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 java.util.Enumeration;
24 import java.util.Hashtable;
25 import java.util.Iterator;
26 import java.util.Vector;
28 import jalview.datamodel.DBRefEntry;
29 import jalview.datamodel.DBRefSource;
30 import jalview.datamodel.FeatureProperties;
31 import jalview.datamodel.Mapping;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceI;
37 * Data model for one entry returned from an EMBL query, as marshalled by a
40 * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
42 * @see embl_mapping.xml
44 public class EmblEntry
60 Vector<String> keywords;
62 Vector<DBRefEntry> dbRefs;
64 Vector<EmblFeature> features;
66 EmblSequence sequence;
69 * @return the accession
71 public String getAccession()
78 * the accession to set
80 public void setAccession(String accession)
82 this.accession = accession;
88 public Vector<DBRefEntry> getDbRefs()
97 public void setDbRefs(Vector<DBRefEntry> dbRefs)
105 public String getDesc()
114 public void setDesc(String desc)
120 * @return the features
122 public Vector<EmblFeature> getFeatures()
129 * the features to set
131 public void setFeatures(Vector<EmblFeature> features)
133 this.features = features;
137 * @return the keywords
139 public Vector<String> getKeywords()
146 * the keywords to set
148 public void setKeywords(Vector<String> keywords)
150 this.keywords = keywords;
154 * @return the lastUpdated
156 public String getLastUpdated()
163 * the lastUpdated to set
165 public void setLastUpdated(String lastUpdated)
167 this.lastUpdated = lastUpdated;
171 * @return the releaseCreated
173 public String getRCreated()
179 * @param releaseCreated
180 * the releaseCreated to set
182 public void setRCreated(String releaseCreated)
184 this.rCreated = releaseCreated;
188 * @return the releaseLastUpdated
190 public String getRLastUpdated()
196 * @param releaseLastUpdated
197 * the releaseLastUpdated to set
199 public void setRLastUpdated(String releaseLastUpdated)
201 this.rLastUpdated = releaseLastUpdated;
205 * @return the sequence
207 public EmblSequence getSequence()
214 * the sequence to set
216 public void setSequence(EmblSequence sequence)
218 this.sequence = sequence;
222 * @return the taxDivision
224 public String getTaxDivision()
231 * the taxDivision to set
233 public void setTaxDivision(String taxDivision)
235 this.taxDivision = taxDivision;
239 * @return the version
241 public String getVersion()
250 public void setVersion(String version)
252 this.version = version;
256 * EMBL Feature support is limited. The text below is included for the benefit
257 * of any developer working on improving EMBL feature import in Jalview.
258 * Extract from EMBL feature specification see
259 * http://www.embl-ebi.ac.uk/embl/Documentation
260 * /FT_definitions/feature_table.html 3.5 Location 3.5.1 Purpose
262 * The location indicates the region of the presented sequence which
263 * corresponds to a feature.
265 * 3.5.2 Format and conventions The location contains at least one sequence
266 * location descriptor and may contain one or more operators with one or more
267 * sequence location descriptors. Base numbers refer to the numbering in the
268 * entry. This numbering designates the first base (5' end) of the presented
269 * sequence as base 1. Base locations beyond the range of the presented
270 * sequence may not be used in location descriptors, the only exception being
271 * location in a remote entry (see 3.5.2.1, e).
273 * Location operators and descriptors are discussed in more detail below.
275 * 3.5.2.1 Location descriptors
277 * The location descriptor can be one of the following: (a) a single base
278 * number (b) a site between two indicated adjoining bases (c) a single base
279 * chosen from within a specified range of bases (not allowed for new entries)
280 * (d) the base numbers delimiting a sequence span (e) a remote entry
281 * identifier followed by a local location descriptor (i.e., a-d)
283 * A site between two adjoining nucleotides, such as endonucleolytic cleavage
284 * site, is indicated by listing the two points separated by a carat (^). The
285 * permitted formats for this descriptor are n^n+1 (for example 55^56), or,
286 * for circular molecules, n^1, where "n" is the full length of the molecule,
287 * ie 1000^1 for circular molecule with length 1000.
289 * A single base chosen from a range of bases is indicated by the first base
290 * number and the last base number of the range separated by a single period
291 * (e.g., '12.21' indicates a single base taken from between the indicated
292 * points). From October 2006 the usage of this descriptor is restricted : it
293 * is illegal to use "a single base from a range" (c) either on its own or in
294 * combination with the "sequence span" (d) descriptor for newly created
295 * entries. The existing entries where such descriptors exist are going to be
298 * Sequence spans are indicated by the starting base number and the ending
299 * base number separated by two periods (e.g., '34..456'). The '<' and '>'
300 * symbols may be used with the starting and ending base numbers to indicate
301 * that an end point is beyond the specified base number. The starting and
302 * ending base positions can be represented as distinct base numbers
303 * ('34..456') or a site between two indicated adjoining bases.
