From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Fri, 2 Nov 2018 06:50:46 +0000 (-0500)
Subject: Marshalling produces valid ZIP file. Unmarshalling hanging on getting a
X-Git-Tag: Release_2_11_4_0~45^2~18^2~428^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=59d9dfb7b746fcc396af9b572b40636028df9fed;p=jalview.git

Marshalling produces valid ZIP file. Unmarshalling hanging on getting a
system JAXBContextFactory -- simple enough to do, just haven't done it.
---

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 390e8cd..f244d14 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -338,7 +338,8 @@ public class FileLoader implements Runnable
                   "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
+        // BH 2018 switch to File object here instead of filename
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
       }
       else
       {
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 42328b8..194cbf2 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -130,6 +130,7 @@ import java.awt.Color;
 import java.awt.Font;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.DataInputStream;
 import java.io.DataOutputStream;
 import java.io.File;
@@ -2478,7 +2479,7 @@ public class Jalview2XML
    * @param file
    *          - HTTP URL or filename
    */
-  public AlignFrame loadJalviewAlign(final String file)
+  public AlignFrame loadJalviewAlign(final Object file)
   {
 
     jalview.gui.AlignFrame af = null;
@@ -2522,9 +2523,33 @@ public class Jalview2XML
     return af;
   }
 
-  private jarInputStreamProvider createjarInputStreamProvider(
-          final String file) throws MalformedURLException
+  @SuppressWarnings("unused")
+private jarInputStreamProvider createjarInputStreamProvider(
+          final Object ofile) throws MalformedURLException
   {
+	
+	  // BH 2018 allow for bytes already attached to File object
+	final String file = ofile.toString();
+	byte[] bytes = /** @j2sNative ofile._bytes ||*/null;
+	if (bytes != null) {
+
+	    return new jarInputStreamProvider()
+	    {
+
+	      @Override
+	      public JarInputStream getJarInputStream() throws IOException
+	      {
+	          return new JarInputStream(new ByteArrayInputStream(bytes));
+	      }
+
+	      @Override
+	      public String getFilename()
+	      {
+	        return file;
+	      }
+	    };
+
+	}
     URL url = null;
     errorMessage = null;
     uniqueSetSuffix = null;
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index c56ecfc..c29d77b 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/timestamp b/swingjs/timestamp
index d1276fe..75fd0a4 100644
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20181101203541 
+20181101233424 
diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip
index c56ecfc..c29d77b 100644
Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ
diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp
index d1276fe..75fd0a4 100644
--- a/swingjs/ver/3.2.4/timestamp
+++ b/swingjs/ver/3.2.4/timestamp
@@ -1 +1 @@
-20181101203541 
+20181101233424