#!/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 $OPEN "$@"