X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=ccfe460ffb9324c8c09683fde0dee130b7cad57d;hb=9cd3ff27d8a47b2e8b1f3be9ff07d47ea9bc6fd1;hp=186f7866b2e7fdbe3652af5660ab2f7815789a67;hpb=d99084464d534fd58df437bcee706e20acc17db9;p=jalview.git

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++)