+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
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;
/**
* @param accession
- * the accession to set
+ * the accession to set
*/
public void setAccession(String accession)
{
/**
* @param dbRefs
- * the dbRefs to set
+ * the dbRefs to set
*/
public void setDbRefs(Vector dbRefs)
{
/**
* @param desc
- * the desc to set
+ * the desc to set
*/
public void setDesc(String desc)
{
/**
* @param features
- * the features to set
+ * the features to set
*/
public void setFeatures(Vector features)
{
/**
* @param keywords
- * the keywords to set
+ * the keywords to set
*/
public void setKeywords(Vector keywords)
{
/**
* @param lastUpdated
- * the lastUpdated to set
+ * the lastUpdated to set
*/
public void setLastUpdated(String lastUpdated)
{
/**
* @param refs
- * the refs to set
+ * the refs to set
*/
public void setRefs(Vector refs)
{
/**
* @param releaseCreated
- * the releaseCreated to set
+ * the releaseCreated to set
*/
public void setRcreated(String releaseCreated)
{
/**
* @param releaseLastUpdated
- * the releaseLastUpdated to set
+ * the releaseLastUpdated to set
*/
public void setRLastUpdated(String releaseLastUpdated)
{
/**
* @param sequence
- * the sequence to set
+ * the sequence to set
*/
public void setSequence(EmblSequence sequence)
{
/**
* @param taxDivision
- * the taxDivision to set
+ * the taxDivision to set
*/
public void setTaxDivision(String taxDivision)
{
/**
* @param version
- * the version to set
+ * the version to set
*/
public void setVersion(String version)
{
* Recover annotated sequences from EMBL file
*
* @param noNa
- * don't return nucleic acid sequences
+ * don't return nucleic acid sequences
* @param sourceDb
- * TODO
+ * TODO
* @param noProtein
- * don't return any translated protein sequences marked in features
+ * 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);
dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
{
for (Iterator i = features.iterator(); i.hasNext();)
{
- boolean nextFeature=false;
EmblFeature feature = (EmblFeature) i.next();
if (!noNa)
{
;
}
}
- if (feature.getName().equalsIgnoreCase("CDS"))
+ if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
- // 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;
- }
- }
- }
- 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)
- {
- 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());
- }
- }
- }
- Sequence product = null;
- if (prseq != null && prname != null && prid != 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)
- {
- 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);
- }
- }
- // add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
- {
- 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);
- }
- }
-
+ parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
}
else
{
} 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());
+ 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)
+ if (!noNa && dna != null)
{
seqs.add(dna);
}
}
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 && 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;
+ }
+ }
+ }
+ 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)
+ {
+ for (Iterator quals = feature.getQualifiers().iterator(); quals
+ .hasNext();)
+ {
+ Qualifier q = (Qualifier) quals.next();
+ if (q.getName().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;
+
+ }
+ 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
+ String[] s = q.getValues();
+ StringBuffer sb = new StringBuffer();
+ if (s != null)
+ {
+ for (int i = 0; i < s.length; i++)
+ {
+ sb.append(s[i]);
+ sb.append("\n");
+ }
+ }
+ vals.put(q.getName(), sb.toString());
+ }
+ }
+ }
+ Sequence product = null;
+ if (prseq != null && prname != null && prid != null)
+ {
+ // extract proteins.
+ product = new Sequence(prid, prseq, prstart, prstart + prseq.length()
+ - 1);
+ 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 == dna.getSequence().length)
+ {
+ // 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);
+ }
+ if ((prseq.length() + 1) * 3 == 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);
+ }
+ }
+ else
+ {
+ 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);
+ // reconstruct the EMBLCDS entry
+ 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);
+ pcdnaref.setMap(new Mapping(mp));
+ if (product != null)
+ product.addDBRef(pcdnaref);
+
+ }
+ }
+ // 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 + (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)
+ {
+ for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+ {
+ 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.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());
+ }
+ }
+ }
+ 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);
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff