/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
-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 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;
}
* 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,
+ public 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();
+ Vector<SequenceI> seqs = new Vector<SequenceI>();
Sequence dna = null;
if (!noNa)
{
{ 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);
+ }
}
}
}
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;
* flag for generation of Peptide sequence objects
*/
private void parseCodingFeature(EmblFeature feature, String sourceDb,
- Vector seqs, Sequence dna, boolean noPeptide)
+ Vector<SequenceI> seqs, Sequence dna, boolean noPeptide)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
// extract coding region(s)
- jalview.datamodel.Mapping map = null;
+ 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];
}
{
// throw anything else into the additional properties hash
String[] s = q.getValues();
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
if (s != null)
{
for (int i = 0; i < s.length; i++)
sb.append("\n");
}
}
- vals.put(q.getName(), sb.toString());
+ 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)
{
// marked.
exon = new int[]
{ dna.getStart() + (prstart - 1), dna.getEnd() };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
+ map = new Mapping(product, exon, new int[]
{ 1, prseq.length() }, 3, 1);
}
if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
.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[]
+ map = new Mapping(product, exon, new int[]
{ 1, prseq.length() }, 3, 1);
}
}
{
// final product length trunctation check
- map = new jalview.datamodel.Mapping(product,
+ map = new Mapping(product,
adjustForProteinLength(prseq.length(), exon), new int[]
{ 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
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[]
+ MapList mp = new MapList(new int[]
{ 1, prseq.length() }, new int[]
{ 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
// { 1 + (prstart - 1) * 3,
// { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
pcdnaref.setMap(new Mapping(mp));
if (product != null)
+ {
product.addDBRef(pcdnaref);
+ protEMBLCDS = new DBRefEntry(pcdnaref);
+ protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+ product.addDBRef(protEMBLCDS);
+
+ }
}
}
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.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
+ ref.setSource(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(DBRefSource.UNIPROT))
{
ref.setMap(map);
if (map != null && map.getTo() != null)
if (map.getTo().getName().indexOf(prid) == 0)
{
map.getTo().setName(
- jalview.datamodel.DBRefSource.UNIPROT + "|"
+ DBRefSource.UNIPROT + "|"
+ ref.getAccessionId());
}
}
+ 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);
+ }
+ }
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff