+++ /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.bin.Cache;
-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.DnaUtils;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.StringUtils;
-
-import java.text.ParseException;
-import java.util.Arrays;
-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/ena/data/view/J03321&display=xml
- *
- * @see embl_mapping.xml
- */
-public class EmblEntry
-{
- private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
- String accession;
-
- String entryVersion;
-
- String sequenceVersion;
-
- String dataClass;
-
- String moleculeType;
-
- String topology;
-
- String sequenceLength;
-
- String taxonomicDivision;
-
- String description;
-
- String firstPublicDate;
-
- String firstPublicRelease;
-
- String lastUpdatedDate;
-
- String lastUpdatedRelease;
-
- 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 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 sequence
- */
- public EmblSequence getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(EmblSequence sequence)
- {
- this.sequence = sequence;
- }
-
- /**
- * 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 = makeSequence(sourceDb);
- if (dna == null)
- {
- return null;
- }
- dna.setDescription(description);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb, getSequenceVersion(),
- 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));
-
- /*
- * transform EMBL Database refs to canonical form
- */
- if (dbRefs != null)
- {
- for (DBRefEntry dbref : dbRefs)
- {
- dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
- dna.addDBRef(dbref);
- }
- }
-
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
- try
- {
- for (EmblFeature feature : features)
- {
- if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
- {
- parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
- }
- }
- } 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;
- }
-
- /**
- * @param sourceDb
- * @return
- */
- SequenceI makeSequence(String sourceDb)
- {
- if (sequence == null)
- {
- System.err.println(
- "No sequence was returned for ENA accession " + accession);
- return null;
- }
- SequenceI dna = new Sequence(sourceDb + "|" + accession,
- sequence.getSequence());
- 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
- * @param matcher
- * helper to match xrefs in already retrieved sequences
- */
- void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides,
- SequenceIdMatcher matcher)
- {
- boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
-
- int[] exons = getCdsRanges(feature);
-
- String translation = null;
- String proteinName = "";
- String proteinId = null;
- Map<String, String> vals = new Hashtable<>();
-
- /*
- * 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(" ", ""))
- translation = SPACE_PATTERN.matcher(q.getValues()[0])
- .replaceAll("");
- }
- else if (qname.equals("protein_id"))
- {
- proteinId = q.getValues()[0].trim();
- }
- else if (qname.equals("codon_start"))
- {
- try
- {
- codonStart = Integer.parseInt(q.getValues()[0].trim());
- } 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
- proteinName = q.getValues()[0].trim();
- }
- 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);
- }
- }
- }
- }
-
- DBRefEntry proteinToEmblProteinRef = null;
- exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
-
- SequenceI product = null;
- Mapping dnaToProteinMapping = null;
- if (translation != null && proteinName != null && proteinId != null)
- {
- int translationLength = translation.length();
-
- /*
- * look for product in peptides list, if not found, add it
- */
- product = matcher.findIdMatch(proteinId);
- if (product == null)
- {
- product = new Sequence(proteinId, translation, 1,
- translationLength);
- product.setDescription(((proteinName.length() == 0)
- ? "Protein Product from " + sourceDb
- : proteinName));
- peptides.add(product);
- matcher.add(product);
- }
-
- // we have everything - create the mapping and perhaps the protein
- // sequence
- if (exons == null || exons.length == 0)
- {
- /*
- * workaround until we handle dna location for CDS sequence
- * e.g. location="X53828.1:60..1058" correctly
- */
- System.err.println(
- "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
- + sourceDb + ":" + getAccession() + ")");
- int dnaLength = dna.getLength();
- if (translationLength * 3 == (1 - codonStart + dnaLength))
- {
- 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
- exons = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() };
- dnaToProteinMapping = new Mapping(product, exons,
- new int[]
- { 1, translationLength }, 3, 1);
- }
- if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
- {
- System.err.println(
- "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
- exons = new int[] { dna.getStart() + (codonStart - 1),
- dna.getEnd() - 3 };
- dnaToProteinMapping = new Mapping(product, exons,
- new int[]
- { 1, translationLength }, 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
- int[] cdsRanges = adjustForProteinLength(translationLength,
- exons);
- dnaToProteinMapping = new Mapping(product, cdsRanges,
- new int[]
- { 1, translationLength }, 3, 1);
- if (product != null)
- {
- /*
- * make xref with mapping from protein to EMBL dna
- */
- DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
- getSequenceVersion(), proteinId,
- new Mapping(dnaToProteinMapping.getMap().getInverse()));
- product.addDBRef(proteinToEmblRef);
-
- /*
- * make xref from protein to EMBLCDS; we assume here that the
- * CDS sequence version is same as dna sequence (?!)
- */
- MapList proteinToCdsMapList = new MapList(
- new int[]
- { 1, translationLength },
- new int[]
- { 1 + (codonStart - 1),
- (codonStart - 1) + 3 * translationLength },
- 1, 3);
- DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
- DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
- new Mapping(proteinToCdsMapList));
- product.addDBRef(proteinToEmblCdsRef);
-
- /*
- * make 'direct' xref from protein to EMBLCDSPROTEIN
- */
- proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
- proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
- proteinToEmblProteinRef.setMap(null);
- product.addDBRef(proteinToEmblProteinRef);
- }
- }
- }
-
- /*
- * add cds features to dna sequence
- */
- String cds = feature.getName(); // "CDS"
- for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
- {
- int exonStart = exons[xint];
- int exonEnd = exons[xint + 1];
- int begin = Math.min(exonStart, exonEnd);
- int end = Math.max(exonStart, exonEnd);
- int exonNumber = xint / 2 + 1;
- String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
- exonNumber, proteinName, proteinId);
-
- SequenceFeature sf = makeCdsFeature(cds, desc, begin, end,
- sourceDb, vals);
-
- sf.setEnaLocation(feature.getLocation());
- boolean forwardStrand = exonStart <= exonEnd;
- sf.setStrand(forwardStrand ? "+" : "-");
- sf.setPhase(String.valueOf(codonStart - 1));
- sf.setValue(FeatureProperties.EXONPOS, exonNumber);
- sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
-
- dna.addSequenceFeature(sf);
- }
- }
-
- /*
- * add feature dbRefs to sequence, and mappings for Uniprot xrefs
- */
- boolean hasUniprotDbref = false;
- if (feature.dbRefs != null)
- {
- boolean mappingUsed = false;
- for (DBRefEntry ref : feature.dbRefs)
- {
- /*
- * ensure UniProtKB/Swiss-Prot converted to UNIPROT
- */
- String source = DBRefUtils.getCanonicalName(ref.getSource());
- ref.setSource(source);
- DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
- ref.getVersion(), ref.getAccessionId());
- if (source.equals(DBRefSource.UNIPROT))
- {
- String proteinSeqName = DBRefSource.UNIPROT + "|"
- + ref.getAccessionId();
- if (dnaToProteinMapping != null
- && dnaToProteinMapping.getTo() != null)
- {
- if (mappingUsed)
- {
- /*
- * two or more Uniprot xrefs for the same CDS -
- * each needs a distinct Mapping (as to a different sequence)
- */
- dnaToProteinMapping = new Mapping(dnaToProteinMapping);
- }
- mappingUsed = true;
-
- /*
- * try to locate the protein mapped to (possibly by a
- * previous CDS feature); if not found, construct it from
- * the EMBL translation
- */
- SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
- if (proteinSeq == null)
- {
- proteinSeq = new Sequence(proteinSeqName,
- product.getSequenceAsString());
- matcher.add(proteinSeq);
- peptides.add(proteinSeq);
- }
- dnaToProteinMapping.setTo(proteinSeq);
- dnaToProteinMapping.setMappedFromId(proteinId);
- proteinSeq.addDBRef(proteinDbRef);
- ref.setMap(dnaToProteinMapping);
- }
- hasUniprotDbref = true;
- }
- if (product != null)
- {
- /*
- * copy feature dbref to our protein product
- */
- DBRefEntry pref = proteinDbRef;
- pref.setMap(null); // reference is direct
- product.addDBRef(pref);
- // Add converse mapping reference
- if (dnaToProteinMapping != null)
- {
- Mapping pmap = new Mapping(dna,
- dnaToProteinMapping.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getSequenceVersion(),
- this.getAccession());
- pref.setMap(pmap);
- if (dnaToProteinMapping.getTo() != null)
- {
- dnaToProteinMapping.getTo().addDBRef(pref);
- }
- }
- }
- dna.addDBRef(ref);
- }
- }
-
- /*
- * if we have a product (translation) but no explicit Uniprot dbref
- * (example: EMBL AAFI02000057 protein_id EAL65544.1)
- * then construct mappings to an assumed EMBLCDSPROTEIN accession
- */
- if (!hasUniprotDbref && product != null)
- {
- if (proteinToEmblProteinRef == null)
- {
- // assuming CDSPROTEIN sequence version = dna version (?!)
- proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
- getSequenceVersion(), proteinId);
- }
- product.addDBRef(proteinToEmblProteinRef);
-
- if (dnaToProteinMapping != null
- && dnaToProteinMapping.getTo() != null)
- {
- DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, getSequenceVersion(),
- proteinId);
- dnaToEmblProteinRef.setMap(dnaToProteinMapping);
- dnaToProteinMapping.setMappedFromId(proteinId);
- dna.addDBRef(dnaToEmblProteinRef);
- }
- }
- }
-
- /**
- * Helper method to construct a SequenceFeature for one cds range
- *
- * @param type
- * feature type ("CDS")
- * @param desc
- * description
- * @param begin
- * start position
- * @param end
- * end position
- * @param group
- * feature group
- * @param vals
- * map of 'miscellaneous values' for feature
- * @return
- */
- protected SequenceFeature makeCdsFeature(String type, String desc,
- int begin, int end, String group, Map<String, String> vals)
- {
- SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
- 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 single array 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.location == null)
- {
- return new int[] {};
- }
-
- try
- {
- List<int[]> ranges = DnaUtils.parseLocation(feature.location);
- return listToArray(ranges);
- } catch (ParseException e)
- {
- Cache.log.warn(
- String.format("Not parsing inexact CDS location %s in ENA %s",
- feature.location, this.accession));
- return new int[] {};
- }
- }
-
- /**
- * Converts a list of [start, end] ranges to a single array of [start, end,
- * start, end ...]
