upgrade to latest paradise services model using JSon response.

[jalview.git] / src / jalview / ws / jws1 / Annotate3D.java

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index a30a9a1..e90b2d2 100644 (file)
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -31,6 +31,7 @@ import java.io.Reader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLEncoder;
+import java.util.Iterator;
 
 public class Annotate3D
 {
@@ -76,12 +77,21 @@ public class Annotate3D
           sb.append(cbuff[i]);
         }
       }
-
-      FileParse fp = new InputStreamParser(
-              jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
-                      .toString()), source.getDataName());
-      AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
-      return nal;
+      Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+              .getRNAMLForPDBFileAsString(sb.toString());
+      AlignmentI al=null;
+      while (r.hasNext())
+      {
+        FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+        AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+        if (al==null)
+        {
+          al = nal;
+        } else {
+          al.append(nal);
+        }
+      }
+      return al;
     } catch (Throwable x)
     {
       if (x instanceof IOException)