JAL-1675 Chimera highlight side-chain; timeout added to REST calls

[jalview.git] / src / jalview / ext / paradise / Annotate3D.java

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 4842033..68625bc 100644 (file)
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/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.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.ext.paradise;
 
+import jalview.util.MessageManager;
 import jalview.ws.HttpClientUtils;
 
 import java.io.IOException;
@@ -28,7 +29,6 @@ import java.io.Reader;
 import java.io.StringReader;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Iterator;
 import java.util.List;
 
@@ -36,7 +36,6 @@ import org.apache.http.NameValuePair;
 import org.apache.http.message.BasicNameValuePair;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
-import org.json.simple.JSONStreamAware;
 import org.json.simple.parser.ContentHandler;
 import org.json.simple.parser.ParseException;
 
@@ -137,7 +136,7 @@ public class Annotate3D
     // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
     // vals));
     ArrayList<Reader> readers = new ArrayList<Reader>();
-    readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+    readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0));
     return readers.iterator();
 
   }
@@ -189,14 +188,14 @@ public class Annotate3D
         @Override
         public void remove()
         {
-          throw new Error("Remove: Not implemented");
+          throw new Error(MessageManager.getString("error.not_implemented_remove"));
 
         }
 
         @Override
         protected Object clone() throws CloneNotSupportedException
         {
-          throw new CloneNotSupportedException("Clone: Not implemented");
+          throw new CloneNotSupportedException(MessageManager.getString("error.not_implemented_clone"));
         }
 
         @Override
@@ -217,8 +216,7 @@ public class Annotate3D
       };
     } catch (Exception foo)
     {
-      throw new Exception(
-              "Couldn't parse response from Annotate3d server.", foo);
+      throw new Exception(MessageManager.getString("exception.couldnt_parse_responde_from_annotated3d_server"), foo);
     }
 
   }