Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[jalview.git] / src / jalview / ws / dbsources / Xfam.java

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index f0cb14b..e39f0ab 100644 (file)
--- 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;
@@ -63,10 +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);
@@ -75,11 +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();
@@ -88,7 +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();
   }