Description: JSONObject was wrongly invoked
 It was called with a wrong package name, "simple" being forgotten.
 Moreover it is called on an AlignmentPojo object, I added the getAppSettings
 method in the call to get a HashMap<String, Object>.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: jalview-dev@jalview.org
Last-Update: 2020-11-15

--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -255,8 +255,8 @@
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
       }
-      org.json.JSONObject generatedJSon = new org.json.JSONObject(
-              jsonAlignmentPojo);
+      org.json.simple.JSONObject generatedJSon = new org.json.simple.JSONObject(
+              jsonAlignmentPojo.getAppSettings());
       jsonOutput = generatedJSon.toString();
       return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
               "xEnd");