+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel.xdb.embl;
-
-import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.StringUtils;
-
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-/**
- * Data model for one entry returned from an EMBL query, as marshalled by a
- * Castor binding file
- *
- * For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
- *
- * @see embl_mapping.xml
- */
-public class EmblEntry
-{
- private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
- String accession;
-
- String version;
-
- String taxDivision;
-
- String desc;
-
- String rCreated;
-
- String rLastUpdated;
-
- String lastUpdated;
-
- Vector<String> keywords;
-
- Vector<DBRefEntry> dbRefs;
-
- Vector<EmblFeature> features;
-
- EmblSequence sequence;
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-
- /**
- * @return the dbRefs
- */
- public Vector<DBRefEntry> getDbRefs()
- {
- return dbRefs;
- }
-
- /**
- * @param dbRefs
- * the dbRefs to set
- */
- public void setDbRefs(Vector<DBRefEntry> dbRefs)
- {
- this.dbRefs = dbRefs;
- }
-
- /**
- * @return the desc
- */
- public String getDesc()
- {
- return desc;
- }
-
- /**
- * @param desc
- * the desc to set
- */
- public void setDesc(String desc)
- {
- this.desc = desc;
- }
-
- /**
- * @return the features
- */
- public Vector<EmblFeature> getFeatures()
- {
- return features;
- }
-
- /**
- * @param features
- * the features to set
- */
- public void setFeatures(Vector<EmblFeature> features)
- {
- this.features = features;
- }
-
- /**
- * @return the keywords
- */
- public Vector<String> getKeywords()
- {
- return keywords;
- }
-
- /**
- * @param keywords
- * the keywords to set
- */
- public void setKeywords(Vector<String> keywords)
- {
- this.keywords = keywords;
- }
-
- /**
- * @return the lastUpdated
- */
- public String getLastUpdated()
- {
- return lastUpdated;
- }
-
- /**
- * @param lastUpdated
- * the lastUpdated to set
- */
- public void setLastUpdated(String lastUpdated)
- {
- this.lastUpdated = lastUpdated;
- }
-
- /**
- * @return the releaseCreated
- */
- public String getRCreated()
- {
- return rCreated;
- }
-
- /**
- * @param releaseCreated
- * the releaseCreated to set
- */
- public void setRCreated(String releaseCreated)
- {
- this.rCreated = releaseCreated;
- }
-
- /**
- * @return the releaseLastUpdated
- */
- public String getRLastUpdated()
- {
- return rLastUpdated;
- }
-
- /**
- * @param releaseLastUpdated
- * the releaseLastUpdated to set
- */
- public void setRLastUpdated(String releaseLastUpdated)
- {
- this.rLastUpdated = releaseLastUpdated;
- }
-
- /**
- * @return the sequence
- */
- public EmblSequence getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(EmblSequence sequence)
- {
- this.sequence = sequence;
- }
-
- /**
- * @return the taxDivision
- */
- public String getTaxDivision()
- {
- return taxDivision;
- }
-
- /**
- * @param taxDivision
- * the taxDivision to set
- */
- public void setTaxDivision(String taxDivision)
- {
- this.taxDivision = taxDivision;
- }
-
- /**
- * @return the version
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- */
- public void setVersion(String version)
- {
- this.version = version;
- }
-
- /**
- * Recover annotated sequences from EMBL file
- *
- * @param sourceDb
- * @param peptides
- * a list of protein products found so far (to add to)
- * @return dna dataset sequence with DBRefs and features
- */
- public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
- {
- SequenceI dna = new Sequence(sourceDb + "|" + accession,
- sequence.getSequence());
- dna.setDescription(desc);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
- dna.addDBRef(retrievedref);
- // add map to indicate the sequence is a valid coordinate frame for the
- // dbref
- retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
- new int[] { 1, dna.getLength() }, 1, 1));
- // TODO: transform EMBL Database refs to canonical form
- if (dbRefs != null)
- {
- for (DBRefEntry dbref : dbRefs)
- {
- dna.addDBRef(dbref);
- }
- }
-
- try
- {
- for (EmblFeature feature : features)
- {
- if (feature.dbRefs != null)
- {
- for (DBRefEntry dbref : feature.dbRefs)
- {
- dna.addDBRef(dbref);
- }
- }
- if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
- {
- parseCodingFeature(feature, sourceDb, dna, peptides);
- }
- }
- } catch (Exception e)
- {
- System.err.println("EMBL Record Features parsing error!");
- System.err
- .println("Please report the following to help@jalview.org :");
- System.err.println("EMBL Record " + accession);
- System.err.println("Resulted in exception: " + e.getMessage());
- e.printStackTrace(System.err);
- }
-
- return dna;
- }
-
- /**
- * Extracts coding region and product from a CDS feature and properly decorate
- * it with annotations.
