X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=022ae6d6ff399be4ee3f8a1a6bb03ef27c3eea06;hb=aad3640b07f836362df7ea025fa09127a0a06145;hp=a30a9a1c161a9a7fc82865facc8670c27c62a991;hpb=1af953b3f29ffe11b7bf298ef3fce773012c49e9;p=jalview.git

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index a30a9a1..022ae6d 100644
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,27 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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;
+import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -31,6 +35,7 @@ import java.io.Reader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLEncoder;
+import java.util.Iterator;
 
 public class Annotate3D
 {
@@ -76,12 +81,25 @@ public class Annotate3D
           sb.append(cbuff[i]);
         }
       }
-
-      FileParse fp = new InputStreamParser(
-              jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
-                      .toString()), source.getDataName());
-      AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
-      return nal;
+      Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+              .getRNAMLForPDBFileAsString(sb.toString());
+      AlignmentI al = null;
+      while (r.hasNext())
+      {
+        FileParse fp = new InputStreamParser(r.next(),
+                source.getDataName());
+        AlignmentI nal = new FormatAdapter().readFromFile(fp,
+                FileFormat.Rnaml);
+        if (al == null)
+        {
+          al = nal;
+        }
+        else
+        {
+          al.append(nal);
+        }
+      }
+      return al;
     } catch (Throwable x)
     {
       if (x instanceof IOException)
@@ -90,8 +108,8 @@ public class Annotate3D
       }
       else
       {
-        throw new IOException(
-                "Unexpected exception when handling RNAML translation of PDB data",
+        throw new IOException(MessageManager.getString(
+                "exception.unexpected_handling_rnaml_translation_for_pdb"),
                 x);
       }
     }
@@ -162,8 +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)
       {