From 102c4a5e44f17f965387d203f8274803104863b5 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 8 Feb 2021 11:57:20 +0000
Subject: [PATCH] JAL-3521 Adjusted wrapper shell script and .desktop file to
 cater for opening a file with or without -open arg

---
 utils/debian/debian/jalview.desktop   |    2 +-
 utils/debian/debian/wrappers/jalview  |   17 +++++++++++++++++
 utils/debian/mime_types_for_debian.pl |    2 +-
 3 files changed, 19 insertions(+), 2 deletions(-)
 create mode 100755 utils/debian/debian/wrappers/jalview

diff --git a/utils/debian/debian/jalview.desktop b/utils/debian/debian/jalview.desktop
index d4cc896..7cf0afb 100644
--- a/utils/debian/debian/jalview.desktop
+++ b/utils/debian/debian/jalview.desktop
@@ -6,7 +6,7 @@ Comment=Multiple Sequence Alignment Editor
 Icon=jalview-icon
 Type=Application
 TryExec=jalview
-Exec=jalview -open %u
+Exec=jalview %u
 Terminal=false
 Categories=Science;Biology;
 Keywords=alignment;sequence;
diff --git a/utils/debian/debian/wrappers/jalview b/utils/debian/debian/wrappers/jalview
new file mode 100755
index 0000000..4823bee
--- /dev/null
+++ b/utils/debian/debian/wrappers/jalview
@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+set -e
+ARG1=$1
+
+# copy the debian default settings if no user jalview settings file exist
+if [ -n "${HOME}" -a \! -e ${HOME}/.jalview_properties ]; then
+  /bin/cp /etc/jalview_properties ${HOME}/.jalview_properties
+fi
+
+# check to see if $1 is set and is not start of other cli set args
+OPEN=""
+if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" ]; then
+  # first argument exists and does not start with a "-"
+  OPEN="-open"
+fi
+  
+java -jar /usr/share/java/jalview.jar $OPEN "$@"
diff --git a/utils/debian/mime_types_for_debian.pl b/utils/debian/mime_types_for_debian.pl
index 9cbfc40..15e1ea1 100755
--- a/utils/debian/mime_types_for_debian.pl
+++ b/utils/debian/mime_types_for_debian.pl
@@ -233,7 +233,7 @@ Comment=Multiple Sequence Alignment Editor
 Icon=jalview-icon
 Type=Application
 TryExec=jalview
-Exec=jalview -open %u
+Exec=jalview %u
 Terminal=false
 Categories=Science;Biology;
 Keywords=alignment;sequence;
-- 
1.7.10.2