- *
- * @param feature
- * coding feature
- * @param sourceDb
- * source database for the EMBLXML
- * @param dna
- * parent dna sequence for this record
- * @param peptides
- * list of protein product sequences for Embl entry
- */
- void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides)
- {
- boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
-
- int[] exon = getCdsRanges(feature);
-
- String prseq = null;
- String prname = "";
- String prid = null;
- Map<String, String> vals = new Hashtable<String, String>();
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
-
- /*
- * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
- * (phase is required for CDS features in GFF3 format)
- */
- int codonStart = 1;
-
- /*
- * parse qualifiers, saving protein translation, protein id,
- * codon start position, product (name), and 'other values'
- */
- if (feature.getQualifiers() != null)
- {
- for (Qualifier q : feature.getQualifiers())
- {
- String qname = q.getName();
- if (qname.equals("translation"))
- {
- // remove all spaces (precompiled String.replaceAll(" ", ""))
- prseq = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
- }
- else if (qname.equals("protein_id"))
- {
- prid = q.getValues()[0];
- }
- else if (qname.equals("codon_start"))
- {
- try
- {
- codonStart = Integer.parseInt(q.getValues()[0]);
- } catch (NumberFormatException e)
- {
- System.err.println("Invalid codon_start in XML for "
- + accession + ": " + e.getMessage());
- }
- }
- else if (qname.equals("product"))
- {
- // sometimes name is returned e.g. for V00488
- prname = q.getValues()[0];
- }
- else
- {
- // throw anything else into the additional properties hash
- String[] qvals = q.getValues();
- if (qvals != null)
- {
- String commaSeparated = StringUtils.arrayToSeparatorList(qvals,
- ",");
- vals.put(qname, commaSeparated);
- }
- }
- }
- }
-
- // SequenceI product = null;
- DBRefEntry protEMBLCDS = null;
- exon = MappingUtils.removeStartPositions(codonStart - 1, exon);
- boolean noProteinDbref = true;
-
- SequenceI product = null;
- Mapping map = null;
- if (prseq != null && prname != null && prid != null)
- {
- /*
- * look for product in peptides list, if not found, add it
- */
- product = matcher.findIdMatch(prid);
- if (product == null)
- {
- product = new Sequence(prid, prseq, 1, prseq.length());
- product.setDescription(((prname.length() == 0) ? "Protein Product from "
- + sourceDb
- : prname));
- peptides.add(product);
- matcher.add(product);
- }
-
- // we have everything - create the mapping and perhaps the protein
- // sequence
- if (exon == null || exon.length == 0)
- {
- System.err
- .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
- + sourceDb + ":" + getAccession() + ")");
- if (prseq.length() * 3 == (1 - codonStart + dna.getSequence().length))
- {
- System.err
- .println("Not allowing for additional stop codon at end of cDNA fragment... !");
- // this might occur for CDS sequences where no features are
- // marked.
- exon = new int[] { dna.getStart() + (codonStart - 1), dna.getEnd() };
- map = new Mapping(product, exon, new int[] { 1, prseq.length() },
- 3, 1);
- }
- if ((prseq.length() + 1) * 3 == (1 - codonStart + dna.getSequence().length))
- {
- System.err
- .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
- exon = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() - 3 };
- map = new Mapping(product, exon, new int[] { 1, prseq.length() },
- 3, 1);
- }
- }
- else
- {
- // Trim the exon mapping if necessary - the given product may only be a
- // fragment of a larger protein. (EMBL:AY043181 is an example)
-
- if (isEmblCdna)
- {
- // TODO: Add a DbRef back to the parent EMBL sequence with the exon
- // map
- // if given a dataset reference, search dataset for parent EMBL
- // sequence if it exists and set its map
- // make a new feature annotating the coding contig
- }
- else
- {
- // final product length truncation check
- // TODO should from range include stop codon even if not in protein
- // in order to include stop codon in CDS sequence (as done for
- // Ensembl)?
