/*
* 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.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 java.util.Hashtable;
import java.util.Map.Entry;
import java.util.Vector;
/**
* 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/embl/x53828/emblxml
*
* @see embl_mapping.xml
*/
public class EmblEntry
{
String accession;
String version;
String taxDivision;
String desc;
String rCreated;
String rLastUpdated;
String lastUpdated;
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 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 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 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;
}
/*
* EMBL Feature support is limited. The text below is included for the benefit
* of any developer working on improving EMBL feature import in Jalview.
* Extract from EMBL feature specification see
* http://www.embl-ebi.ac.uk/embl/Documentation
* /FT_definitions/feature_table.html 3.5 Location 3.5.1 Purpose
*
* The location indicates the region of the presented sequence which
* corresponds to a feature.
*
* 3.5.2 Format and conventions The location contains at least one sequence
* location descriptor and may contain one or more operators with one or more
* sequence location descriptors. Base numbers refer to the numbering in the
* entry. This numbering designates the first base (5' end) of the presented
* sequence as base 1. Base locations beyond the range of the presented
* sequence may not be used in location descriptors, the only exception being
* location in a remote entry (see 3.5.2.1, e).
*
* Location operators and descriptors are discussed in more detail below.
*
* 3.5.2.1 Location descriptors
*
* The location descriptor can be one of the following: (a) a single base
* number (b) a site between two indicated adjoining bases (c) a single base
* chosen from within a specified range of bases (not allowed for new entries)
* (d) the base numbers delimiting a sequence span (e) a remote entry
* identifier followed by a local location descriptor (i.e., a-d)
*
* A site between two adjoining nucleotides, such as endonucleolytic cleavage
* site, is indicated by listing the two points separated by a carat (^). The
* permitted formats for this descriptor are n^n+1 (for example 55^56), or,
* for circular molecules, n^1, where "n" is the full length of the molecule,
* ie 1000^1 for circular molecule with length 1000.
*
* A single base chosen from a range of bases is indicated by the first base
* number and the last base number of the range separated by a single period
* (e.g., '12.21' indicates a single base taken from between the indicated
* points). From October 2006 the usage of this descriptor is restricted : it
* is illegal to use "a single base from a range" (c) either on its own or in
* combination with the "sequence span" (d) descriptor for newly created
* entries. The existing entries where such descriptors exist are going to be
* retrofitted.
*
* Sequence spans are indicated by the starting base number and the ending
* base number separated by two periods (e.g., '34..456'). The '<' and '>'
* symbols may be used with the starting and ending base numbers to indicate
* that an end point is beyond the specified base number. The starting and
* ending base positions can be represented as distinct base numbers
* ('34..456') or a site between two indicated adjoining bases.
*
* A location in a remote entry (not the entry to which the feature table
* belongs) can be specified by giving the accession-number and sequence
* version of the remote entry, followed by a colon ":", followed by a
* location descriptor which applies to that entry's sequence (i.e.
* J12345.1:1..15, see also examples below)
*
* 3.5.2.2 Operators
*
* The location operator is a prefix that specifies what must be done to the
* indicated sequence to find or construct the location corresponding to the
* feature. A list of operators is given below with their definitions and most
* common format.
*
* complement(location) Find the complement of the presented sequence in the
* span specified by " location" (i.e., read the complement of the presented
* strand in its 5'-to-3' direction)
*
* join(location,location, ... location) The indicated elements should be
* joined (placed end-to-end) to form one contiguous sequence
*
* order(location,location, ... location) The elements can be found in the
* specified order (5' to 3' direction), but nothing is implied about the
* reasonableness about joining them
*
* Note : location operator "complement" can be used in combination with
* either " join" or "order" within the same location; combinations of "join"
* and "order" within the same location (nested operators) are illegal.
