+ vals.add(new BasicNameValuePair("output", "rnaml"));
+ return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+ }
+ 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("Remove: Not implemented");
+
+ }@Override
+ protected Object clone() throws CloneNotSupportedException
+ {
+ throw new CloneNotSupportedException("Clone: Not implemented");
+ }@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("Couldn't parse response from Annotate3d server.",foo);
+ }
+
+