/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
+import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.util.StringUtils;
-import java.util.Enumeration;
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/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
+ * &format=emblxml
+ *
+ * @see embl_mapping.xml
+ */
public class EmblEntry
{
+ private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
+
String accession;
String version;
String lastUpdated;
- Vector keywords;
-
- Vector refs;
+ Vector<String> keywords;
- Vector dbRefs;
+ Vector<DBRefEntry> dbRefs;
- Vector features;
+ 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 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 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()
* @param releaseCreated
* the releaseCreated to set
*/
- public void setRcreated(String releaseCreated)
+ public void setRCreated(String releaseCreated)
{
this.rCreated = releaseCreated;
}
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
+ * @param peptides
+ * a list of protein products found so far (to add to)
+ * @return dna dataset sequence with DBRefs and features
*/
- 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)
+ public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
+ {
+ SequenceI dna = new Sequence(sourceDb + "|" + accession,
+ sequence.getSequence());
+ dna.setDescription(desc);
+ DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+ dna.addDBRef(retrievedref);
+ // add map to indicate the sequence is a valid coordinate frame for the
+ // dbref
+ retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
+ new int[] { 1, dna.getLength() }, 1, 1));
+ // TODO: transform EMBL Database refs to canonical form
+ if (dbRefs != null)
{
- // 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 (Iterator i = dbRefs.iterator(); i.hasNext(); dna
- .addDBRef((DBRefEntry) i.next()))
- ;
+ for (DBRefEntry dbref : dbRefs)
+ {
+ dna.addDBRef(dbref);
+ }
}
+
try
{
- for (Iterator i = features.iterator(); i.hasNext();)
+ for (EmblFeature feature : features)
{
- EmblFeature feature = (EmblFeature) i.next();
- if (!noNa)
+ if (feature.dbRefs != null)
{
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ for (DBRefEntry dbref : feature.dbRefs)
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
+ dna.addDBRef(dbref);
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
- parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
- }
- else
- {
- // General feature type.
- if (!noNa)
- {
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
- }
- }
+ parseCodingFeature(feature, sourceDb, dna, peptides);
}
}
} catch (Exception e)
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] = (SequenceI) seqs.elementAt(i);
- seqs.set(i, null);
- }
- return sqs;
+
+ return dna;
}
/**
- * attempt to extract coding region and product from a feature and properly
- * decorate it with annotations.
+ * 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 seqs
- * place where sequences go
* @param dna
* parent dna sequence for this record
- * @param noPeptide
- * flag for generation of Peptide sequence objects
+ * @param peptides
+ * list of protein product sequences for Embl entry
*/
- private void parseCodingFeature(EmblFeature feature, String sourceDb,
- Vector seqs, Sequence dna, boolean noPeptide)
+ void parseCodingFeature(EmblFeature feature, String sourceDb,
+ SequenceI dna, List<SequenceI> peptides)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
- // extract coding region(s)
- jalview.datamodel.Mapping map = null;
- int[] exon = null;
- if (feature.locations != null && feature.locations.size() > 0)
- {
- 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;
- }
- }
- }
+
+ int[] exon = getCdsRanges(feature);
+
String prseq = null;
- String prname = new String();
+ String prname = "";
String prid = null;
- Hashtable vals = new Hashtable();
- int prstart = 1;
- // get qualifiers
- if (feature.getQualifiers() != null
- && feature.getQualifiers().size() > 0)
+ Map<String, String> vals = new Hashtable<String, String>();
+ SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
+
+ /*
+ * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
+ * (phase is required for CDS features in GFF3 format)
+ */
+ int codonStart = 1;
+
+ /*
+ * parse qualifiers, saving protein translation, protein id,
+ * codon start position, product (name), and 'other values'
+ */
+ if (feature.getQualifiers() != null)
{
- for (Iterator quals = feature.getQualifiers().iterator(); quals
- .hasNext();)
+ for (Qualifier q : feature.getQualifiers())
{
- Qualifier q = (Qualifier) quals.next();
- if (q.getName().equals("translation"))
+ String qname = q.getName();
+ if (qname.equals("translation"))
{
- StringBuffer prsq = new StringBuffer(q.getValues()[0]);
- int p = prsq.indexOf(" ");
- while (p > -1)
- {
- prsq.deleteCharAt(p);
- p = prsq.indexOf(" ", p);
- }
- prseq = prsq.toString();
- prsq = null;
-
+ // remove all spaces (precompiled String.replaceAll(" ", ""))
+ prseq = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
}
- else if (q.getName().equals("protein_id"))
+ else if (qname.equals("protein_id"))
{
prid = q.getValues()[0];
}
- else if (q.getName().equals("codon_start"))
+ else if (qname.equals("codon_start"))
{
- prstart = Integer.parseInt(q.getValues()[0]);
+ try
+ {
+ codonStart = Integer.parseInt(q.getValues()[0]);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Invalid codon_start in XML for "
+ + accession + ": " + e.getMessage());
+ }
}
- else if (q.getName().equals("product"))
+ else if (qname.equals("product"))
{
+ // sometimes name is returned e.g. for V00488
prname = q.getValues()[0];
}
else
{
// throw anything else into the additional properties hash
- String[] s = q.getValues();
- StringBuffer sb = new StringBuffer();
- if (s != null)
+ String[] qvals = q.getValues();
+ if (qvals != null)
{
- for (int i = 0; i < s.length; i++)
- {
- sb.append(s[i]);
- sb.append("\n");
- }
+ String commaSeparated = StringUtils.arrayToSeparatorList(qvals,
+ ",");
+ vals.put(qname, commaSeparated);
}
- vals.put(q.getName(), sb.toString());
}
}
}
- Sequence product = null;
- exon = adjustForPrStart(prstart, exon);
+ // SequenceI product = null;
+ DBRefEntry protEMBLCDS = null;
+ exon = MappingUtils.removeStartPositions(codonStart - 1, exon);
+ boolean noProteinDbref = true;
+
+ SequenceI product = null;
+ Mapping map = null;
if (prseq != null && prname != null && prid != null)
{
- // extract proteins.
