JAL-1269 RNAML returned directly from Annotate3d rather than embedded in a JSON array

diff --git a/src/jalview/ext/paradise/Annotate3D.java b/src/jalview/ext/paradise/Annotate3D.java
index 114de42..64d39d0 100644 (file)
--- a/src/jalview/ext/paradise/Annotate3D.java
+++ b/src/jalview/ext/paradise/Annotate3D.java
@@ -111,7 +111,11 @@ public class Annotate3D
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("data", pdbfile));
     vals.add(new BasicNameValuePair("output", "rnaml"));
-    return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+    // return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+    ArrayList<Reader> readers = new ArrayList<Reader>();
+    readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals));
+    return readers.iterator();
+
   }
   public static Iterator<Reader> processJsonResponseFor(Reader respons) throws Exception
   {
@@ -179,9 +183,12 @@ public class Annotate3D
     List<NameValuePair> vals = new ArrayList<NameValuePair>();
     vals.add(new BasicNameValuePair("tool", "rnaview"));
     vals.add(new BasicNameValuePair("pdbid", pdbid));
-    vals.add(new BasicNameValuePair("format", "rnaml"));
-    java.net.URL geturl = new URL(twoDtoolsURL+"?tool=rnaview&output=rnaml&pdbid="+pdbid);
-    return processJsonResponseFor(new InputStreamReader(geturl.openStream()));
+    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();
   }
 
 }