*
*
*
* 3.5.3 Location examples
*
* The following is a list of common location descriptors with their meanings:
*
* Location Description
*
* 467 Points to a single base in the presented sequence
*
* 340..565 Points to a continuous range of bases bounded by and including the
* starting and ending bases
*
* <345..500 Indicates that the exact lower boundary point of a feature is
* unknown. The location begins at some base previous to the first base
* specified (which need not be contained in the presented sequence) and
* continues to and includes the ending base
*
* <1..888 The feature starts before the first sequenced base and continues to
* and includes base 888
*
* 1..>888 The feature starts at the first sequenced base and continues beyond
* base 888
*
* 102.110 Indicates that the exact location is unknown but that it is one of
* the bases between bases 102 and 110, inclusive
*
* 123^124 Points to a site between bases 123 and 124
*
* join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
* form one contiguous sequence
*
*
* complement(34..126) Start at the base complementary to 126 and finish at
* the base complementary to base 34 (the feature is on the strand
* complementary to the presented strand)
*
*
* complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
* to 5163, then complements the joined segments (the feature is on the strand
* complementary to the presented strand)
*
* join(complement(4918..5163),complement(2691..4571)) Complements regions
* 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
* feature is on the strand complementary to the presented strand)
*
* J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
* this database) with primary accession number 'J00194'
*
* join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
* with the region 100..202 of remote entry J00194
*/
/**
* Recover annotated sequences from EMBL file
*
* @param noNa
* don't return nucleic acid sequences
* @param sourceDb
* TODO
* @param noProtein
* don't return any translated protein sequences marked in features
* @return dataset sequences with DBRefs and features - DNA always comes first
*/
public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
boolean noPeptide, String sourceDb)
{ // TODO: ensure emblEntry.getSequences behaves correctly for returning all
// cases of noNa and noPeptide
Vector seqs = new Vector();
Sequence dna = null;
if (!noNa)
{
// In theory we still need to create this if noNa is set to avoid a null
// pointer exception
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 (!noNa)
{
if (feature.dbRefs != null)
{
for (DBRefEntry dbref : feature.dbRefs)
{
dna.addDBRef(dbref);
}
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
}
else
{
// General feature type.
// TODO this is just duplicated code ??
if (!noNa)
{
if (feature.dbRefs != null)
{
for (DBRefEntry dbref : feature.dbRefs)
{
dna.addDBRef(dbref);
}
}
}
}
}
} 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);
}
if (!noNa && dna != null)
{
seqs.add(dna);
}
SequenceI[] sqs = new SequenceI[seqs.size()];
for (int i = 0, j = seqs.size(); i < j; i++)
{
sqs[i] = seqs.elementAt(i);
seqs.set(i, null);
}
return sqs;
}
/**
* attempt to extract coding region and product from a feature and properly
* decorate it with annotations.
*
* @param feature
* coding feature
* @param sourceDb
* source database for the EMBLXML
* @param seqs
* place where sequences go
* @param dna
* parent dna sequence for this record
* @param noPeptide
* flag for generation of Peptide sequence objects
*/
private void parseCodingFeature(EmblFeature feature, String sourceDb,
Vector seqs, Sequence dna, boolean noPeptide)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
// extract coding region(s)
jalview.datamodel.Mapping map = null;
int[] exon = null;
if (feature.locations != null)
{
for (EmblFeatureLocations loc : feature.locations)
{
int[] se = loc.getElementRanges(accession);
if (exon == null)
{
exon = se;
}
else
{
int[] t = new int[exon.length + se.length];
System.arraycopy(exon, 0, t, 0, exon.length);
System.arraycopy(se, 0, t, exon.length, se.length);
exon = t;
}
}
}
String prseq = null;
String prname = new String();
String prid = null;
Hashtable vals = new Hashtable();
int prstart = 1;
// get qualifiers
if (feature.getQualifiers() != null)
{
for (Qualifier q : feature.getQualifiers())
{
String qname = q.getName();
if (qname.equals("translation"))
{
StringBuilder prsq = new StringBuilder(q.getValues()[0]);
int p = prsq.indexOf(" ");
while (p > -1)
{
prsq.deleteCharAt(p);
p = prsq.indexOf(" ", p);
}
prseq = prsq.toString();
prsq = null;
}
else if (qname.equals("protein_id"))
{
prid = q.getValues()[0];
}
else if (qname.equals("codon_start"))
{
prstart = Integer.parseInt(q.getValues()[0]);
}
else if (qname.equals("product"))
{
prname = q.getValues()[0];
}
else
{
// throw anything else into the additional properties hash
String[] s = q.getValues();
StringBuilder sb = new StringBuilder();
if (s != null)
{
for (int i = 0; i < s.length; i++)
{
sb.append(s[i]);
sb.append("\n");
}
}
vals.put(qname, sb.toString());
}
}
}
Sequence product = null;
DBRefEntry protEMBLCDS = null;
exon = adjustForPrStart(prstart, exon);
boolean noProteinDbref = true;
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
product = new Sequence(prid, prseq, 1, prseq.length());
product.setDescription(((prname.length() == 0) ? "Protein Product from "
+ sourceDb
: prname));
if (!noPeptide)
{
// Protein is also added to vector of sequences returned
seqs.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 - prstart + 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() + (prstart - 1), dna.getEnd() };
map = new jalview.datamodel.Mapping(product, exon, new int[]
{ 1, prseq.length() }, 3, 1);
}
if ((prseq.length() + 1) * 3 == (1 - prstart + 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() + (prstart - 1), dna.getEnd() - 3 };
map = new jalview.datamodel.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 trunctation check
map = new jalview.datamodel.Mapping(product,
adjustForProteinLength(prseq.length(), exon), 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.
jalview.util.MapList mp = new jalview.util.MapList(new int[]
{ 1, prseq.length() }, new int[]
{ 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
// { 1 + (prstart - 1) * 3,
// 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
// { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
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 = new SequenceFeature();
sf.setBegin(exon[xint]);
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
sf.setDescription("Exon " + (1 + xint / 2) + " for protein '"
+ prname + "' EMBLCDS:" + prid);
sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
sf.setValue(FeatureProperties.EXONPRODUCT, prname);
if (vals != null)
{
for (Entry val : vals.entrySet())
{
sf.setValue(val.getKey(), val.getValue());
}
}
dna.addSequenceFeature(sf);
}
}
// add dbRefs to sequence
if (feature.dbRefs != null)
{
for (DBRefEntry ref : feature.dbRefs)
{
ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
.getSource()));
// Hard code the kind of protein product accessions that EMBL cite
if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
{
ref.setMap(map);
if (map != null && map.getTo() != null)
{
map.getTo().addDBRef(
new DBRefEntry(ref.getSource(), ref.getVersion(), ref
.getAccessionId())); // don't copy map over.
if (map.getTo().getName().indexOf(prid) == 0)
{
map.getTo().setName(
jalview.datamodel.DBRefSource.UNIPROT + "|"
+ ref.getAccessionId());
}
}
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);
}
}
}
}
}
private int[] adjustForPrStart(int prstart, int[] exon)
{
int origxon[], sxpos = -1;
int sxstart, sxstop; // unnecessary variables used for debugging
// first adjust range for codon start attribute
if (prstart > 1)
{
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 += exon[x + 1] - exon[x] + 1;
if (prstart <= cdspos)
{
sxpos = x;
sxstart = exon[x];
sxstop = exon[x + 1];
// and adjust start boundary of first exon.
exon[x] = exon[x + 1] - cdspos + prstart;
break;
}
}
if (sxpos > 0)
{
int[] nxon = new int[exon.length - sxpos];
System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
exon = nxon;
}
}
return exon;
}
/**
* 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;
int sxstart, sxstop; // unnecessary variables used for debugging
// 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 += exon[x + 1] - exon[x] + 1;
if (cdslength <= cdspos)
{
// advanced beyond last codon.
sxpos = x;
sxstart = exon[x];
sxstop = exon[x + 1];
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;
}
}