From d86d8ec0d76b7265c856ebcb337c22fb9e3830ac Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 28 Jul 2011 11:30:55 +0100
Subject: [PATCH] refer to local default setting for proxy when connecting to
 www.jalview.org (JAL-864)

---
 src/jalview/bin/Cache.java        |    7 +++----
 src/jalview/bin/Jalview.java      |    2 +-
 src/jalview/gui/Desktop.java      |    2 +-
 src/jalview/gui/Preferences.java  |    2 +-
 src/jalview/gui/SplashScreen.java |    2 +-
 5 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f67377b..68edf1b 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -106,7 +106,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
  * (false)</li>
  * <li>VERSION_CHECK (true) check for the latest release version from
- * www.jalview.org</li>
+ * www.jalview.org (or the alias given by the www.jalview.org property)</li>
  * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
  * ID tooltip</li>
  * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
@@ -132,8 +132,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * warning dialog box is displayed.</li>
  * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation when shading by annotation</li>
  * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation when shading by annotation</li>
- * 
- * <li></li>
+ * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP requests to be redirected to a mirror of http://www.jalview.org</li>
  * 
  * <li></li>
  * 
@@ -331,7 +330,7 @@ public class Cache
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
             java.net.URL url = new java.net.URL(
-                    "http://www.jalview.org/webstart/jalview.jnlp");
+                    Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp");
             BufferedReader in = new BufferedReader(new InputStreamReader(
                     url.openStream()));
             String line = null;
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9383656..b83bdc0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -504,7 +504,7 @@ public class Jalview
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
-              "http://www.jalview.org/examples/exampleFile_2_3.jar");
+              jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_3.jar");
 
       protocol = "File";
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index afae5fb..8a96ec4 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -946,7 +946,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       message.append("\n\n!! Jalview version "
               + jalview.bin.Cache.getProperty("LATEST_VERSION")
-              + " is available for download from http://www.jalview.org !!\n");
+              + " is available for download from "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!\n");
 
     }
     // TODO: update this text for each release or centrally store it for lite
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index fac25e9..a4de985 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -189,7 +189,7 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org","http://www.jalview.org")+"/examples/exampleFile_2_3.jar"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index e855057..2bc4f9e 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -193,7 +193,7 @@ public class SplashScreen extends JPanel implements Runnable
               "!! Jalview version "
                       + jalview.bin.Cache.getDefault("LATEST_VERSION",
                               "..Checking..")
-                      + " is available for download from http://www.jalview.org !!",
+                      + " is available for download from "+jalview.bin.Cache.getDefault("www.jalview.org","http://www.jalview.org")+" !!",
               50, y += fontSize + 10);
       y += 5;
       g.setColor(Color.black);
-- 
1.7.10.2