X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=022ae6d6ff399be4ee3f8a1a6bb03ef27c3eea06;hb=9a68d6293a1d0ded59716fa34826fb4af793c330;hp=4502b3956fc8fbf4623849b63ad52c8c30134bec;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index 4502b39..022ae6d 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,8 @@
  */
 package jalview.ws.jws1;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.InputStreamParser;
@@ -86,8 +86,10 @@ public class Annotate3D
       AlignmentI al = null;
       while (r.hasNext())
       {
-        FileParse fp = new InputStreamParser(r.next(), source.getDataName());
-        AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+        FileParse fp = new InputStreamParser(r.next(),
+                source.getDataName());
+        AlignmentI nal = new FormatAdapter().readFromFile(fp,
+                FileFormat.Rnaml);
         if (al == null)
         {
           al = nal;
@@ -106,7 +108,8 @@ public class Annotate3D
       }
       else
       {
-        throw new IOException(MessageManager.getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+        throw new IOException(MessageManager.getString(
+                "exception.unexpected_handling_rnaml_translation_for_pdb"),
                 x);
       }
     }
@@ -177,8 +180,8 @@ public class Annotate3D
       URL url = new URL(
               "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
                       + content);
-      BufferedReader is = new BufferedReader(new InputStreamReader(
-              url.openStream()));
+      BufferedReader is = new BufferedReader(
+              new InputStreamReader(url.openStream()));
       String str4;
       while ((str4 = is.readLine()) != null)
       {