From 97708f316b561ec5f9f03d402945b522085b0d5b Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 24 Jan 2023 07:48:07 +0000
Subject: [PATCH] =?utf8?q?JAL-629=20don=E2=80=99t=20trash=20user=E2=80=99s=20?=
 =?utf8?q?system=20property=20file=20when=20adjusting=20settings=20to=20proc?=
 =?utf8?q?ess=20CL=20args?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 src/jalview/bin/Cache.java    |   19 +++++++++++++++----
 src/jalview/bin/Commands.java |    4 ++++
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 370a243..7ff7309 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -322,6 +322,16 @@ public class Cache
 
   private static boolean propsAreReadOnly = Platform.isJS();
 
+  public static boolean isPropsAreReadOnly()
+  {
+    return propsAreReadOnly;
+  }
+
+  public static void setPropsAreReadOnly(boolean propsAreReadOnly)
+  {
+    Cache.propsAreReadOnly = propsAreReadOnly;
+  }
+
   private final static String JS_PROPERTY_PREFIX = "jalview_";
 
   /**
@@ -1401,10 +1411,11 @@ public class Cache
                 if (customProxySet &&
                 // we have a username but no password for the scheme being
                 // requested
-                (protocol.equalsIgnoreCase("http")
-                        && (httpUser != null && httpUser.length() > 0
-                                && (httpPassword == null
-                                        || httpPassword.length == 0)))
+                        (protocol.equalsIgnoreCase("http")
+                                && (httpUser != null
+                                        && httpUser.length() > 0
+                                        && (httpPassword == null
+                                                || httpPassword.length == 0)))
                         || (protocol.equalsIgnoreCase("https")
                                 && (httpsUser != null
                                         && httpsUser.length() > 0
diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 5b3e199..289d962 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -476,6 +476,10 @@ public class Commands
             }
           }
         }
+        // for moment we disable JSON export
+        Cache.setPropsAreReadOnly(true);
+        Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
         switch (type)
         {
         case "svg":
-- 
1.7.10.2