/*
* 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 .
* 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 keywords;
Vector dbRefs;
Vector 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 getDbRefs()
{
return dbRefs;
}
/**
* @param dbRefs
* the dbRefs to set
*/
public void setDbRefs(Vector dbRefs)
{
this.dbRefs = dbRefs;
}
/**
* @return the features
*/
public Vector getFeatures()
{
return features;
}
/**
* @param features
* the features to set
*/
public void setFeatures(Vector features)
{
this.features = features;
}
/**
* @return the keywords
*/
public Vector getKeywords()
{
return keywords;
}
/**
* @param keywords
* the keywords to set
*/
public void setKeywords(Vector 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 peptides)
{
SequenceI dna = makeSequence(sourceDb);
if (dna == null)
{
return null;
}
dna.setDescription(description);
DBRefEntry retrievedref = new DBRefEntry(sourceDb,
getSequenceVersion(), accession);
dna.addDBRef(retrievedref);
dna.setSourceDBRef(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 peptides, SequenceIdMatcher matcher)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
int[] exons = getCdsRanges(feature);
String translation = null;
String proteinName = "";
String proteinId = null;
Map 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() + ")");
if (translationLength * 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
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 + dna
.getSequence().length))
{
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
*/
for (int xint = 0; exons != null && xint < exons.length; xint += 2)
{
SequenceFeature sf = makeCdsFeature(exons, xint, proteinName,
proteinId, vals, codonStart);
sf.setType(feature.getName()); // "CDS"
sf.setEnaLocation(feature.getLocation());
sf.setFeatureGroup(sourceDb);
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);
proteinSeq.setSourceDBRef(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);
product.setSourceDBRef(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 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 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 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 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 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;
}
}