From 9cd3ff27d8a47b2e8b1f3be9ff07d47ea9bc6fd1 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Tue, 8 Oct 2019 19:21:24 +0200
Subject: [PATCH] JAL-3436 fix for reload not reloading files

 -- fix for Jalview projects reload where reload was using just the file
name.

 -- will test further to ensure this is only in relation to JVP files
---
 src/jalview/gui/AlignFrame.java      |    5 ++++-
 src/jalview/project/Jalview2XML.java |   16 ++++++++++++++--
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0271506..0c25262 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1053,6 +1053,7 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void reload_actionPerformed(ActionEvent e)
   {
+    System.out.println("AlignFrame.reload " + fileName);
     if (fileName != null)
     {
       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
@@ -1084,7 +1085,9 @@ public class AlignFrame extends GAlignFrame
         DataSourceType protocol = fileName.startsWith("http:")
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
-        loader.loadFile(viewport, fileName, protocol, currentFileFormat);
+        loader.loadFile(viewport,
+                (fileObject == null ? fileName : fileObject), protocol,
+                currentFileFormat);
       }
       else
       {
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 186f786..ccfe460 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2742,6 +2742,13 @@ public class Jalview2XML
   public boolean attemptversion1parse = false;
 
   /**
+   * JalviewJS only -- to preserve bytes in AlignFrame
+   * 
+   * BH 2019 JAL-3436
+   */
+  private File file;
+
+  /**
    * Load a jalview project archive from a jar file
    * 
    * @param file
@@ -2800,6 +2807,10 @@ public class Jalview2XML
 			String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
       byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
               : null;
+      if (bytes != null)
+      {
+        this.file = (File) ofile;
+      }
 			URL url = null;
 			errorMessage = null;
 			uniqueSetSuffix = null;
@@ -4997,7 +5008,7 @@ public class Jalview2XML
     }
   }
 
-  AlignFrame loadViewport(String file, List<JSeq> JSEQ,
+  AlignFrame loadViewport(String fileName, List<JSeq> JSEQ,
           List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
           Viewport view, String uniqueSeqSetId, String viewId,
           List<JvAnnotRow> autoAlan)
@@ -5017,7 +5028,8 @@ public class Jalview2XML
     // }
     ;
     af.alignPanel.setHoldRepaint(true);
-    af.setFileName(file, FileFormat.Jalview);
+    af.setFileName(fileName, FileFormat.Jalview);
+    af.setFileObject(file); // BH 2019 JAL-3436
 
     final AlignViewport viewport = af.getViewport();
     for (int i = 0; i < JSEQ.size(); i++)
-- 
1.7.10.2