From b77e5440f9a866b464b0077478b604df513cf3fc Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 21 Jul 2010 15:06:07 +0000
Subject: [PATCH] URLs that begin with javascript: are opened in the same
 window. See http://issues.jalview.org/browse/JAL-604

---
 src/jalview/appletgui/AlignFrame.java |    8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ccf7c06..14606b7 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2580,8 +2580,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           System.out.println("Show url: " + url);
         }
-        viewport.applet.getAppletContext().showDocument(
+        if (url.indexOf("javascript:")==0)
+        {
+          // no target for the javascript context
+          viewport.applet.getAppletContext().showDocument(new java.net.URL(url));
+        } else{
+          viewport.applet.getAppletContext().showDocument(
                 new java.net.URL(url), target);
+        }
       } catch (Exception ex)
       {
         ex.printStackTrace();
-- 
1.7.10.2