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JAL-2353 primary ref candidates that should be promoted should preserve original...
[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
286fc36
..
c9db7f2
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-193,7
+193,7
@@
public class Uniprot extends DbSourceProxyImpl
SequenceI sequence = new Sequence(id, seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
SequenceI sequence = new Sequence(id, seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
-
+ final String uniprotRecordVersion = "" + entry.getVersion();
/*
* add a 'self' DBRefEntry for each accession
*/
/*
* add a 'self' DBRefEntry for each accession
*/
@@
-202,8
+202,8
@@
public class Uniprot extends DbSourceProxyImpl
boolean canonical = true;
for (String accessionId : entry.getAccession())
{
boolean canonical = true;
for (String accessionId : entry.getAccession())
{
- DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
- accessionId, null, canonical);
+ DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT,
+ uniprotRecordVersion, accessionId, null, canonical);
canonical = false;
dbRefs.add(dbRef);
}
canonical = false;
dbRefs.add(dbRef);
}
@@
-241,8
+241,11
@@
public class Uniprot extends DbSourceProxyImpl
// remove version
String[] vrs = cdsId.split("\\.");
String version = vrs.length > 1 ? vrs[1]
// remove version
String[] vrs = cdsId.split("\\.");
String version = vrs.length > 1 ? vrs[1]
- : DBRefSource.UNIPROT + ":" + dbVersion;
+ : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
+ // TODO: process VARIANT features to allow EMBLCDS record's product to
+ // match Uniprot
+ dbr.setCanonical(true);
dbRefs.add(dbr);
}
}
dbRefs.add(dbr);
}
}
@@
-252,7
+255,7
@@
public class Uniprot extends DbSourceProxyImpl
// remove version
String[] vrs = dbref.getId().split("\\.");
String version = vrs.length > 1 ? vrs[1]
// remove version
String[] vrs = dbref.getId().split("\\.");
String version = vrs.length > 1 ? vrs[1]
- : DBRefSource.UNIPROT + ":" + dbVersion;
+ : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
dbr.setAccessionId(vrs[0]);
dbr.setVersion(version);
/*
dbr.setAccessionId(vrs[0]);
dbr.setVersion(version);
/*
@@
-270,7
+273,7
@@
public class Uniprot extends DbSourceProxyImpl
// remove version
String[] cdsVrs = cdsId.split("\\.");
String cdsVersion = cdsVrs.length > 1 ? cdsVrs[1]
// remove version
String[] cdsVrs = cdsId.split("\\.");
String cdsVersion = cdsVrs.length > 1 ? cdsVrs[1]
- : DBRefSource.UNIPROT + ":" + dbVersion;
+ : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
dbr = new DBRefEntry(DBRefSource.ENSEMBL,
DBRefSource.UNIPROT + ":" + cdsVersion, cdsVrs[0]);
dbRefs.add(dbr);
dbr = new DBRefEntry(DBRefSource.ENSEMBL,
DBRefSource.UNIPROT + ":" + cdsVersion, cdsVrs[0]);
dbRefs.add(dbr);