X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=b6f53cd1408a8a321d87c13cf8ab312236c34588;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=8cc0ce440b521a1e60def704cd43cd0ad3f7f54b;hpb=65d7b70ce9788fd1680a5e81b1eaae30126b8ed2;p=jalview.git diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index 8cc0ce4..b6f53cd 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -193,7 +193,8 @@ public class Uniprot extends DbSourceProxyImpl * 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()); @@ -205,10 +206,10 @@ public class Uniprot extends DbSourceProxyImpl { DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion, accessionId); + + // mark dbRef as a primary reference for this sequence dbRefs.add(dbRef); } - sequence.setSourceDBRef((dbRefs != null && dbRefs.size() > 0) ? dbRefs - .get(0) : null); Vector onlyPdbEntries = new Vector(); for (PDBEntry pdb : entry.getDbReference()) @@ -222,6 +223,38 @@ public class Uniprot extends DbSourceProxyImpl { onlyPdbEntries.addElement(pdb); } + if ("EMBL".equals(pdb.getType())) + { + // look for a CDS reference and add it, too. + String cdsId = (String) pdb.getProperty("protein sequence ID"); + if (cdsId != null && cdsId.trim().length() > 0) + { + // remove version + String[] vrs = cdsId.split("\\."); + dbr = new DBRefEntry(DBRefSource.EMBLCDS, vrs.length > 1 ? vrs[1] + : DBRefSource.UNIPROT + ":" + dbVersion, vrs[0]); + dbRefs.add(dbr); + } + } + if ("Ensembl".equals(pdb.getType())) + { + /*UniprotXML + * + * + * + * + * + */ + String cdsId = (String) pdb.getProperty("protein sequence ID"); + if (cdsId != null && cdsId.trim().length() > 0) + { + dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT + + ":" + dbVersion, cdsId.trim()); + dbRefs.add(dbr); + + } + } + } sequence.setPDBId(onlyPdbEntries); @@ -233,7 +266,10 @@ public class Uniprot extends DbSourceProxyImpl sequence.addSequenceFeature(sf); } } - sequence.setDBRefs(dbRefs.toArray(new DBRefEntry[0])); + for (DBRefEntry dbr : dbRefs) + { + sequence.addDBRef(dbr); + } return sequence; }