From 6b74ef88014ba574bd60a14eae8167390e012421 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 17 Oct 2019 16:48:06 +0100
Subject: [PATCH] JAL-3436 null large object reference, tidy method visibility

---
 src/jalview/project/Jalview2XML.java |   16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 9507a87..b0315e8 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -445,7 +445,7 @@ public class Jalview2XML
    * @param _jmap
    * @return
    */
-  public SeqFref newMappingRef(final String sref,
+  protected SeqFref newMappingRef(final String sref,
           final jalview.datamodel.Mapping _jmap)
   {
     SeqFref fref = new SeqFref(sref, "Mapping")
@@ -467,7 +467,7 @@ public class Jalview2XML
     return fref;
   }
 
-  public SeqFref newAlcodMapRef(final String sref,
+  protected SeqFref newAlcodMapRef(final String sref,
           final AlignedCodonFrame _cf,
           final jalview.datamodel.Mapping _jmap)
   {
@@ -499,7 +499,7 @@ public class Jalview2XML
     return fref;
   }
 
-  public void resolveFrefedSequences()
+  protected void resolveFrefedSequences()
   {
     Iterator<SeqFref> nextFref = frefedSequence.iterator();
     int toresolve = frefedSequence.size();
@@ -867,7 +867,7 @@ public class Jalview2XML
    * @param out
    *          jar entry name
    */
-  public JalviewModel saveState(AlignmentPanel ap, String fileName,
+  protected JalviewModel saveState(AlignmentPanel ap, String fileName,
           JarOutputStream jout, List<String> viewIds)
   {
     return saveState(ap, fileName, false, jout, viewIds);
@@ -889,7 +889,7 @@ public class Jalview2XML
    * @param out
    *          jar entry name
    */
-  public JalviewModel saveState(AlignmentPanel ap, String fileName,
+  protected JalviewModel saveState(AlignmentPanel ap, String fileName,
           boolean storeDS, JarOutputStream jout, List<String> viewIds)
   {
     if (viewIds == null)
@@ -2798,6 +2798,7 @@ public class Jalview2XML
         System.err.println("Error loading alignment: " + x.getMessage());
       }
     }
+    this.jarFile = null;
     return af;
   }
 
@@ -5632,7 +5633,7 @@ public class Jalview2XML
     return false;
   }
 
-  public void addToSkipList(AlignFrame af)
+  protected void addToSkipList(AlignFrame af)
   {
     if (skipList == null)
     {
@@ -5641,7 +5642,7 @@ public class Jalview2XML
     skipList.put(af.getViewport().getSequenceSetId(), af);
   }
 
-  public void clearSkipList()
+  protected void clearSkipList()
   {
     if (skipList != null)
     {
@@ -6126,6 +6127,7 @@ public class Jalview2XML
     af.getAlignPanels().clear();
     af.closeMenuItem_actionPerformed(true);
     af.alignPanel.setHoldRepaint(false);
+    this.jarFile = null;
 
     return af.alignPanel;
   }
-- 
1.7.10.2