+/*
+ * 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 java.util.Enumeration;
+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.Iterator;
+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 version;
+ String entryVersion;
+
+ String sequenceVersion;
+
+ String dataClass;
- String taxDivision;
+ String moleculeType;
- String desc;
+ String topology;
- String rCreated;
+ String sequenceLength;
- String rLastUpdated;
+ String taxonomicDivision;
- String lastUpdated;
+ String description;
- Vector keywords;
+ String firstPublicDate;
- Vector refs;
+ String firstPublicRelease;
- Vector dbRefs;
+ String lastUpdatedDate;
- Vector features;
+ String lastUpdatedRelease;
+
+ Vector<String> keywords;
+
+ Vector<DBRefEntry> dbRefs;
+
+ Vector<EmblFeature> features;
EmblSequence sequence;
/**
* @return the dbRefs
*/
- public Vector getDbRefs()
+ public Vector<DBRefEntry> getDbRefs()
{
return dbRefs;
}
* @param dbRefs
* the dbRefs to set
*/
- public void setDbRefs(Vector dbRefs)
+ 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 getFeatures()
+ public Vector<EmblFeature> getFeatures()
{
return features;
}
* @param features
* the features to set
*/
- public void setFeatures(Vector features)
+ public void setFeatures(Vector<EmblFeature> features)
{
this.features = features;
}
/**
* @return the keywords
*/
- public Vector getKeywords()
+ public Vector<String> getKeywords()
{
return keywords;
}
* @param keywords
* the keywords to set
*/
- public void setKeywords(Vector keywords)
+ 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 refs
- */
- public Vector getRefs()
- {
- return refs;
- }
-
- /**
- * @param refs
- * the refs to set
- */
- public void setRefs(Vector refs)
- {
- this.refs = refs;
- }
-
- /**
- * @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 the taxDivision
+ * 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 String getTaxDivision()
+ public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
{
- return taxDivision;
- }
+ 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);
+ }
+ }
- /**
- * @param taxDivision
- * the taxDivision to set
- */
- public void setTaxDivision(String taxDivision)
- {
- this.taxDivision = taxDivision;
- }
+ 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 the version
- */
- public String getVersion()
- {
- return version;
+ return dna;
}
/**
- * @param version
- * the version to set
+ * @param sourceDb
+ * @return
*/
- public void setVersion(String version)
+ SequenceI makeSequence(String sourceDb)
{
- this.version = version;
+ 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;
}
- /*
- * 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
+ * Extracts coding region and product from a CDS feature and properly decorate
+ * it with annotations.
*
- * @param noNa
- * don't return nucleic acid sequences
+ * @param feature
+ * coding feature
* @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
+ * 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
*/
- public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
- boolean noPeptide, String sourceDb)
+ void parseCodingFeature(EmblFeature feature, String sourceDb,
+ SequenceI dna, List<SequenceI> peptides,
+ SequenceIdMatcher matcher)
{
- Vector seqs = new Vector();
- Sequence dna = null;
- if (!noNa)
- {
- dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
- dna.setDescription(desc);
- dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
- // TODO: add mapping for parentAccession attribute
- // TODO: transform EMBL Database refs to canonical form
- if (dbRefs != null)
- for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
- .addDBRef((DBRefEntry) i.next()))
- ;
- }
- try
+ 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 (Iterator i = features.iterator(); i.hasNext();)
+ for (Qualifier q : feature.getQualifiers())
{
- boolean nextFeature=false;
- EmblFeature feature = (EmblFeature) i.next();
- if (!noNa)
+ 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"))
{
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ try
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
+ codonStart = Integer.parseInt(q.getValues()[0].trim());
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Invalid codon_start in XML for " + accession
+ + ": " + e.getMessage());
}
}
- if (feature.getName().equalsIgnoreCase("CDS"))
+ else if (qname.equals("product"))
{
- // extract coding region(s)
- jalview.datamodel.Mapping map = null;
- int[] exon = null;
- if (feature.locations != null && feature.locations.size() > 0)
