X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=e39f0ab2f0eb3a95c610229b59d2441239795c83;hb=1724567f3dfc3b4637aac7bdeb6633628e6a8335;hp=b83f558a9cb5582ea9ea868fb29000389e8d9a0e;hpb=7b9c6bc2db695c996b7bd4e536a6718b22042125;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index b83f558..e39f0ab 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -20,7 +20,9 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.bin.Cache;
+import java.util.Locale;
+
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.io.DataSourceType;
@@ -36,7 +38,6 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
  */
 public abstract class Xfam extends DbSourceProxyImpl
 {
-
   public Xfam()
   {
     super();
@@ -64,10 +65,7 @@ public abstract class Xfam extends DbSourceProxyImpl
     // TODO: trap HTTP 404 exceptions and return null
     String xfamUrl = getURL(queries);
 
-    if (Cache.log != null)
-    {
-      Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
-    }
+    Console.debug("XFAM URL for retrieval is: " + xfamUrl);
 
     AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
             DataSourceType.URL, FileFormat.Stockholm);
@@ -76,11 +74,11 @@ public abstract class Xfam extends DbSourceProxyImpl
     {
       rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
               // getDbSource(),
-              getDbVersion(), queries.trim().toUpperCase()));
+              getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
       if (!getDbSource().equals(getXfamSource()))
       { // add the specific ref too
         rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
-                getDbVersion(), queries.trim().toUpperCase()));
+                getDbVersion(), queries.trim().toUpperCase(Locale.ROOT)));
       }
     }
     stopQuery();
@@ -89,7 +87,7 @@ public abstract class Xfam extends DbSourceProxyImpl
 
   String getURL(String queries)
   {
-    return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
+    return getURLPrefix() + "/family/" + queries.trim().toUpperCase(Locale.ROOT)
             + getURLSuffix();
   }