X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;fp=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=c9db7f2979a4b729f1d60fe4c15452bcb8331456;hp=286fc36a142cc4e40972231fca14c70ea603c459;hb=a8c998b5e5debd0dc8a17daa8005a1cc3ca07078;hpb=5221c772a071266446c5c959f34ec89c8e874201

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 286fc36..c9db7f2 100644
--- 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));
-
+    final String uniprotRecordVersion = "" + entry.getVersion();
     /*
      * add a 'self' DBRefEntry for each accession
      */
@@ -202,8 +202,8 @@ public class Uniprot extends DbSourceProxyImpl
     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);
     }
@@ -241,8 +241,11 @@ public class Uniprot extends DbSourceProxyImpl
           // 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]);
+          // TODO: process VARIANT features to allow EMBLCDS record's product to
+          // match Uniprot
+          dbr.setCanonical(true);
           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]
-                : DBRefSource.UNIPROT + ":" + dbVersion;
+                : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
         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]
-                  : DBRefSource.UNIPROT + ":" + dbVersion;
+                  : DBRefSource.UNIPROT + ":" + uniprotRecordVersion;
           dbr = new DBRefEntry(DBRefSource.ENSEMBL,
                   DBRefSource.UNIPROT + ":" + cdsVersion, cdsVrs[0]);
           dbRefs.add(dbr);