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 jalview.analysis.SequenceIdMatcher;
24 import jalview.bin.Cache;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.DBRefEntry;
28 import jalview.datamodel.DBRefSource;
29 import jalview.datamodel.FeatureProperties;
30 import jalview.datamodel.Mapping;
31 import jalview.datamodel.Sequence;
32 import jalview.datamodel.SequenceFeature;
33 import jalview.datamodel.SequenceI;
34 import jalview.util.DBRefUtils;
35 import jalview.util.DnaUtils;
36 import jalview.util.MapList;
37 import jalview.util.MappingUtils;
38 import jalview.util.MessageManager;
39 import jalview.ws.ebi.EBIFetchClient;
40 import jalview.xml.binding.embl.EntryType;
41 import jalview.xml.binding.embl.EntryType.Feature;
42 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
43 import jalview.xml.binding.jalview.JalviewModel;
44 import jalview.xml.binding.embl.ROOT;
45 import jalview.xml.binding.embl.XrefType;
48 import java.io.FileInputStream;
49 import java.io.InputStream;
50 import java.text.ParseException;
51 import java.util.ArrayList;
52 import java.util.Arrays;
53 import java.util.Hashtable;
54 import java.util.List;
56 import java.util.Map.Entry;
57 import java.util.regex.Pattern;
59 import javax.xml.bind.JAXBContext;
60 import javax.xml.bind.JAXBElement;
61 import javax.xml.bind.JAXBException;
62 import javax.xml.stream.FactoryConfigurationError;
63 import javax.xml.stream.XMLInputFactory;
64 import javax.xml.stream.XMLStreamException;
65 import javax.xml.stream.XMLStreamReader;
67 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
70 * JAL-1856 Embl returns this text for query not found
72 private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
74 private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
76 public EmblXmlSource()
82 * Retrieves and parses an emblxml file, and returns an alignment containing
83 * the parsed sequences, or null if none were found
86 * "EMBL" or "EMBLCDS" - anything else will not retrieve emblxml
91 protected AlignmentI getEmblSequenceRecords(String emprefx, String query)
95 EBIFetchClient dbFetch = new EBIFetchClient();
99 reply = dbFetch.fetchDataAsFile(
100 emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
102 } catch (Exception e)
105 throw new Exception(MessageManager.formatMessage(
106 "exception.ebiembl_retrieval_failed_on", new String[]
107 { emprefx.toLowerCase(), query.trim() }), e);
109 return getEmblSequenceRecords(emprefx, query, reply);
113 * parse an emblxml file stored locally
116 * either EMBL or EMBLCDS strings are allowed - anything else will
117 * not retrieve emblxml
120 * the EMBL XML file containing the results of a query
124 protected AlignmentI getEmblSequenceRecords(String emprefx, String query,
125 File reply) throws Exception
127 List<EntryType> entries = null;
128 if (reply != null && reply.exists())
130 file = reply.getAbsolutePath();
131 if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
133 InputStream is = new FileInputStream(reply);
134 entries = getEmblEntries(is);
139 * invalid accession gets a reply with no <entry> elements, text content of
140 * EmbFile reads something like (e.g.) this ungrammatical phrase
141 * Entry: <acc> display type is either not supported or entry is not found.
143 AlignmentI al = null;
144 List<SequenceI> seqs = new ArrayList<>();
145 List<SequenceI> peptides = new ArrayList<>();
148 for (EntryType entry : entries)
150 SequenceI seq = getSequence(emprefx, entry, peptides);
153 seqs.add(seq.deriveSequence());
154 // place DBReferences on dataset and refer
159 al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
164 "No record found for '" + emprefx + ":" + query + "'");
173 * Reads the XML reply from file and unmarshals it to Java objects. Answers a
174 * (possibly empty) list of <code>EntryType</code> objects.