305 * A location in a remote entry (not the entry to which the feature table
306 * belongs) can be specified by giving the accession-number and sequence
307 * version of the remote entry, followed by a colon ":", followed by a
308 * location descriptor which applies to that entry's sequence (i.e.
309 * J12345.1:1..15, see also examples below)
313 * The location operator is a prefix that specifies what must be done to the
314 * indicated sequence to find or construct the location corresponding to the
315 * feature. A list of operators is given below with their definitions and most
318 * complement(location) Find the complement of the presented sequence in the
319 * span specified by " location" (i.e., read the complement of the presented
320 * strand in its 5'-to-3' direction)
322 * join(location,location, ... location) The indicated elements should be
323 * joined (placed end-to-end) to form one contiguous sequence
325 * order(location,location, ... location) The elements can be found in the
326 * specified order (5' to 3' direction), but nothing is implied about the
327 * reasonableness about joining them
329 * Note : location operator "complement" can be used in combination with
330 * either " join" or "order" within the same location; combinations of "join"
331 * and "order" within the same location (nested operators) are illegal.
335 * 3.5.3 Location examples
337 * The following is a list of common location descriptors with their meanings:
339 * Location Description
341 * 467 Points to a single base in the presented sequence
343 * 340..565 Points to a continuous range of bases bounded by and including the
344 * starting and ending bases
346 * <345..500 Indicates that the exact lower boundary point of a feature is
347 * unknown. The location begins at some base previous to the first base
348 * specified (which need not be contained in the presented sequence) and
349 * continues to and includes the ending base
351 * <1..888 The feature starts before the first sequenced base and continues to
352 * and includes base 888
354 * 1..>888 The feature starts at the first sequenced base and continues beyond
357 * 102.110 Indicates that the exact location is unknown but that it is one of
358 * the bases between bases 102 and 110, inclusive
360 * 123^124 Points to a site between bases 123 and 124
362 * join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
363 * form one contiguous sequence
366 * complement(34..126) Start at the base complementary to 126 and finish at
367 * the base complementary to base 34 (the feature is on the strand
368 * complementary to the presented strand)
371 * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
372 * to 5163, then complements the joined segments (the feature is on the strand
373 * complementary to the presented strand)
375 * join(complement(4918..5163),complement(2691..4571)) Complements regions
376 * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
377 * feature is on the strand complementary to the presented strand)
379 * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
380 * this database) with primary accession number 'J00194'
382 * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
383 * with the region 100..202 of remote entry J00194
386 * Recover annotated sequences from EMBL file
389 * don't return nucleic acid sequences
393 * don't return any translated protein sequences marked in features
394 * @return dataset sequences with DBRefs and features - DNA always comes first
396 public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
397 boolean noPeptide, String sourceDb)
398 { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
399 // cases of noNa and noPeptide
400 Vector seqs = new Vector();
404 // In theory we still need to create this if noNa is set to avoid a null
406 dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
407 dna.setDescription(desc);
408 DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
409 dna.addDBRef(retrievedref);
410 // add map to indicate the sequence is a valid coordinate frame for the
412 retrievedref.setMap(new Mapping(null, new int[]
413 { 1, dna.getLength() }, new int[]
414 { 1, dna.getLength() }, 1, 1));
415 // TODO: transform EMBL Database refs to canonical form
418 for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
419 .addDBRef((DBRefEntry) i.next()))
427 for (Iterator i = features.iterator(); i.hasNext();)
429 EmblFeature feature = (EmblFeature) i.next();
432 if (feature.dbRefs != null && feature.dbRefs.size() > 0)
434 for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
435 .addDBRef((DBRefEntry) dbr.next()))
441 if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
443 parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
447 // General feature type.
450 if (feature.dbRefs != null && feature.dbRefs.size() > 0)
452 for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
453 .addDBRef((DBRefEntry) dbr.next()))
461 } catch (Exception e)
463 System.err.println("EMBL Record Features parsing error!");
465 .println("Please report the following to help@jalview.org :");
466 System.err.println("EMBL Record " + accession);
467 System.err.println("Resulted in exception: " + e.getMessage());
468 e.printStackTrace(System.err);
470 if (!noNa && dna != null)
474 SequenceI[] sqs = new SequenceI[seqs.size()];
475 for (int i = 0, j = seqs.size(); i < j; i++)
477 sqs[i] = (SequenceI) seqs.elementAt(i);
484 * attempt to extract coding region and product from a feature and properly
485 * decorate it with annotations.
