Merge branch 'develop' into Jalview-JS/develop

[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..caff3bb 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);
@@ -151,15 +151,20 @@ 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();
+         // BH 2019 never called?
     try
     {
-      final JSONArray responses = (JSONArray) jp.parse(respons);
-      final Iterator rvals = responses.iterator();
-      return new Iterator<Reader>()
+      @SuppressWarnings("unchecked")
+       final Iterator<Object> rvals = ((List<Object>) JSONUtils.parse(respons)).iterator();
+      return new Iterator<>()
       {
         @Override
         public boolean hasNext()
@@ -167,10 +172,11 @@ public class Annotate3D
           return rvals.hasNext();
         }
 
-        @Override
+        @SuppressWarnings("unchecked")
+               @Override
         public Reader next()
         {
-          JSONObject val = (JSONObject) rvals.next();
+          Map<String, Object> val = (Map<String, Object>) rvals.next();
 
           Object sval = null;
           try
@@ -180,7 +186,6 @@ public class Annotate3D
           {
             x.printStackTrace();
           }
-          ;
           if (sval == null)
           {
             System.err.println(
@@ -189,9 +194,7 @@ public class Annotate3D
 
             sval = "";
           }
-          return new StringReader((sval instanceof JSONObject)
-                  ? ((JSONObject) sval).toString()
-                  : sval.toString());
+          return new StringReader(sval.toString());
 
         }
 
@@ -232,13 +235,12 @@ public class Annotate3D
               "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"));
@@ -246,7 +248,7 @@ 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();
   }