180 List<EntryType> getEmblEntries(InputStream is)
182 List<EntryType> entries = new ArrayList<>();
185 JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.embl");
186 XMLStreamReader streamReader = XMLInputFactory.newInstance()
187 .createXMLStreamReader(is);
188 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
189 JAXBElement<ROOT> rootElement = um.unmarshal(streamReader, ROOT.class);
190 ROOT root = rootElement.getValue();
193 * document root contains either "entry" or "entrySet"
199 if (root.getEntrySet() != null)
201 entries = root.getEntrySet().getEntry();
203 else if (root.getEntry() != null)
205 entries.add(root.getEntry());
207 } catch (JAXBException | XMLStreamException
208 | FactoryConfigurationError e)
216 * A helper method to parse XML data and construct a sequence, with any
217 * available database references and features
224 SequenceI getSequence(String sourceDb, EntryType entry,
225 List<SequenceI> peptides)
227 String seqString = entry.getSequence();
228 if (seqString == null)
232 seqString = seqString.replace(" ", "").replace("\n", "").replace("\t",
234 String accession = entry.getAccession();
235 SequenceI dna = new Sequence(sourceDb + "|" + accession, seqString);
237 dna.setDescription(entry.getDescription());
238 String sequenceVersion = String.valueOf(entry.getVersion().intValue());
239 DBRefEntry selfRref = new DBRefEntry(sourceDb, sequenceVersion,
241 dna.addDBRef(selfRref);
243 new Mapping(null, new int[]
244 { 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
250 List<XrefType> xrefs = entry.getXref();
253 for (XrefType xref : xrefs)
255 String acc = xref.getId();
256 String source = DBRefUtils.getCanonicalName(xref.getDb());
257 String version = xref.getSecondaryId();
258 if (version == null || "".equals(version))
262 dna.addDBRef(new DBRefEntry(source, version, acc));
266 SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
269 List<Feature> features = entry.getFeature();
270 if (features != null)
272 for (Feature feature : features)
274 if (FeatureProperties.isCodingFeature(sourceDb,
277 parseCodingFeature(entry, feature, sourceDb, dna, peptides,
282 } catch (Exception e)
284 System.err.println("EMBL Record Features parsing error!");
286 .println("Please report the following to help@jalview.org :");
287 System.err.println("EMBL Record " + accession);
288 System.err.println("Resulted in exception: " + e.getMessage());
289 e.printStackTrace(System.err);
296 * Extracts coding region and product from a CDS feature and decorates it with
306 void parseCodingFeature(EntryType entry, Feature feature, String sourceDb,
307 SequenceI dna, List<SequenceI> peptides,
308 SequenceIdMatcher matcher)
310 final boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
311 final String accession = entry.getAccession();
312 final String sequenceVersion = entry.getVersion().toString();
314 int[] exons = getCdsRanges(entry.getAccession(), feature);
316 String translation = null;
317 String proteinName = "";
318 String proteinId = null;
319 Map<String, String> vals = new Hashtable<>();
322 * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
323 * (phase is required for CDS features in GFF3 format)
328 * parse qualifiers, saving protein translation, protein id,
329 * codon start position, product (name), and 'other values'
331 if (feature.getQualifier() != null)
333 for (Qualifier q : feature.getQualifier())
335 String qname = q.getName();
336 String value = q.getValue();
337 value = value == null ? ""
338 : value.trim().replace(" ", "").replace("\n", "")
340 if (qname.equals("translation"))
344 else if (qname.equals("protein_id"))
348 else if (qname.equals("codon_start"))
352 codonStart = Integer.parseInt(value.trim());
353 } catch (NumberFormatException e)
355 System.err.println("Invalid codon_start in XML for "
356 + entry.getAccession() + ": " + e.getMessage());
359 else if (qname.equals("product"))
361 // sometimes name is returned e.g. for V00488
366 // throw anything else into the additional properties hash
367 if (!"".equals(value))
369 vals.put(qname, value);
375 DBRefEntry proteinToEmblProteinRef = null;
376 exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
378 SequenceI product = null;
379 Mapping dnaToProteinMapping = null;
380 if (translation != null && proteinName != null && proteinId != null)
382 int translationLength = translation.length();
385 * look for product in peptides list, if not found, add it
387 product = matcher.findIdMatch(proteinId);
390 product = new Sequence(proteinId, translation, 1,
392 product.setDescription(((proteinName.length() == 0)
393 ? "Protein Product from " + sourceDb
395 peptides.add(product);
396 matcher.add(product);
399 // we have everything - create the mapping and perhaps the protein
401 if (exons == null || exons.length == 0)
404 * workaround until we handle dna location for CDS sequence
405 * e.g. location="X53828.1:60..1058" correctly
408 "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
409 + sourceDb + ":" + entry.getAccession() + ")");
410 int dnaLength = dna.getLength();
411 if (translationLength * 3 == (1 - codonStart + dnaLength))
414 "Not allowing for additional stop codon at end of cDNA fragment... !");
415 // this might occur for CDS sequences where no features are marked
416 exons = new int[] { dna.getStart() + (codonStart - 1),
418 dnaToProteinMapping = new Mapping(product, exons,
420 { 1, translationLength }, 3, 1);
422 if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
425 "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
426 exons = new int[] { dna.getStart() + (codonStart - 1),
428 dnaToProteinMapping = new Mapping(product, exons,
430 { 1, translationLength }, 3, 1);
435 // Trim the exon mapping if necessary - the given product may only be a
436 // fragment of a larger protein. (EMBL:AY043181 is an example)
440 // TODO: Add a DbRef back to the parent EMBL sequence with the exon
442 // if given a dataset reference, search dataset for parent EMBL
443 // sequence if it exists and set its map
444 // make a new feature annotating the coding contig
448 // final product length truncation check
449 int[] cdsRanges = adjustForProteinLength(translationLength,
451 dnaToProteinMapping = new Mapping(product, cdsRanges,
453 { 1, translationLength }, 3, 1);
457 * make xref with mapping from protein to EMBL dna
459 DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
460 sequenceVersion, proteinId,
461 new Mapping(dnaToProteinMapping.getMap().getInverse()));
462 product.addDBRef(proteinToEmblRef);
465 * make xref from protein to EMBLCDS; we assume here that the
466 * CDS sequence version is same as dna sequence (?!)
