From 4ecd680a70a52359793d2cdc082d48a07573de79 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@stolaf.edu>
Date: Mon, 2 Jul 2018 19:00:29 +0100
Subject: [PATCH] JAL-3026  File...Reload working

---
 src/jalview/gui/AlignFrame.java |   35 ++++++++++++++++++++++++++++-------
 src/jalview/io/FileLoader.java  |   19 +++++++++++++++++++
 2 files changed, 47 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ee2875a..c07cfe0 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -181,6 +181,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   String fileName = null;
 
+  File fileObject;
+
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -533,6 +535,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setFileFormat(format);
     reload.setEnabled(true);
   }
+  
+  /**
+   * JavaScript will have this, maybe others. More dependable than a file name
+   * and maintains a reference to the actual bytes loaded.
+   * 
+   * @param file
+   */
+  public void setFileObject(File file) {
+    this.fileObject = file;
+  }
 
   /**
    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
@@ -1064,8 +1076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         FileLoader loader = new FileLoader();
         DataSourceType protocol = fileName.startsWith("http:")
-                ? DataSourceType.URL
-                : DataSourceType.FILE;
+                ? DataSourceType.URL : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
@@ -1073,11 +1084,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Rectangle bounds = this.getBounds();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
-                ? DataSourceType.URL
-                : DataSourceType.FILE;
-        AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
-                protocol, currentFileFormat);
+
+        AlignFrame newframe = null;
+
+        if (fileObject == null)
+        {
+
+          DataSourceType protocol = (fileName.startsWith("http:")
+                  ? DataSourceType.URL : DataSourceType.FILE);
+          newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+                  currentFileFormat);
+        }
+        else
+        {
+          newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat);
+        }
 
         newframe.setBounds(bounds);
         if (featureSettings != null && featureSettings.isShowing())
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index eda3899..8e68067 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -170,6 +170,24 @@ public class FileLoader implements Runnable
   }
 
   /**
+   * Load alignment from (file, protocol) of type format and wait till loaded
+   * 
+   * @param file
+   * @param sourceType
+   * @param format
+   * @return alignFrame constructed from file contents
+   */
+  public AlignFrame LoadFileWaitTillLoaded(File file,
+          DataSourceType sourceType, FileFormatI format)
+  {
+    this.selectedFile = file;
+    this.file = file.getPath();
+    this.protocol = sourceType;
+    this.format = format;
+    return _LoadFileWaitTillLoaded();
+  }
+
+  /**
    * Load alignment from FileParse source of type format and wait till loaded
    * 
    * @param source
@@ -443,6 +461,7 @@ public class FileLoader implements Runnable
             if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
+              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
             if (proxyColourScheme != null)
             {
-- 
1.7.10.2