+ // 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)
{
- for (Enumeration locs = feature.locations.elements(); locs
- .hasMoreElements();)
- {
- EmblFeatureLocations loc = (EmblFeatureLocations) locs
- .nextElement();
- 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 commaSeparated = StringUtils.arrayToSeparatorList(qvals,
+ ",");
+ vals.put(qname, commaSeparated);
}
- String prseq = null;
- String prname = new String();
- String prid = null;
- Hashtable vals = new Hashtable();
- int prstart = 1;
- // get qualifiers
- if (feature.getQualifiers() != null
- && feature.getQualifiers().size() > 0)
+ }
+ }
+ }
+
+ 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)
{
- for (Iterator quals = feature.getQualifiers().iterator(); quals
- .hasNext();)
- {
- Qualifier q = (Qualifier) quals.next();
- if (q.getName().equals("translation"))
- {
- prseq = q.getValues()[0];
- }
- else if (q.getName().equals("protein_id"))
- {
- prid = q.getValues()[0];
- }
- else if (q.getName().equals("codon_start"))
- {
- prstart = Integer.parseInt(q.getValues()[0]);
- }
- else if (q.getName().equals("product"))
- {
- prname = q.getValues()[0];
- }
- else
- {
- // throw anything else into the additional properties hash
- vals.put(q.getName(), q.getValues().toString());
- }
- }
+ /*
+ * 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);
}
- Sequence product = null;
- if (prseq != null && prname != null && prid != null)
+ }
+ }
+
+ /*
+ * 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)
{
- // extract proteins.
- if (!noPeptide)
- {
- product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
- + "|" + prname, prseq, prstart, prstart
- + prseq.length() - 1);
- product.setDescription("Protein Product from " + sourceDb);
- seqs.add(product);
- }
- // we have everything - create the mapping and perhaps the protein
- // sequence
- map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
- // add cds feature to dna seq - this may include the stop codon
- for (int xint = 0; xint < exon.length; xint += 2)
+ if (mappingUsed)
{
- SequenceFeature sf = new SequenceFeature();
- sf.setBegin(exon[xint]);
- sf.setEnd(exon[xint + 1]);
- sf.setType(feature.getName());
- sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL);
- sf.setDescription("Exon " + (1 + xint) + " for protein '"
- + prname + "' EMBLCDS:" + prid);
- if (vals != null && vals.size() > 0)
- {
- Enumeration kv = vals.elements();
- while (kv.hasMoreElements())
- {
- Object key = kv.nextElement();
- if (key != null)
- sf.setValue(key.toString(), vals.get(key));
- }
- }
- dna.addSequenceFeature(sf);
+ /*
+ * two or more Uniprot xrefs for the same CDS -
+ * each needs a distinct Mapping (as to a different sequence)
+ */
+ dnaToProteinMapping = new Mapping(dnaToProteinMapping);
}
- }
- // add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ 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)
{
- DBRefEntry ref = (DBRefEntry) dbr.next();
- ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
- .getSource()));
- if (ref.getSource().equals(
- jalview.datamodel.DBRefSource.UNIPROT))
- {
- ref.setMap(map);
- }
- if (product != null)
- {
- DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
- .getVersion(), ref.getAccessionId());
- pref.setMap(null); // reference is direct
- }
- dna.addDBRef(ref);
+ 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;
}
- else
+ if (product != null)
{
- // General feature type.
- if (!noNa)
+ /*
+ * 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)
{
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ Mapping pmap = new Mapping(dna,
+ dnaToProteinMapping.getMap().getInverse());
+ pref = new DBRefEntry(sourceDb, getSequenceVersion(),
+ this.getAccession());
+ pref.setMap(pmap);
+ if (dnaToProteinMapping.getTo() != null)
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
+ dnaToProteinMapping.getTo().addDBRef(pref);
}
}
}
+ dna.addDBRef(ref);
}
- } catch (Exception e)
+ }
+
+ /*
+ * 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)
{
- 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 (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];
}
- if (!noNa && dna!=null)
+ 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)
{
- seqs.add(dna);
+ return exon;
}
- SequenceI[] sqs = new SequenceI[seqs.size()];
- for (int i = 0, j = seqs.size(); i < j; i++)
+ 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)
{
- sqs[i] = (SequenceI) seqs.elementAt(i);
- seqs.set(i, null);
+ return exon;
}
- return sqs;
+
+ 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