468 MapList proteinToCdsMapList = new MapList(
470 { 1, translationLength },
472 { 1 + (codonStart - 1),
473 (codonStart - 1) + 3 * translationLength },
475 DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
476 DBRefSource.EMBLCDS, sequenceVersion, proteinId,
477 new Mapping(proteinToCdsMapList));
478 product.addDBRef(proteinToEmblCdsRef);
481 * make 'direct' xref from protein to EMBLCDSPROTEIN
483 proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
484 proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
485 proteinToEmblProteinRef.setMap(null);
486 product.addDBRef(proteinToEmblProteinRef);
492 * add cds features to dna sequence
494 String cds = feature.getName(); // "CDS"
495 for (int xint = 0; exons != null
496 && xint < exons.length - 1; xint += 2)
498 int exonStart = exons[xint];
499 int exonEnd = exons[xint + 1];
500 int begin = Math.min(exonStart, exonEnd);
501 int end = Math.max(exonStart, exonEnd);
502 int exonNumber = xint / 2 + 1;
503 String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
504 exonNumber, proteinName, proteinId);
506 SequenceFeature sf = makeCdsFeature(cds, desc, begin, end, sourceDb,
509 sf.setEnaLocation(feature.getLocation());
510 boolean forwardStrand = exonStart <= exonEnd;
511 sf.setStrand(forwardStrand ? "+" : "-");
512 sf.setPhase(String.valueOf(codonStart - 1));
513 sf.setValue(FeatureProperties.EXONPOS, exonNumber);
514 sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
516 dna.addSequenceFeature(sf);
521 * add feature dbRefs to sequence, and mappings for Uniprot xrefs
523 boolean hasUniprotDbref = false;
524 List<XrefType> xrefs = feature.getXref();
527 boolean mappingUsed = false;
528 for (XrefType xref : xrefs)
531 * ensure UniProtKB/Swiss-Prot converted to UNIPROT
533 String source = DBRefUtils.getCanonicalName(xref.getDb());
534 String version = xref.getSecondaryId();
535 if (version == null || "".equals(version))
539 DBRefEntry dbref = new DBRefEntry(source, version, xref.getId());
540 DBRefEntry proteinDbRef = new DBRefEntry(source, version,
541 dbref.getAccessionId());
542 if (source.equals(DBRefSource.UNIPROT))
544 String proteinSeqName = DBRefSource.UNIPROT + "|"
545 + dbref.getAccessionId();
546 if (dnaToProteinMapping != null
547 && dnaToProteinMapping.getTo() != null)
552 * two or more Uniprot xrefs for the same CDS -
553 * each needs a distinct Mapping (as to a different sequence)
555 dnaToProteinMapping = new Mapping(dnaToProteinMapping);
560 * try to locate the protein mapped to (possibly by a
561 * previous CDS feature); if not found, construct it from
562 * the EMBL translation
564 SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
565 if (proteinSeq == null)
567 proteinSeq = new Sequence(proteinSeqName,
568 product.getSequenceAsString());
569 matcher.add(proteinSeq);
570 peptides.add(proteinSeq);
572 dnaToProteinMapping.setTo(proteinSeq);
573 dnaToProteinMapping.setMappedFromId(proteinId);
574 proteinSeq.addDBRef(proteinDbRef);
575 dbref.setMap(dnaToProteinMapping);
577 hasUniprotDbref = true;
582 * copy feature dbref to our protein product
584 DBRefEntry pref = proteinDbRef;
585 pref.setMap(null); // reference is direct
586 product.addDBRef(pref);
587 // Add converse mapping reference
588 if (dnaToProteinMapping != null)
590 Mapping pmap = new Mapping(dna,
591 dnaToProteinMapping.getMap().getInverse());
592 pref = new DBRefEntry(sourceDb, sequenceVersion, accession);
594 if (dnaToProteinMapping.getTo() != null)
596 dnaToProteinMapping.getTo().addDBRef(pref);
605 * if we have a product (translation) but no explicit Uniprot dbref
606 * (example: EMBL AAFI02000057 protein_id EAL65544.1)
607 * then construct mappings to an assumed EMBLCDSPROTEIN accession
609 if (!hasUniprotDbref && product != null)
611 if (proteinToEmblProteinRef == null)
613 // assuming CDSPROTEIN sequence version = dna version (?!)