- product = new Sequence(prid, prseq, 1, prseq.length());
- product.setDescription(((prname.length() == 0) ? "Protein Product from "
- + sourceDb
- : prname));
- if (!noPeptide)
+ /*
+ * look for product in peptides list, if not found, add it
+ */
+ product = matcher.findIdMatch(prid);
+ if (product == null)
{
- // Protein is also added to vector of sequences returned
- seqs.add(product);
+ product = new Sequence(prid, prseq, 1, prseq.length());
+ product.setDescription(((prname.length() == 0) ? "Protein Product from "
+ + sourceDb
+ : prname));
+ peptides.add(product);
+ matcher.add(product);
}
+
// we have everything - create the mapping and perhaps the protein
// sequence
if (exon == null || exon.length == 0)
System.err
.println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ sourceDb + ":" + getAccession() + ")");
- if (prseq.length() * 3 == (1 - prstart + dna.getSequence().length))
+ if (prseq.length() * 3 == (1 - codonStart + dna.getSequence().length))
{
System.err
.println("Not allowing for additional stop codon at end of cDNA fragment... !");
// this might occur for CDS sequences where no features are
// marked.
- exon = new int[]
- { dna.getStart() + (prstart - 1), dna.getEnd() };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
- { 1, prseq.length() }, 3, 1);
+ exon = new int[] { dna.getStart() + (codonStart - 1), dna.getEnd() };
+ map = new Mapping(product, exon, new int[] { 1, prseq.length() },
+ 3, 1);
}
- if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
+ if ((prseq.length() + 1) * 3 == (1 - codonStart + dna.getSequence().length))
{
System.err
.println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
- exon = new int[]
- { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
- { 1, prseq.length() }, 3, 1);
+ exon = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() - 3 };
+ map = new Mapping(product, exon, new int[] { 1, prseq.length() },
+ 3, 1);
}
}
else
}
else
{
- // final product length trunctation check
-
- map = new jalview.datamodel.Mapping(product,
- adjustForProteinLength(prseq.length(), exon), new int[]
- { 1, prseq.length() }, 3, 1);
+ // final product length truncation check
+ // TODO should from range include stop codon even if not in protein
+ // in order to include stop codon in CDS sequence (as done for
+ // Ensembl)?
