Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[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 4030d8c..3afe8ec 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",
-              ".xml");
+              "xml");
       Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
 
       if (entries != null)
@@ -226,8 +226,7 @@ public class Uniprot extends DbSourceProxyImpl
       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)
         {
           // remove version
@@ -246,8 +245,7 @@ public class Uniprot extends DbSourceProxyImpl
         * <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)
         {
           dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT