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JAL-2609 enabled (still broken/incomplete) fast paint
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Uniprot.java
diff --git
a/src/jalview/ws/dbsources/Uniprot.java
b/src/jalview/ws/dbsources/Uniprot.java
index
7ecd324
..
7261cba
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-28,9
+28,9
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
-import jalview.util.DBRefUtils;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.UniprotFile;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
@@
-166,7
+166,7
@@
public class Uniprot extends DbSourceProxyImpl
// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
- ".xml");
+ "xml");
Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
if (entries != null)
Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
if (entries != null)
@@
-194,7
+194,8
@@
public class Uniprot extends DbSourceProxyImpl
* UniprotEntry
* @return SequenceI instance created from the UniprotEntry instance
*/
* UniprotEntry
* @return SequenceI instance created from the UniprotEntry instance
*/
- public SequenceI uniprotEntryToSequenceI(UniprotEntry entry){
+ public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
+ {
String id = getUniprotEntryId(entry);
SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
.getContent());
String id = getUniprotEntryId(entry);
SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
.getContent());
@@
-226,17
+227,17
@@
public class Uniprot extends DbSourceProxyImpl
if ("EMBL".equals(pdb.getType()))
{
// look for a CDS reference and add it, too.
if ("EMBL".equals(pdb.getType()))
{
// look for a CDS reference and add it, too.
- String cdsId = (String) pdb.getProperty()
- .get("protein sequence ID");
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
if (cdsId != null && cdsId.trim().length() > 0)
{
- dbr = new DBRefEntry(DBRefSource.EMBLCDS, DBRefSource.UNIPROT
- + ":"
- + dbVersion, cdsId.trim());
+ // remove version
+ String[] vrs = cdsId.split("\\.");
+ dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1]
+ : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]);
dbRefs.add(dbr);
}
}
dbRefs.add(dbr);
}
}
- if (false) // "Ensembl".equals(pdb.getType()))
+ if ("Ensembl".equals(pdb.getType()))
{
/*UniprotXML
* <dbReference type="Ensembl" id="ENST00000321556">
{
/*UniprotXML
* <dbReference type="Ensembl" id="ENST00000321556">
@@
-245,36
+246,32
@@
public class Uniprot extends DbSourceProxyImpl
* <property type="gene ID" value="ENSG00000158828"/>
* </dbReference>
*/
* <property type="gene ID" value="ENSG00000158828"/>
* </dbReference>
*/
- String cdsId = (String) pdb.getProperty()
- .get("protein sequence ID");
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
if (cdsId != null && cdsId.trim().length() > 0)
{
- // Only add the product ID
- dbRefs.remove(dbr);
dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
+ ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
}
}
dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
+ ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
}
}
-
}
sequence.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
}
sequence.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
- for (SequenceFeature sf : entry.getFeature())
+ for (UniprotFeature uf : entry.getFeature())
{
{
- sf.setFeatureGroup("Uniprot");
- sequence.addSequenceFeature(sf);
+ SequenceFeature copy = new SequenceFeature(uf.getType(),
+ uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+ copy.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(copy);
}
}
}
}
- // we use setDBRefs to assign refs quickly.
- sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0]));
- // need to use ensurePrimaries to reify any refs that should become primary
- // refs
- DBRefUtils.ensurePrimaries(sequence); // promote any direct refs to primary
- // source dbs
+ for (DBRefEntry dbr : dbRefs)
+ {
+ sequence.addDBRef(dbr);
+ }
return sequence;
}
return sequence;
}