Merge branch 'develop' into trialMerge

[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 d50ad87..3c443de 100644 (file)
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.paradise;
 
+import jalview.util.JSONUtils;
 import jalview.util.MessageManager;
 import jalview.ws.HttpClientUtils;
 
@@ -32,11 +33,10 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 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;
 
@@ -137,13 +137,13 @@ public class Annotate3D
   public static Iterator<Reader> getRNAMLForPDBFileAsString(String pdbfile)
           throws Exception
   {
-    List<NameValuePair> vals = new ArrayList<NameValuePair>();
+    List<NameValuePair> vals = new ArrayList<>();
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("data", pdbfile));
     vals.add(new BasicNameValuePair("output", "rnaml"));
     // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
     // vals));
-    ArrayList<Reader> readers = new ArrayList<Reader>();
+    ArrayList<Reader> readers = new ArrayList<>();
     final BufferedReader postResponse = HttpClientUtils
             .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
     readers.add(postResponse);
@@ -151,94 +151,31 @@ public class Annotate3D
 
   }
 
+  /**
+   * @param respons
+   * @return
+   * @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();
-        }
-      };
+      @SuppressWarnings("unchecked")
+       List<Object> responses = (List<Object>) JSONUtils.parse(respons);
+      return new RvalsIterator(responses);
     } 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>();
+    List<NameValuePair> vals = new ArrayList<>();
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("pdbid", pdbid));
     vals.add(new BasicNameValuePair("output", "rnaml"));
@@ -246,9 +183,70 @@ public class Annotate3D
             + pdbid + "&output=rnaml");
     // return processJsonResponseFor(new
     // InputStreamReader(geturl.openStream()));
-    ArrayList<Reader> readers = new ArrayList<Reader>();
+    ArrayList<Reader> readers = new ArrayList<>();
     readers.add(new InputStreamReader(geturl.openStream()));
     return readers.iterator();
   }
 
 }
+
+class RvalsIterator implements Iterator<Reader>, AutoCloseable
+{
+  private Iterator<Object> rvals;
+
+  protected RvalsIterator(List<Object> responses)
+  {
+    this.rvals = responses.iterator();
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return rvals.hasNext();
+  }
+
+  @Override
+  public Reader next()
+  {
+    Map<String, Object> val = (Map<String, Object>) 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.toString());
+  }
+
+  @Override
+  public void remove()
+  {
+    throw new UnsupportedOperationException();
+  }
+
+  @Override
+  protected Object clone() throws CloneNotSupportedException
+  {
+    throw new UnsupportedOperationException();
+  }
+
+  @Override
+  public void close()
+  {
+    while (rvals.hasNext())
+    {
+      rvals.next();
+    }
+  }
+}