X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fparadise%2FAnnotate3D.java;h=8b74d59cadfe38b23c2bfc06273989373acfcacd;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=b0adb45eca276af14549c58fc7b344b7ec40565a;hpb=ccd574c354cee52f67ab73d28381f44ffe3e5a7c;p=jalview.git

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index b0adb45..8b74d59 100644
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -1,34 +1,248 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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.Iterator;
 import java.util.List;
 
 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.parser.ContentHandler;
+import org.json.simple.parser.ParseException;
 
+/**
+ * simple methods for calling the various paradise RNA tools
+ * 
+ * @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
+ */
 public class Annotate3D
 {
+  private static String twoDtoolsURL = "http://arn-ibmc.in2p3.fr/api/compute/2d";
 
-  public static Reader getRNAMLForPDBFileAsString(String pdbfile)
+  private static ContentHandler createContentHandler()
+  {
+    ContentHandler ch = new ContentHandler()
+    {
+
+      @Override
+      public void startJSON() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public void endJSON() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public boolean startObject() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean endObject() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean startObjectEntry(String key) throws ParseException,
+              IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean endObjectEntry() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean startArray() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean endArray() throws ParseException, IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public boolean primitive(Object value) throws ParseException,
+              IOException
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+    };
+    return ch;
+  }
+
+  public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
           throws Exception
   {
     List<NameValuePair> vals = new ArrayList<NameValuePair>();
+    vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("data", pdbfile));
-    return HttpClientUtils.doHttpUrlPost(
-            "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d",
-            vals);
+    vals.add(new BasicNameValuePair("output", "rnaml"));
+    // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
+    // vals));
+    ArrayList<Reader> readers = new ArrayList<Reader>();
+    final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
+            twoDtoolsURL, vals, 0, 0);
+    readers.add(postResponse);
+    return readers.iterator();
+
   }
 
-  public static Reader getRNAMLForPDBId(String pdbid) throws Exception
+  public static Iterator<Reader> processJsonResponseFor(Reader respons)
+          throws Exception
+  {
+    org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser();
+    try
+    {
+      final JSONArray responses = (JSONArray) jp.parse(respons);
+      final Iterator rvals = responses.iterator();
+      return new Iterator<Reader>()
+      {
+        @Override
+        public boolean hasNext()
+        {
+          return rvals.hasNext();
+        }
+
+        @Override
+        public Reader next()
+        {
+          JSONObject val = (JSONObject) rvals.next();
+
+          Object sval = null;
+          try
+          {
+            sval = val.get("2D");
+          } catch (Exception x)
+          {
+            x.printStackTrace();
+          }
+          ;
+          if (sval == null)
+          {
+            System.err
+                    .println("DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+                            + val.toString());
+
+            sval = "";
+          }
+          return new StringReader(
+                  (sval instanceof JSONObject) ? ((JSONObject) sval)
+                          .toString() : sval.toString());
+
+        }
+
+        @Override
+        public void 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"));
+        }
+
+        @Override
+        public boolean equals(Object obj)
+        {
+          return super.equals(obj);
+        }
+
+        @Override
+        protected void finalize() throws Throwable
+        {
+          while (rvals.hasNext())
+          {
+            rvals.next();
+          }
+          super.finalize();
+        }
+      };
+    } catch (Exception foo)
+    {
+      throw new Exception(
+              MessageManager
+                      .getString("exception.couldnt_parse_responde_from_annotated3d_server"),
+              foo);
+    }
+
+  }
+
+  public static Iterator<Reader> getRNAMLForPDBId(String pdbid)
+          throws Exception
   {
     List<NameValuePair> vals = new ArrayList<NameValuePair>();
+    vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("pdbid", pdbid));
-    return HttpClientUtils.doHttpUrlPost(
-            "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d",
-            vals);
+    vals.add(new BasicNameValuePair("output", "rnaml"));
+    java.net.URL geturl = new URL(twoDtoolsURL + "?tool=rnaview&pdbid="
+            + pdbid + "&output=rnaml");
+    // return processJsonResponseFor(new
+    // InputStreamReader(geturl.openStream()));
+    ArrayList<Reader> readers = new ArrayList<Reader>();
+    readers.add(new InputStreamReader(geturl.openStream()));
+    return readers.iterator();
   }
 
 }