X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=3f890ba7293f7eabd9a11872e2d830d39c54c103;hb=d62b90cb6effb7b380e5f7d590691dd884b024cf;hp=bc1e5ab9b0bef65ff61b796012035845ce54940d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index bc1e5ab..3f890ba 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,22 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
@@ -25,11 +33,14 @@ import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-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;
@@ -46,13 +57,11 @@ public class EmblEntry
String lastUpdated;
- Vector keywords;
+ Vector keywords;
- Vector refs;
+ Vector dbRefs;
- Vector dbRefs;
-
- Vector features;
+ Vector features;
EmblSequence sequence;
@@ -76,7 +85,7 @@ public class EmblEntry
/**
* @return the dbRefs
*/
- public Vector getDbRefs()
+ public Vector getDbRefs()
{
return dbRefs;
}
@@ -85,7 +94,7 @@ public class EmblEntry
* @param dbRefs
* the dbRefs to set
*/
- public void setDbRefs(Vector dbRefs)
+ public void setDbRefs(Vector dbRefs)
{
this.dbRefs = dbRefs;
}
@@ -110,7 +119,7 @@ public class EmblEntry
/**
* @return the features
*/
- public Vector getFeatures()
+ public Vector getFeatures()
{
return features;
}
@@ -119,7 +128,7 @@ public class EmblEntry
* @param features
* the features to set
*/
- public void setFeatures(Vector features)
+ public void setFeatures(Vector features)
{
this.features = features;
}
@@ -127,7 +136,7 @@ public class EmblEntry
/**
* @return the keywords
*/
- public Vector getKeywords()
+ public Vector getKeywords()
{
return keywords;
}
@@ -136,7 +145,7 @@ public class EmblEntry
* @param keywords
* the keywords to set
*/
- public void setKeywords(Vector keywords)
+ public void setKeywords(Vector keywords)
{
this.keywords = keywords;
}
@@ -159,23 +168,6 @@ public class EmblEntry
}
/**
- * @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()
@@ -187,7 +179,7 @@ public class EmblEntry
* @param releaseCreated
* the releaseCreated to set
*/
- public void setRcreated(String releaseCreated)
+ public void setRCreated(String releaseCreated)
{
this.rCreated = releaseCreated;
}
@@ -422,9 +414,13 @@ public class EmblEntry
{ 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()))
+ {
;
+ }
+ }
}
try
{
@@ -437,7 +433,9 @@ public class EmblEntry
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
@@ -453,7 +451,9 @@ public class EmblEntry
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
}
@@ -579,16 +579,17 @@ public class EmblEntry
}
}
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(prid, prseq, 1, prseq.length());
- product
- .setDescription(((prname.length() == 0) ? "Protein Product from "
- + sourceDb
- : prname));
+ product.setDescription(((prname.length() == 0) ? "Protein Product from "
+ + sourceDb
+ : prname));
if (!noPeptide)
{
// Protein is also added to vector of sequences returned
@@ -657,8 +658,14 @@ public class EmblEntry
// { 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);
+
+ }
+
}
}
// add cds feature to dna seq - this may include the stop codon
@@ -669,18 +676,20 @@ public class EmblEntry
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + (int) (xint / 2))
+ 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)
{
- Enumeration kv = vals.elements();
+ Enumeration kv = vals.keys();
while (kv.hasMoreElements())
{
Object key = kv.nextElement();
if (key != null)
+ {
sf.setValue(key.toString(), vals.get(key));
+ }
}
}
dna.addSequenceFeature(sf);
@@ -710,19 +719,20 @@ public class EmblEntry
+ 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)
{
@@ -732,6 +742,33 @@ public class EmblEntry
}
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);
+ }
+ }
+ }
}
}