X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=5b75206147a3fc549f58ed6f3cf31b03764450d4;hb=61ba3fbbcf553e5945051ae4f7ab185ddd2e6dca;hp=66a3564dcb86c6d6e111c0749920d56a9eee741b;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 66a3564..5b75206 100644
--- 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 2.8.2b1)
- * 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.
  * 
@@ -23,13 +23,13 @@ package jalview.ext.paradise;
 import jalview.util.MessageManager;
 import jalview.ws.HttpClientUtils;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
 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;
 
@@ -37,7 +37,6 @@ 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;
 
@@ -46,13 +45,20 @@ import org.json.simple.parser.ParseException;
  * 
  * @author jimp
  * 
- *         History: v1.0 revised from original due to refactoring of
- *         paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
- *         http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview
+ * @version v1.0 revised from original due to refactoring of
+ *          paradise-ubmc.u-strasbg.fr/webservices/annotate3d to
+ *          http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview <br/>
+ *          See also testing URL from fjossinet:<br/>
+ *          http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d <br/>
+ *          If in doubt, check against the REST client at:
+ *          https://github.com/fjossinet/RNA-Science
+ *          -Toolbox/blob/master/pyrna/restclient.py
  */
 public class Annotate3D
 {
-  private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
+  // also test with
+  // "http://charn2-ibmc.u-strasbg.fr:8080/api/compute/2d";
+  private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d?tool=rnaview";
 
   private static ContentHandler createContentHandler()
   {
@@ -138,7 +144,9 @@ public class Annotate3D
     // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
     // vals));
     ArrayList<Reader> readers = new ArrayList<Reader>();
-    readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+    final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
+            twoDtoolsURL, vals, 0, 0);
+    readers.add(postResponse);
     return readers.iterator();
 
   }
@@ -190,14 +198,16 @@ public class Annotate3D
         @Override
         public void remove()
         {
-          throw new Error(MessageManager.getString("error.not_implemented_remove"));
+          throw new Error(
+                  MessageManager.getString("error.not_implemented_remove"));
 
         }
 
         @Override
         protected Object clone() throws CloneNotSupportedException
         {
-          throw new CloneNotSupportedException(MessageManager.getString("error.not_implemented_clone"));
+          throw new CloneNotSupportedException(
+                  MessageManager.getString("error.not_implemented_clone"));
         }
 
         @Override
@@ -218,7 +228,10 @@ public class Annotate3D
       };
     } catch (Exception foo)
     {
-      throw new Exception(MessageManager.getString("exception.couldnt_parse_responde_from_annotated3d_server"), foo);
+      throw new Exception(
+              MessageManager
+                      .getString("exception.couldnt_parse_responde_from_annotated3d_server"),
+              foo);
     }
 
   }