From cc6197585bf74c9562c0b869a4d28646af5b13bc Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 17 Apr 2019 16:34:58 +0100
Subject: [PATCH] JAL-3026 fix bug loading Jalview Project (in Java)

---
 src/jalview/io/AnnotationFile.java   |    2 +-
 src/jalview/io/FileLoader.java       |    2 +-
 src/jalview/project/Jalview2XML.java |    9 ++++-----
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index aa29ced..02667c5 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -684,7 +684,7 @@ public class AnnotationFile
     {
       if (sourceType == DataSourceType.FILE)
       {
-        in = FileLoader.getBuffereReader(file);
+        in = FileLoader.getBufferedReader(file);
       }
       else if (sourceType == DataSourceType.URL)
       {
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 2169715..38cf3e6 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -647,7 +647,7 @@ public class FileLoader implements Runnable
    * @throws FileNotFoundException 
    */
   @SuppressWarnings("unused")
-  public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
+  public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
     if (file instanceof String)
     {
       return new BufferedReader(new FileReader((String) file));
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 41dd2f9..4d772a1 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -462,7 +462,7 @@ public class Jalview2XML
       public boolean isResolvable()
       {
         return super.isResolvable() && mp.getTo() != null;
-      };
+      }
 
       @Override
       boolean resolve()
@@ -694,7 +694,6 @@ public class Jalview2XML
       } catch (Exception foo)
       {
       }
-      ;
       jout.close();
     } catch (Exception ex)
     {
@@ -780,7 +779,6 @@ public class Jalview2XML
       } catch (Exception foo)
       {
       }
-      ;
       jout.close();
       boolean success = true;
 
@@ -2763,7 +2761,7 @@ public class Jalview2XML
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();
-          };
+          }
         });
       } catch (Exception x)
       {
@@ -2779,7 +2777,8 @@ public class Jalview2XML
 		// BH 2018 allow for bytes already attached to File object
 		try {
 			String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
-      byte[] bytes = Platform.getFileBytes((File) ofile);
+      byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
+              : null;
 			URL url = null;
 			errorMessage = null;
 			uniqueSetSuffix = null;
-- 
1.7.10.2