490 * source database for the EMBLXML
492 * place where sequences go
494 * parent dna sequence for this record
496 * flag for generation of Peptide sequence objects
498 private void parseCodingFeature(EmblFeature feature, String sourceDb,
499 Vector seqs, Sequence dna, boolean noPeptide)
501 boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
502 // extract coding region(s)
503 jalview.datamodel.Mapping map = null;
505 if (feature.locations != null && feature.locations.size() > 0)
507 for (Enumeration locs = feature.locations.elements(); locs
510 EmblFeatureLocations loc = (EmblFeatureLocations) locs
512 int[] se = loc.getElementRanges(accession);
519 int[] t = new int[exon.length + se.length];
520 System.arraycopy(exon, 0, t, 0, exon.length);
521 System.arraycopy(se, 0, t, exon.length, se.length);
527 String prname = new String();
529 Hashtable vals = new Hashtable();
532 if (feature.getQualifiers() != null
533 && feature.getQualifiers().size() > 0)
535 for (Iterator quals = feature.getQualifiers().iterator(); quals
538 Qualifier q = (Qualifier) quals.next();
539 if (q.getName().equals("translation"))
541 StringBuffer prsq = new StringBuffer(q.getValues()[0]);
542 int p = prsq.indexOf(" ");
545 prsq.deleteCharAt(p);
546 p = prsq.indexOf(" ", p);
548 prseq = prsq.toString();
552 else if (q.getName().equals("protein_id"))
554 prid = q.getValues()[0];
556 else if (q.getName().equals("codon_start"))
558 prstart = Integer.parseInt(q.getValues()[0]);
560 else if (q.getName().equals("product"))
562 prname = q.getValues()[0];
566 // throw anything else into the additional properties hash
567 String[] s = q.getValues();
568 StringBuffer sb = new StringBuffer();
571 for (int i = 0; i < s.length; i++)
577 vals.put(q.getName(), sb.toString());
581 Sequence product = null;
582 DBRefEntry protEMBLCDS = null;
583 exon = adjustForPrStart(prstart, exon);
584 boolean noProteinDbref=true;
586 if (prseq != null && prname != null && prid != null)
589 product = new Sequence(prid, prseq, 1, prseq.length());
590 product.setDescription(((prname.length() == 0) ? "Protein Product from "
595 // Protein is also added to vector of sequences returned
598 // we have everything - create the mapping and perhaps the protein
600 if (exon == null || exon.length == 0)
603 .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
604 + sourceDb + ":" + getAccession() + ")");
605 if (prseq.length() * 3 == (1 - prstart + dna.getSequence().length))
608 .println("Not allowing for additional stop codon at end of cDNA fragment... !");
609 // this might occur for CDS sequences where no features are
612 { dna.getStart() + (prstart - 1), dna.getEnd() };
613 map = new jalview.datamodel.Mapping(product, exon, new int[]
614 { 1, prseq.length() }, 3, 1);
616 if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
619 .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
621 { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
622 map = new jalview.datamodel.Mapping(product, exon, new int[]
623 { 1, prseq.length() }, 3, 1);
628 // Trim the exon mapping if necessary - the given product may only be a
629 // fragment of a larger protein. (EMBL:AY043181 is an example)
633 // TODO: Add a DbRef back to the parent EMBL sequence with the exon
635 // if given a dataset reference, search dataset for parent EMBL
636 // sequence if it exists and set its map
637 // make a new feature annotating the coding contig
641 // final product length trunctation check
643 map = new jalview.datamodel.Mapping(product,
644 adjustForProteinLength(prseq.length(), exon), new int[]
645 { 1, prseq.length() }, 3, 1);
646 // reconstruct the EMBLCDS entry
647 // TODO: this is only necessary when there codon annotation is
648 // complete (I think JBPNote)
649 DBRefEntry pcdnaref = new DBRefEntry();
650 pcdnaref.setAccessionId(prid);
651 pcdnaref.setSource(DBRefSource.EMBLCDS);
652 pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
653 jalview.util.MapList mp = new jalview.util.MapList(new int[]
654 { 1, prseq.length() }, new int[]
655 { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
656 // { 1 + (prstart - 1) * 3,
657 // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
658 // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
659 pcdnaref.setMap(new Mapping(mp));
662 product.addDBRef(pcdnaref);
663 protEMBLCDS = new DBRefEntry(pcdnaref);