- int[] cdsRanges = adjustForProteinLength(prseq.length(),
- exon);
- map = new Mapping(product, cdsRanges, new int[] { 1, prseq.length() }, 3, 1);
- // reconstruct the EMBLCDS entry
- // TODO: this is only necessary when there codon annotation is
- // complete (I think JBPNote)
- DBRefEntry pcdnaref = new DBRefEntry();
- pcdnaref.setAccessionId(prid);
- pcdnaref.setSource(DBRefSource.EMBLCDS);
- pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
- MapList mp = new MapList(new int[] { 1, prseq.length() },
- new int[] { 1 + (codonStart - 1),
- (codonStart - 1) + 3 * prseq.length() }, 1, 3);
- pcdnaref.setMap(new Mapping(mp));
- if (product != null)
- {
- product.addDBRef(pcdnaref);
- protEMBLCDS = new DBRefEntry(pcdnaref);
- protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
- product.addDBRef(protEMBLCDS);
- }
- }
- }
- // add cds feature to dna seq - this may include the stop codon
- for (int xint = 0; exon != null && xint < exon.length; xint += 2)
- {
- SequenceFeature sf = makeCdsFeature(exon, xint, prname, prid, vals,
- codonStart);
- sf.setType(feature.getName()); // "CDS"
- sf.setFeatureGroup(sourceDb);
- dna.addSequenceFeature(sf);
- }
- }
-
- /*
- * add dbRefs to sequence, and mappings for Uniprot xrefs
- */
- if (feature.dbRefs != null)
- {
- boolean mappingUsed = false;
- for (DBRefEntry ref : feature.dbRefs)
- {
- ref.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
- if (ref.getSource().equals(DBRefSource.UNIPROT))
- {
- String proteinSeqName = DBRefSource.UNIPROT + "|"
- + ref.getAccessionId();
- if (map != null && map.getTo() != null)
- {
- if (mappingUsed)
- {
- /*
- * two or more Uniprot xrefs for the same CDS -
- * each needs a distinct Mapping (as to a different sequence)
- */
- map = new Mapping(map);
- }
- mappingUsed = true;
-
- /*
- * try to locate the protein mapped to (possibly by a
- * previous CDS feature)
- */
- SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
- if (proteinSeq == null)
- {
- proteinSeq = new Sequence(proteinSeqName,
- product
- .getSequenceAsString());
- matcher.add(proteinSeq);
- peptides.add(proteinSeq);
- }
- map.setTo(proteinSeq);
- map.getTo().addDBRef(
- new DBRefEntry(ref.getSource(), ref.getVersion(), ref
- .getAccessionId()));
- ref.setMap(map);
- }
- noProteinDbref = false;
- }
- if (product != null)
- {
- DBRefEntry pref = new DBRefEntry(ref.getSource(),
- ref.getVersion(), ref.getAccessionId());
- pref.setMap(null); // reference is direct
- product.addDBRef(pref);
- // Add converse mapping reference
- if (map != null)
- {
- Mapping pmap = new Mapping(dna, map.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getVersion(),
- this.getAccession());
- pref.setMap(pmap);
- if (map.getTo() != null)
- {
- map.getTo().addDBRef(pref);
- }
- }
- }
- dna.addDBRef(ref);
- }
- if (noProteinDbref && product != null)
- {
- // add protein coding reference to dna sequence so xref matches
- if (protEMBLCDS == null)
- {
- protEMBLCDS = new DBRefEntry();
- protEMBLCDS.setAccessionId(prid);
- protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
- protEMBLCDS.setVersion(getVersion());
- protEMBLCDS
- .setMap(new Mapping(product, map.getMap().getInverse()));
- }
- product.addDBRef(protEMBLCDS);
-
- // Add converse mapping reference
- if (map != null)
- {
- Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
- .getInverse());
- DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
- ncMap.setMap(pmap);
- if (map.getTo() != null)
- {
- dna.addDBRef(ncMap);
- }
- }
- }
- }
- }
-
- /**
- * Helper method to construct a SequenceFeature for one cds range
- *
- * @param exons
