JAL-1919 code improvement to make PDB sequence fetcher file format configurable....

[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 455dcb5..17f1842 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -165,7 +165,7 @@ public class Uniprot extends DbSourceProxyImpl
       // uniprotxml parameter required since december 2007
       // uniprotkb dbname changed introduced december 2008
       File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
-              null);
+              null, ".xml");
       Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
 
       if (entries != null)
@@ -271,7 +271,9 @@ public class Uniprot extends DbSourceProxyImpl
   public static String getUniprotEntryId(UniprotEntry entry)
   {
     StringBuilder name = new StringBuilder(32);
-    name.append("UniProt/Swiss-Prot");
+    // name.append("UniProt/Swiss-Prot");
+    // use 'canonicalised' name for optimal id matching
+    name.append(DBRefSource.UNIPROT);
     for (String accessionId : entry.getAccession())
     {
       name.append(BAR_DELIMITER);