JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...

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

diff --git a/src/jalview/ws/dbsources/EmblFlatfileSource.java b/src/jalview/ws/dbsources/EmblFlatfileSource.java
index 2353f22..7d3c6dd 100644 (file)
--- a/src/jalview/ws/dbsources/EmblFlatfileSource.java
+++ b/src/jalview/ws/dbsources/EmblFlatfileSource.java
@@ -1,5 +1,7 @@
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
 import java.io.File;
 import java.io.IOException;
 
@@ -73,13 +75,13 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              dbName.toLowerCase() + ":" + query.trim(), null, "txt");
+              dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
     } catch (Exception e)
     {
       stopQuery();
       throw new Exception(
-              String.format("EBI EMBL XML retrieval failed for %s:%s",
-                      dbName.toLowerCase(), query.trim()),
+              String.format("EBI EMBL retrieval failed for %s:%s",
+                      dbName.toLowerCase(Locale.ROOT), query.trim()),
               e);
     }
     return getEmblSequenceRecords(dbName, query, reply);
@@ -112,4 +114,10 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
     stopQuery();
     return al;
   }
+
+  @Override
+  public boolean isDnaCoding()
+  {
+    return true;
+  }
 }