- * array of cds [start, end, ...] positions
- * @param exonStartIndex
- * offset into the exons array
- * @param proteinName
- * @param proteinAccessionId
- * @param vals
- * map of 'miscellaneous values' for feature
- * @param codonStart
- * codon start position for CDS (1/2/3, normally 1)
- * @return
- */
- protected SequenceFeature makeCdsFeature(int[] exons, int exonStartIndex,
- String proteinName, String proteinAccessionId,
- Map<String, String> vals, int codonStart)
- {
- int exonNumber = exonStartIndex / 2 + 1;
- SequenceFeature sf = new SequenceFeature();
- sf.setBegin(Math.min(exons[exonStartIndex], exons[exonStartIndex + 1]));
- sf.setEnd(Math.max(exons[exonStartIndex], exons[exonStartIndex + 1]));
- sf.setDescription(String.format(
- "Exon %d for protein '%s' EMBLCDS:%s", exonNumber, proteinName,
- proteinAccessionId));
- sf.setPhase(String.valueOf(codonStart - 1));
- sf.setStrand(exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+" : "-");
- sf.setValue(FeatureProperties.EXONPOS, exonNumber);
- sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
- if (!vals.isEmpty())
- {
- StringBuilder sb = new StringBuilder();
- boolean first = true;
- for (Entry<String, String> val : vals.entrySet())
- {
- if (!first)
- {
- sb.append(";");
- }
- sb.append(val.getKey()).append("=").append(val.getValue());
- first = false;
- sf.setValue(val.getKey(), val.getValue());
- }
- sf.setAttributes(sb.toString());
- }
- return sf;
- }
-
- /**
- * Returns the CDS positions as a list of [start, end, start, end...]
- * positions. If on the reverse strand, these will be in descending order.
- *
- * @param feature
- * @return
- */
- protected int[] getCdsRanges(EmblFeature feature)
- {
- if (feature.locations == null)
- {
- return new int[] {};
- }
- int cdsBoundaryCount = 0; // count of all start/stop locations
- int[][] cdsLocations = new int[feature.locations.size()][];
- int locationNumber = 0;
- for (EmblFeatureLocations loc : feature.locations)
- {
- int[] locationRanges = loc.getElementRanges(accession);
- cdsLocations[locationNumber++] = locationRanges;
- cdsBoundaryCount += locationRanges.length;
- }
- int[] cdsRanges = new int[cdsBoundaryCount];
- int copyTo = 0;
- for (int[] ranges : cdsLocations)
- {
- System.arraycopy(ranges, 0, cdsRanges, copyTo, ranges.length);
- copyTo += ranges.length;
- }
- return cdsRanges;
-
- }
-
- /**
- * truncate the last exon interval to the prlength'th codon
- *
- * @param prlength
- * @param exon
- * @return new exon
- */
- private int[] adjustForProteinLength(int prlength, int[] exon)
- {
-
- int origxon[], sxpos = -1, endxon = 0, cdslength = prlength * 3;
- // first adjust range for codon start attribute
- if (prlength >= 1 && exon != null)
- {
- origxon = new int[exon.length];
- System.arraycopy(exon, 0, origxon, 0, exon.length);
- int cdspos = 0;
- for (int x = 0; x < exon.length && sxpos == -1; x += 2)
- {
- cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
- if (cdslength <= cdspos)
- {
- // advanced beyond last codon.
- sxpos = x;
- if (cdslength != cdspos)
- {
- System.err
- .println("Truncating final exon interval on region by "
- + (cdspos - cdslength));
- }
- // locate the new end boundary of final exon as endxon
- endxon = exon[x + 1] - cdspos + cdslength;
- break;
- }
- }
-
- if (sxpos != -1)
- {
- // and trim the exon interval set if necessary
- int[] nxon = new int[sxpos + 2];
- System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
- nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
- // set
- exon = nxon;
- }
- }
- return exon;
- }
-}
git://source.jalview.org / jalview.git / blobdiff