+ int[] cdsRanges = adjustForProteinLength(prseq.length(),
+ exon);
+ map = new Mapping(product, cdsRanges, new int[] { 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
// TODO: this is only necessary when there codon annotation is
// complete (I think JBPNote)
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);
+ MapList mp = new MapList(new int[] { 1, prseq.length() },
+ new int[] { 1 + (codonStart - 1),
+ (codonStart - 1) + 3 * prseq.length() }, 1, 3);
pcdnaref.setMap(new Mapping(mp));
if (product != null)
+ {
product.addDBRef(pcdnaref);
-
+ protEMBLCDS = new DBRefEntry(pcdnaref);
+ protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+ product.addDBRef(protEMBLCDS);
+ }
}
}
// add cds feature to dna seq - this may include the stop codon
for (int xint = 0; exon != null && xint < exon.length; xint += 2)
{
- SequenceFeature sf = new SequenceFeature();
- sf.setBegin(exon[xint]);
- sf.setEnd(exon[xint + 1]);
- sf.setType(feature.getName());
+ SequenceFeature sf = makeCdsFeature(exon, xint, prname, prid, vals,
+ codonStart);
+ sf.setType(feature.getName()); // "CDS"
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + (int) (xint / 2))
- + " for protein '" + prname + "' EMBLCDS:" + prid);
- sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
- sf.setValue(FeatureProperties.EXONPRODUCT, prname);
- 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);
}
}
- // add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+
+ /*
+ * add dbRefs to sequence, and mappings for Uniprot xrefs
+ */
+ if (feature.dbRefs != null)
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ boolean mappingUsed = false;
+ for (DBRefEntry ref : feature.dbRefs)
{
- DBRefEntry ref = (DBRefEntry) dbr.next();
- 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.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
+ if (ref.getSource().equals(DBRefSource.UNIPROT))
{
- ref.setMap(map);
+ String proteinSeqName = DBRefSource.UNIPROT + "|"
+ + ref.getAccessionId();
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)
+ if (mappingUsed)
+ {
+ /*
+ * two or more Uniprot xrefs for the same CDS -
+ * each needs a distinct Mapping (as to a different sequence)
+ */
+ map = new Mapping(map);
+ }
+ mappingUsed = true;
+
+ /*
+ * try to locate the protein mapped to (possibly by a
+ * previous CDS feature)
+ */
+ SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
+ if (proteinSeq == null)
{
- map.getTo().setName(
- jalview.datamodel.DBRefSource.UNIPROT + "|"
- + ref.getAccessionId());
+ proteinSeq = new Sequence(proteinSeqName,
+ product
+ .getSequenceAsString());
+ matcher.add(proteinSeq);
+ peptides.add(proteinSeq);
}
+ map.setTo(proteinSeq);
+ map.getTo().addDBRef(
+ new DBRefEntry(ref.getSource(), ref.getVersion(), ref
+ .getAccessionId()));
+ ref.setMap(map);
}
+ noProteinDbref = false;
}
if (product != null)
{
}
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)
+ /**
+ * Helper method to construct a SequenceFeature for one cds range
+ *
+ * @param exons
+ * array of cds [start, end, ...] positions
+ * @param exonStartIndex
+ * offset into the exons array
+ * @param proteinName
+ * @param proteinAccessionId
+ * @param vals
+ * map of 'miscellaneous values' for feature
+ * @param codonStart
+ * codon start position for CDS (1/2/3, normally 1)
+ * @return
+ */
+ protected SequenceFeature makeCdsFeature(int[] exons, int exonStartIndex,
+ String proteinName, String proteinAccessionId,
+ Map<String, String> vals, int codonStart)
{
-
- int origxon[], sxpos = -1;
- int sxstart, sxstop; // unnecessary variables used for debugging
- // first adjust range for codon start attribute
- if (prstart > 1)
+ 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())
{
- 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)
+ StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for (Entry<String, String> val : vals.entrySet())
{
- cdspos += exon[x + 1] - exon[x] + 1;
- if (prstart <= cdspos)
+ if (!first)
{
- sxpos = x;
- sxstart = exon[x];
- sxstop = exon[x + 1];
- // and adjust start boundary of first exon.
- exon[x] = exon[x + 1] - cdspos + prstart;
- break;
+ sb.append(";");
}
+ sb.append(val.getKey()).append("=").append(val.getValue());
+ first = false;
+ sf.setValue(val.getKey(), val.getValue());
}
+ sf.setAttributes(sb.toString());
+ }
+ return sf;
+ }
- if (sxpos > 0)
- {
- int[] nxon = new int[exon.length - sxpos];
- System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
- exon = nxon;
- }
+ /**
+ * Returns the CDS positions as a list of [start, end, start, end...]
+ * positions. If on the reverse strand, these will be in descending order.
+ *
+ * @param feature
+ * @return
+ */
+ protected int[] getCdsRanges(EmblFeature feature)
+ {
+ if (feature.locations == null)
+ {
+ return new int[] {};
}
- return exon;
+ int cdsBoundaryCount = 0; // count of all start/stop locations
+ int[][] cdsLocations = new int[feature.locations.size()][];
+ int locationNumber = 0;
+ for (EmblFeatureLocations loc : feature.locations)
+ {
+ int[] locationRanges = loc.getElementRanges(accession);
+ cdsLocations[locationNumber++] = locationRanges;
+ cdsBoundaryCount += locationRanges.length;
+ }
+ int[] cdsRanges = new int[cdsBoundaryCount];
+ int copyTo = 0;
+ for (int[] ranges : cdsLocations)
+ {
+ System.arraycopy(ranges, 0, cdsRanges, copyTo, ranges.length);
+ copyTo += ranges.length;
+ }
+ return cdsRanges;
+
}
/**
{
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)
{
int cdspos = 0;
for (int x = 0; x < exon.length && sxpos == -1; x += 2)
{
- cdspos += exon[x + 1] - exon[x] + 1;
+ cdspos += Math.abs(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
git://source.jalview.org / jalview.git / blobdiff