+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import java.util.Enumeration;
import java.util.Hashtable;
-import java.util.Iterator;
+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 lastUpdated;
- Vector keywords;
+ Vector<String> keywords;
- Vector refs;
+ Vector<DBRefEntry> dbRefs;
- Vector 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;
}
* 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
+ * 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.
*
* 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
*/
public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
boolean noPeptide, String sourceDb)
- {
- Vector seqs = new Vector();
+ { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
+ // cases of noNa and noPeptide
+ Vector<SequenceI> seqs = new Vector<SequenceI>();
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);
- dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
- // TODO: add mapping for parentAccession attribute
+ 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 && feature.dbRefs.size() > 0)
+ if (feature.dbRefs != null)
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
+ for (DBRefEntry dbref : feature.dbRefs)
+ {
+ dna.addDBRef(dbref);
+ }
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
else
{
// General feature type.
+ // TODO this is just duplicated code ??
if (!noNa)
{
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ if (feature.dbRefs != null)
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
+ for (DBRefEntry dbref : feature.dbRefs)
+ {
+ dna.addDBRef(dbref);
+ }
}
}
}
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
System.err.println("EMBL Record Features parsing error!");
System.err
SequenceI[] sqs = new SequenceI[seqs.size()];
for (int i = 0, j = seqs.size(); i < j; i++)
{
- sqs[i] = (SequenceI) seqs.elementAt(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
+ * 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)
+ private void parseCodingFeature(EmblFeature feature, String sourceDb,
+ Vector<SequenceI> 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 && feature.locations.size() > 0)
+ if (feature.locations != null)
{
- for (Enumeration locs = feature.locations.elements(); locs
- .hasMoreElements();)
+ for (EmblFeatureLocations loc : feature.locations)
{
- EmblFeatureLocations loc = (EmblFeatureLocations) locs
- .nextElement();
int[] se = loc.getElementRanges(accession);
if (exon == null)
{
String prseq = null;
String prname = new String();
String prid = null;
- Hashtable vals = new Hashtable();
+ Hashtable<String, String> vals = new Hashtable<String, String>();
int prstart = 1;
// get qualifiers
- if (feature.getQualifiers() != null
- && feature.getQualifiers().size() > 0)
+ 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]);
+ StringBuilder prsq = new StringBuilder(q.getValues()[0]);
int p = prsq.indexOf(" ");
while (p > -1)
{
prsq = null;
}
- 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]);
}
- else if (q.getName().equals("product"))
+ else if (qname.equals("product"))
{
prname = q.getValues()[0];
}
else
{
// throw anything else into the additional properties hash
- vals.put(q.getName(), q.getValues().toString());
+ 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(sourceDb + "|" + "EMBLCDS|" + prid
- +((prname.length()==0) ? "" : " " + prname), prseq, prstart, prstart
- + prseq.length() - 1);
- product.setDescription("Protein Product from " + sourceDb);
-
+ 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
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 == dna.getSequence().length)
+ 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(), dna.getEnd() };
- map = new jalview.datamodel.Mapping(product, exon,
- new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ 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 == dna.getSequence().length)
+ if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
{
- exon = new int[]
- { dna.getStart(), dna.getEnd() - 3 };
- map = new jalview.datamodel.Mapping(product, exon,
- new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ 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
{
- map = new jalview.datamodel.Mapping(product, exon,
- new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ // 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+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1);
+ 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)
+ 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
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + xint) + " for protein '"
+ 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 && vals.size() > 0)
+ if (vals != null)
{
- Enumeration kv = vals.elements();
- while (kv.hasMoreElements())
+ for (Entry<String, String> val : vals.entrySet())
{
- Object key = kv.nextElement();
- if (key != null)
- sf.setValue(key.toString(), vals.get(key));
+ sf.setValue(val.getKey(), val.getValue());
}
}
dna.addSequenceFeature(sf);
}
}
// add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+ if (feature.dbRefs != null)
{
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ 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))
+ if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
{
ref.setMap(map);
- /*if (map.getTo()!=null)
+ if (map != null && map.getTo() != null)
{
- map.getTo().setName(map.getTo().getName()+"|"+ref.getSource()+"|"+ref.getAccessionId());
- }*/
+ 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());
+ 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 = new DBRefEntry(sourceDb, getVersion(),
+ this.getAccession());
pref.setMap(pmap);
- if (map.getTo()!=null)
+ 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;
}
}
git://source.jalview.org / jalview.git / blobdiff