Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

diff --cc src/jalview/ws/dbsources/EBIAlfaFold.java
index 4ed28fc,72fd8d9..bee1ae9
--- 1/src/jalview/ws/dbsources/EBIAlfaFold.java
--- 2/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@@ -382,10 -402,29 +382,28 @@@ public class EBIAlfaFold extends EbiFil
        }
      }
  
+     JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
+     if (paeDict == null)
+     {
+       Console.debug("JSON file did not parse properly.");
+       return false;
+     }
+     ContactMatrixI matrix = new PAEContactMatrix(sequence,
+             (Map<String, Object>) paeDict);
+ 
+     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+     pdbAlignment.addAnnotation(cmannot);
+ 
+     return true;
+   }
+ 
+   public static JSONObject parseJSONtoPAEContactMatrix(
 -          InputStream pae_input) throws IOException,ParseException
++          InputStream pae_input) throws IOException, ParseException
+   {
      Object paeJson = Platform.parseJSON(pae_input);
 -    JSONObject paeDict=null;
 +    JSONObject paeDict = null;
      if (paeJson instanceof JSONObject)
      {
 -      Console.debug("***** paeJson is a JSONObject");
        paeDict = (JSONObject) paeJson;
      }
      else if (paeJson instanceof JSONArray)