From e91b3bef83f320e13c59ad5d21d69f0abf3d7507 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 1 Sep 2023 16:22:30 +0100
Subject: [PATCH] JAL-4124 need to repaint alignFrames imported from project
 after resolving references so PAE matrices are displayed

---
 src/jalview/project/Jalview2XML.java |    6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 627aba3..d1e836e 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -3137,6 +3137,7 @@ public class Jalview2XML
       initSeqRefs();
     }
     AlignFrame af = null, _af = null;
+    List<AlignFrame> toRepaint=new ArrayList<AlignFrame>();
     IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
     Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
     final String file = jprovider.getFilename();
@@ -3171,6 +3172,7 @@ public class Jalview2XML
             if (_af != null && object.getViewport().size() > 0)
             // getJalviewModelSequence().getViewportCount() > 0)
             {
+              toRepaint.add(_af);
               if (af == null)
               {
                 // store a reference to the first view
@@ -3200,6 +3202,10 @@ public class Jalview2XML
       } while (jarentry != null);
       jin.close();
       resolveFrefedSequences();
+      for (AlignFrame alignFrame:toRepaint)
+      {
+        alignFrame.repaint();
+      }
     } catch (IOException ex)
     {
       ex.printStackTrace();
-- 
1.7.10.2