ISMACOS=1
fi
+# check for headless mode
+HEADLESS=0
+GUI=0
+HELP=0
+DEBUG=0
+for RAWARG in "${@}"; do
+ ARG="${RAWARG%%=*}"
+ case "${ARG}" in
+ --headless|--output|--image|--structureimage)
+ HEADLESS=1
+ ;;
+ --help|--help-*|--version|-h)
+ HELP=1
+ ;;
+ --gui)
+ GUI=1
+ ;;
+ --debug)
+ DEBUG=1
+ ;;
+ esac
+
+ if [ "${HELP}" = 1 ]; then
+ # --help takes precedence
+ HEADLESS=1
+ GUI=0
+ elif [ "${GUI}" = 1 ]; then
+ # --gui takes precedence over --headless
+ HEADLESS=0
+ fi
+done
+
declare -a JVMARGS=()
# set vars for being inside the macos App Bundle
if [ "${ISMACOS}" = 1 ]; then
# MACOS ONLY
DIR="$(dirname "$(readlinkf "$0")")"
- APP="${DIR%.app/Contents/*}".app
- if [ "${APP}" = "${APP%.app}" ]; then
- echo "Could not find Jalview.app" >&2
- exit 2
- fi
- APPDIR="${APP}/Contents/Resources/app"
+ APPDIR="${DIR%/bin}"
JAVA="${APPDIR}/jre/Contents/Home/bin/java"
JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
else
JAVA="${APPDIR}/jre/bin/java"
fi
+if [ "${HEADLESS}" = 1 ]; then
+ # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes
+ JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+fi
+
SYSJAVA=java
GETDOWNTXT="${APPDIR}/getdown.txt"
declare -a JARPATHS=()
if [ -e "${GETDOWNTXT}" ]; then
# always check grep and sed regexes on macos -- they're not the same
- for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
+for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
+ do
[ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
if [ "$(uname -o)" = "Cygwin" ]; then
# CYGWIN
- echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
CLASSPATH=$(cygpath -pw "${CLASSPATH}")
# now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
ARGS=()
ARGS=( "${ARGS[@]}" "${ARG}" )
fi
done
- elif uname -r | grep Microsoft >/dev/null; then
+ elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
# WSL
- echo "When using relative paths in args within WSL, please start with './' or '../'" >&2
CLASSPATH=""
for JARPATH in "${JARPATHS[@]}"; do
[ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
fi
JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
# Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
if [ \! -e "${JAVA}" ]; then
echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
fi
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -cp \""${CLASSPATH}"\" jalview.bin.Launcher "${ARGS[@]}"
+fi
+
"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"