614 proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
615 sequenceVersion, proteinId);
617 product.addDBRef(proteinToEmblProteinRef);
619 if (dnaToProteinMapping != null
620 && dnaToProteinMapping.getTo() != null)
622 DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
623 DBRefSource.EMBLCDSProduct, sequenceVersion,
625 dnaToEmblProteinRef.setMap(dnaToProteinMapping);
626 dnaToProteinMapping.setMappedFromId(proteinId);
627 dna.addDBRef(dnaToEmblProteinRef);
633 public boolean isDnaCoding()
639 * Returns the CDS positions as a single array of [start, end, start, end...]
640 * positions. If on the reverse strand, these will be in descending order.
646 protected int[] getCdsRanges(String accession, Feature feature)
648 String location = feature.getLocation();
649 if (location == null)
656 List<int[]> ranges = DnaUtils.parseLocation(location);
657 return listToArray(ranges);
658 } catch (ParseException e)
661 String.format("Not parsing inexact CDS location %s in ENA %s",
662 location, accession));
668 * Converts a list of [start, end] ranges to a single array of [start, end,
674 int[] listToArray(List<int[]> ranges)
676 int[] result = new int[ranges.size() * 2];
678 for (int[] range : ranges)
680 result[i++] = range[0];
681 result[i++] = range[1];
687 * Helper method to construct a SequenceFeature for one cds range
690 * feature type ("CDS")
700 * map of 'miscellaneous values' for feature
703 protected SequenceFeature makeCdsFeature(String type, String desc,
704 int begin, int end, String group, Map<String, String> vals)
706 SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
709 StringBuilder sb = new StringBuilder();
710 boolean first = true;
711 for (Entry<String, String> val : vals.entrySet())
717 sb.append(val.getKey()).append("=").append(val.getValue());
719 sf.setValue(val.getKey(), val.getValue());
721 sf.setAttributes(sb.toString());
727 * Truncates (if necessary) the exon intervals to match 3 times the length of
728 * the protein; also accepts 3 bases longer (for stop codon not included in
731 * @param proteinLength
733 * an array of [start, end, start, end...] intervals
734 * @return the same array (if unchanged) or a truncated copy
736 static int[] adjustForProteinLength(int proteinLength, int[] exon)
738 if (proteinLength <= 0 || exon == null)
742 int expectedCdsLength = proteinLength * 3;
743 int exonLength = MappingUtils.getLength(Arrays.asList(exon));
746 * if exon length matches protein, or is shorter, or longer by the
747 * length of a stop codon (3 bases), then leave it unchanged
749 if (expectedCdsLength >= exonLength
750 || expectedCdsLength == exonLength - 3)
758 origxon = new int[exon.length];
759 System.arraycopy(exon, 0, origxon, 0, exon.length);
761 for (int x = 0; x < exon.length; x += 2)
763 cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
764 if (expectedCdsLength <= cdspos)
766 // advanced beyond last codon.
768 if (expectedCdsLength != cdspos)
771 // .println("Truncating final exon interval on region by "
772 // + (cdspos - cdslength));
776 * shrink the final exon - reduce end position if forward
777 * strand, increase it if reverse
779 if (exon[x + 1] >= exon[x])
781 endxon = exon[x + 1] - cdspos + expectedCdsLength;
785 endxon = exon[x + 1] + cdspos - expectedCdsLength;
793 // and trim the exon interval set if necessary
794 int[] nxon = new int[sxpos + 2];
795 System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
796 nxon[sxpos + 1] = endxon; // update the end boundary for the new exon