664 protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
665 product.addDBRef(protEMBLCDS);
671 // add cds feature to dna seq - this may include the stop codon
672 for (int xint = 0; exon != null && xint < exon.length; xint += 2)
674 SequenceFeature sf = new SequenceFeature();
675 sf.setBegin(exon[xint]);
676 sf.setEnd(exon[xint + 1]);
677 sf.setType(feature.getName());
678 sf.setFeatureGroup(sourceDb);
679 sf.setDescription("Exon " + (1 + xint / 2)
680 + " for protein '" + prname + "' EMBLCDS:" + prid);
681 sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
682 sf.setValue(FeatureProperties.EXONPRODUCT, prname);
683 if (vals != null && vals.size() > 0)
685 Enumeration kv = vals.keys();
686 while (kv.hasMoreElements())
688 Object key = kv.nextElement();
691 sf.setValue(key.toString(), vals.get(key));
695 dna.addSequenceFeature(sf);
698 // add dbRefs to sequence
699 if (feature.dbRefs != null && feature.dbRefs.size() > 0)
701 for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
703 DBRefEntry ref = (DBRefEntry) dbr.next();
704 ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
706 // Hard code the kind of protein product accessions that EMBL cite
707 if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
710 if (map != null && map.getTo() != null)
712 map.getTo().addDBRef(
713 new DBRefEntry(ref.getSource(), ref.getVersion(), ref
714 .getAccessionId())); // don't copy map over.
715 if (map.getTo().getName().indexOf(prid) == 0)
718 jalview.datamodel.DBRefSource.UNIPROT + "|"
719 + ref.getAccessionId());
722 noProteinDbref = false;
726 DBRefEntry pref = new DBRefEntry(ref.getSource(),
727 ref.getVersion(), ref.getAccessionId());
728 pref.setMap(null); // reference is direct
729 product.addDBRef(pref);
730 // Add converse mapping reference
733 Mapping pmap = new Mapping(dna, map.getMap().getInverse());
734 pref = new DBRefEntry(sourceDb, getVersion(),
735 this.getAccession());
737 if (map.getTo() != null)
739 map.getTo().addDBRef(pref);
745 if (noProteinDbref && product != null)
747 // add protein coding reference to dna sequence so xref matches
748 if (protEMBLCDS == null)
750 protEMBLCDS = new DBRefEntry();
751 protEMBLCDS.setAccessionId(prid);
752 protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
753 protEMBLCDS.setVersion(getVersion());
755 .setMap(new Mapping(product, map.getMap().getInverse()));
757 product.addDBRef(protEMBLCDS);
759 // Add converse mapping reference
762 Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
764 DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
766 if (map.getTo() != null)
775 private int[] adjustForPrStart(int prstart, int[] exon)
778 int origxon[], sxpos = -1;
779 int sxstart, sxstop; // unnecessary variables used for debugging
780 // first adjust range for codon start attribute
783 origxon = new int[exon.length];
784 System.arraycopy(exon, 0, origxon, 0, exon.length);
786 for (int x = 0; x < exon.length && sxpos == -1; x += 2)
788 cdspos += exon[x + 1] - exon[x] + 1;
789 if (prstart <= cdspos)
793 sxstop = exon[x + 1];
794 // and adjust start boundary of first exon.
795 exon[x] = exon[x + 1] - cdspos + prstart;
802 int[] nxon = new int[exon.length - sxpos];
803 System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
811 * truncate the last exon interval to the prlength'th codon
817 private int[] adjustForProteinLength(int prlength, int[] exon)
820 int origxon[], sxpos = -1, endxon = 0, cdslength = prlength * 3;
821 int sxstart, sxstop; // unnecessary variables used for debugging
822 // first adjust range for codon start attribute
823 if (prlength >= 1 && exon != null)
825 origxon = new int[exon.length];
826 System.arraycopy(exon, 0, origxon, 0, exon.length);
828 for (int x = 0; x < exon.length && sxpos == -1; x += 2)
830 cdspos += exon[x + 1] - exon[x] + 1;
831 if (cdslength <= cdspos)
833 // advanced beyond last codon.
836 sxstop = exon[x + 1];
837 if (cdslength != cdspos)
840 .println("Truncating final exon interval on region by "
841 + (cdspos - cdslength));
843 // locate the new end boundary of final exon as endxon
844 endxon = exon[x + 1] - cdspos + cdslength;
851 // and trim the exon interval set if necessary
852 int[] nxon = new int[sxpos + 2];
853 System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
854 nxon[sxpos + 1] = endxon; // update the end boundary for the new exon