname.equals("codon_start"))
310 codonStart = Integer.parseInt(q.getValues()[0].trim());
311 } catch (NumberFormatException e)
313 System.err.println("Invalid codon_start in XML for "
314 + accession + ": " + e.getMessage());
317 else if (qname.equals("product"))
319 // sometimes name is returned e.g. for V00488
320 proteinName = q.getValues()[0].trim();
324 // throw anything else into the additional properties hash
325 String[] qvals = q.getValues();
328 String commaSeparated = StringUtils.arrayToSeparatorList(qvals,
330 vals.put(qname, commaSeparated);
336 DBRefEntry proteinToEmblProteinRef = null;
337 exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
339 SequenceI product = null;
340 Mapping dnaToProteinMapping = null;
341 if (translation != null && proteinName != null && proteinId != null)
343 int translationLength = translation.length();
346 * look for product in peptides list, if not found, add it
348 product = matcher.findIdMatch(proteinId);
351 product = new Sequence(proteinId, translation, 1, translationLength);
352 product.setDescription(((proteinName.length() == 0) ? "Protein Product from "
355 peptides.add(product);
356 matcher.add(product);
359 // we have everything - create the mapping and perhaps the protein
361 if (exons == null || exons.length == 0)
364 * workaround until we handle dna location for CDS sequence
365 * e.g. location="X53828.1:60..1058" correctly
368 .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
369 + sourceDb + ":" + getAccession() + ")");
370 if (translationLength * 3 == (1 - codonStart + dna.getSequence().length))
373 .println("Not allowing for additional stop codon at end of cDNA fragment... !");
374 // this might occur for CDS sequences where no features are marked
375 exons = new int[] { dna.getStart() + (codonStart - 1),
377 dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
378 translationLength }, 3, 1);
380 if ((translationLength + 1) * 3 == (1 - codonStart + dna
381 .getSequence().length))
384 .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
385 exons = new int[] { dna.getStart() + (codonStart - 1),
387 dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
388 translationLength }, 3, 1);
393 // Trim the exon mapping if necessary - the given product may only be a
394 // fragment of a larger protein. (EMBL:AY043181 is an example)
398 // TODO: Add a DbRef back to the parent EMBL sequence with the exon
400 // if given a dataset reference, search dataset for parent EMBL
401 // sequence if it exists and set its map
402 // make a new feature annotating the coding contig
406 // final product length truncation check
407 int[] cdsRanges = adjustForProteinLength(translationLength, exons);
408 dnaToProteinMapping = new Mapping(product, cdsRanges, new int[] {
409 1, translationLength }, 3, 1);
413 * make xref with mapping from protein to EMBL dna
415 DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
416 getSequenceVersion(), proteinId, new Mapping(
417 dnaToProteinMapping.getMap().getInverse()));
418 product.addDBRef(proteinToEmblRef);
421 * make xref from protein to EMBLCDS; we assume here that the
422 * CDS sequence version is same as dna sequence (?!)
424 MapList proteinToCdsMapList = new MapList(new int[] { 1,
425 translationLength }, new int[] { 1 + (codonStart - 1),
426 (codonStart - 1) + 3 * translationLength }, 1, 3);
427 DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
428 DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
429 new Mapping(proteinToCdsMapList));
430 product.addDBRef(proteinToEmblCdsRef);
433 * make 'direct' xref from protein to EMBLCDSPROTEIN
435 proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
436 proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
437 proteinToEmblProteinRef.setMap(null);
438 product.addDBRef(proteinToEmblProteinRef);
444 * add cds features to dna sequence
446 for (int xint = 0; exons != null && xint < exons.length; xint += 2)
448 SequenceFeature sf = makeCdsFeature(exons, xint, proteinName,
449 proteinId, vals, codonStart);
450 sf.setType(feature.getName()); // "CDS"
451 sf.setEnaLocation(feature.getLocation());
452 sf.setFeatureGroup(sourceDb);
453 dna.addSequenceFeature(sf);