- *
- * @param ranges
- * @return
- */
- int[] listToArray(List<int[]> ranges)
- {
- int[] result = new int[ranges.size() * 2];
- int i = 0;
- for (int[] range : ranges)
- {
- result[i++] = range[0];
- result[i++] = range[1];
- }
- return result;
- }
-
- /**
- * Truncates (if necessary) the exon intervals to match 3 times the length of
- * the protein; also accepts 3 bases longer (for stop codon not included in
- * protein)
- *
- * @param proteinLength
- * @param exon
- * an array of [start, end, start, end...] intervals
- * @return the same array (if unchanged) or a truncated copy
- */
- static int[] adjustForProteinLength(int proteinLength, int[] exon)
- {
- if (proteinLength <= 0 || exon == null)
- {
- return exon;
- }
- int expectedCdsLength = proteinLength * 3;
- int exonLength = MappingUtils.getLength(Arrays.asList(exon));
-
- /*
- * if exon length matches protein, or is shorter, or longer by the
- * length of a stop codon (3 bases), then leave it unchanged
- */
- if (expectedCdsLength >= exonLength
- || expectedCdsLength == exonLength - 3)
- {
- return exon;
- }
-
- int origxon[];
- int sxpos = -1;
- int endxon = 0;
- origxon = new int[exon.length];
- System.arraycopy(exon, 0, origxon, 0, exon.length);
- int cdspos = 0;
- for (int x = 0; x < exon.length; x += 2)
- {
- cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
- if (expectedCdsLength <= cdspos)
- {
- // advanced beyond last codon.
- sxpos = x;
- if (expectedCdsLength != cdspos)
- {
- // System.err
- // .println("Truncating final exon interval on region by "
- // + (cdspos - cdslength));
- }
-
- /*
- * shrink the final exon - reduce end position if forward
- * strand, increase it if reverse
- */
- if (exon[x + 1] >= exon[x])
- {
- endxon = exon[x + 1] - cdspos + expectedCdsLength;
- }
- else
- {
- endxon = exon[x + 1] + cdspos - expectedCdsLength;
- }
- 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;
- }
-
- public String getSequenceVersion()
- {
- return sequenceVersion;
- }
-
- public void setSequenceVersion(String sequenceVersion)
- {
- this.sequenceVersion = sequenceVersion;
- }
-
- public String getSequenceLength()
- {
- return sequenceLength;
- }
-
- public void setSequenceLength(String sequenceLength)
- {
- this.sequenceLength = sequenceLength;
- }
-
- public String getEntryVersion()
- {
- return entryVersion;
- }
-
- public void setEntryVersion(String entryVersion)
- {
- this.entryVersion = entryVersion;
- }
-
- public String getMoleculeType()
- {
- return moleculeType;
- }
-
- public void setMoleculeType(String moleculeType)
- {
- this.moleculeType = moleculeType;
- }
-
- public String getTopology()
- {
- return topology;
- }
-
- public void setTopology(String topology)
- {
- this.topology = topology;
- }
-
- public String getTaxonomicDivision()
- {
- return taxonomicDivision;
- }
-
- public void setTaxonomicDivision(String taxonomicDivision)
- {
- this.taxonomicDivision = taxonomicDivision;
- }
-
- public String getDescription()
- {
- return description;
- }
-
- public void setDescription(String description)
- {
- this.description = description;
- }
-
- public String getFirstPublicDate()
- {
- return firstPublicDate;
- }
-
- public void setFirstPublicDate(String firstPublicDate)
- {
- this.firstPublicDate = firstPublicDate;
- }
-
- public String getFirstPublicRelease()
- {
- return firstPublicRelease;
- }
-
- public void setFirstPublicRelease(String firstPublicRelease)
- {
- this.firstPublicRelease = firstPublicRelease;
- }
-
- public String getLastUpdatedDate()
- {
- return lastUpdatedDate;
- }
-
- public void setLastUpdatedDate(String lastUpdatedDate)
- {
- this.lastUpdatedDate = lastUpdatedDate;
- }
-
- public String getLastUpdatedRelease()
- {
- return lastUpdatedRelease;
- }
-
- public void setLastUpdatedRelease(String lastUpdatedRelease)
- {
- this.lastUpdatedRelease = lastUpdatedRelease;
- }
-
- public String getDataClass()
- {
- return dataClass;
- }
-
- public void setDataClass(String dataClass)
- {
- this.dataClass = dataClass;
- }
-}
git://source.jalview.org / jalview.git / blobdiff