458 * add feature dbRefs to sequence, and mappings for Uniprot xrefs
460 boolean hasUniprotDbref = false;
461 if (feature.dbRefs != null)
463 boolean mappingUsed = false;
464 for (DBRefEntry ref : feature.dbRefs)
467 * ensure UniProtKB/Swiss-Prot converted to UNIPROT
469 String source = DBRefUtils.getCanonicalName(ref.getSource());
470 ref.setSource(source);
471 DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
472 ref.getVersion(), ref.getAccessionId());
473 if (source.equals(DBRefSource.UNIPROT))
475 String proteinSeqName = DBRefSource.UNIPROT + "|"
476 + ref.getAccessionId();
477 if (dnaToProteinMapping != null
478 && dnaToProteinMapping.getTo() != null)
483 * two or more Uniprot xrefs for the same CDS -
484 * each needs a distinct Mapping (as to a different sequence)
486 dnaToProteinMapping = new Mapping(dnaToProteinMapping);
491 * try to locate the protein mapped to (possibly by a
492 * previous CDS feature); if not found, construct it from
493 * the EMBL translation
495 SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
496 if (proteinSeq == null)
498 proteinSeq = new Sequence(proteinSeqName,
499 product.getSequenceAsString());
500 matcher.add(proteinSeq);
501 peptides.add(proteinSeq);
503 dnaToProteinMapping.setTo(proteinSeq);
504 dnaToProteinMapping.setMappedFromId(proteinId);
505 proteinSeq.addDBRef(proteinDbRef);
506 ref.setMap(dnaToProteinMapping);
508 hasUniprotDbref = true;
513 * copy feature dbref to our protein product
515 DBRefEntry pref = proteinDbRef;
516 pref.setMap(null); // reference is direct
517 product.addDBRef(pref);
518 // Add converse mapping reference
519 if (dnaToProteinMapping != null)
521 Mapping pmap = new Mapping(dna, dnaToProteinMapping.getMap()
523 pref = new DBRefEntry(sourceDb, getSequenceVersion(),
524 this.getAccession());
526 if (dnaToProteinMapping.getTo() != null)
528 dnaToProteinMapping.getTo().addDBRef(pref);
537 * if we have a product (translation) but no explicit Uniprot dbref
538 * (example: EMBL AAFI02000057 protein_id EAL65544.1)
539 * then construct mappings to an assumed EMBLCDSPROTEIN accession
541 if (!hasUniprotDbref && product != null)
543 if (proteinToEmblProteinRef == null)
545 // assuming CDSPROTEIN sequence version = dna version (?!)
546 proteinToEmblProteinRef = new DBRefEntry(
547 DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
549 product.addDBRef(proteinToEmblProteinRef);
551 if (dnaToProteinMapping != null
552 && dnaToProteinMapping.getTo() != null)
554 DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
555 DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
556 dnaToEmblProteinRef.setMap(dnaToProteinMapping);
557 dnaToProteinMapping.setMappedFromId(proteinId);
558 dna.addDBRef(dnaToEmblProteinRef);
564 * Helper method to construct a SequenceFeature for one cds range
567 * array of cds [start, end, ...] positions
568 * @param exonStartIndex
569 * offset into the exons array
571 * @param proteinAccessionId
573 * map of 'miscellaneous values' for feature
575 * codon start position for CDS (1/2/3, normally 1)
578 protected SequenceFeature makeCdsFeature(int[] exons, int exonStartIndex,
579 String proteinName, String proteinAccessionId,
580 Map<String, String> vals, int codonStart)
582 int exonNumber = exonStartIndex / 2 + 1;
583 SequenceFeature sf = new SequenceFeature();
584 sf.setBegin(Math.min(exons[exonStartIndex], exons[exonStartIndex + 1]));
585 sf.setEnd(Math.max(exons[exonStartIndex], exons[exonStartIndex + 1]));
586 sf.setDescription(String.format("Exon %d for protein '%s' EMBLCDS:%s",
587 exonNumber, proteinName, proteinAccessionId));
588 sf.setPhase(String.valueOf(codonStart - 1));
589 sf.setStrand(exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+"
591 sf.setValue(FeatureProperties.EXONPOS, exonNumber);
592 sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
595 StringBuilder sb = new StringBuilder();
596 boolean first = true;
597 for (Entry<String, String> val : vals.entrySet())
603 sb.append(val.getKey()).append("=").append(val.getValue());
605 sf.setValue(val.getKey(), val.getValue());
607 sf.setAttributes(sb.toString());
613 * Returns the CDS positions as a single array of [start, end, start, end...]
614 * positions. If on the reverse strand, these will be in descending order.
619 protected int[] getCdsRanges(EmblFeature feature)
621 if (feature.location == null)
628 List<int[]> ranges = DnaUtils.parseLocation(feature.location);
629 return listToArray(ranges);
630 } catch (ParseException e)
632 Cache.log.warn(String.format(
633 "Not parsing inexact CDS location %s in ENA %s",
634 feature.location, this.accession));
640 * Converts a list of [start, end] ranges to a single array of [start, end,
646 int[] listToArray(List<int[]> ranges)
648 int[] result = new int[ranges.size() * 2];
650 for (int[] range : ranges)
652 result[i++] = range[0];
653 result[i++] = range[1];
659 * Truncates (if necessary) the exon intervals to match 3 times the length of
660 * the protein; also accepts 3 bases longer (for stop codon not included in
663 * @param proteinLength
665 * an array of [start, end, start, end...] intervals
666 * @return the same array (if unchanged) or a truncated copy
668 static int[] adjustForProteinLength(int proteinLength, int[] exon)
670 if (proteinLength <= 0 || exon == null)
674 int expectedCdsLength = proteinLength * 3;
675 int exonLength = MappingUtils.getLength(Arrays.asList(exon));
678 * if exon length matches protein, or is shorter, or longer by the
679 * length of a stop codon (3 bases), then leave it unchanged
681 if (expectedCdsLength >= exonLength
682 || expectedCdsLength == exonLength - 3)
690 origxon = new int[exon.length];
691 System.arraycopy(exon, 0, origxon, 0, exon.length);
693 for (int x = 0; x < exon.length; x += 2)
695 cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
696 if (expectedCdsLength <= cdspos)
698 // advanced beyond last codon.
700 if (expectedCdsLength != cdspos)
703 // .println("Truncating final exon interval on region by "
704 // + (cdspos - cdslength));
708 * shrink the final exon - reduce end position if forward
709 * strand, increase it if reverse
711 if (exon[x + 1] >= exon[x])
713 endxon = exon[x + 1] - cdspos + expectedCdsLength;
717 endxon = exon[x + 1] + cdspos - expectedCdsLength;
725 // and trim the exon interval set if necessary
726 int[] nxon = new int[sxpos + 2];
727 System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
728 nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
735 public String getSequenceVersion()
737 return sequenceVersion;
740 public void setSequenceVersion(String sequenceVersion)
742 this.sequenceVersion = sequenceVersion;
745 public String getSequenceLength()
747 return sequenceLength;
750 public void setSequenceLength(String sequenceLength)
752 this.sequenceLength = sequenceLength;
755 public String getEntryVersion()
760 public void setEntryVersion(String entryVersion)
762 this.entryVersion = entryVersion;
765 public String getMoleculeType()
770 public void setMoleculeType(String moleculeType)
772 this.moleculeType = moleculeType;
775 public String getTopology()
780 public void setTopology(String topology)
782 this.topology = topology;
785 public String getTaxonomicDivision()
787 return taxonomicDivision;
790 public void setTaxonomicDivision(String taxonomicDivision)
792 this.taxonomicDivision = taxonomicDivision;
795 public String getDescription()
800 public void setDescription(String description)
802 this.description = description;
805 public String getFirstPublicDate()
807 return firstPublicDate;
810 public void setFirstPublicDate(String firstPublicDate)
812 this.firstPublicDate = firstPublicDate;
815 public String getFirstPublicRelease()
817 return firstPublicRelease;
820 public void setFirstPublicRelease(String firstPublicRelease)
822 this.firstPublicRelease = firstPublicRelease;
825 public String getLastUpdatedDate()
827 return lastUpdatedDate;
830 public void setLastUpdatedDate(String lastUpdatedDate)
832 this.lastUpdatedDate = lastUpdatedDate;
835 public String getLastUpdatedRelease()
837 return lastUpdatedRelease;
840 public void setLastUpdatedRelease(String lastUpdatedRelease)
842 this.lastUpdatedRelease = lastUpdatedRelease;
845 public String getDataClass()
850 public void setDataClass(String dataClass)
852 this.dataClass = dataClass;