4 DIR="$(dirname "$(readlink -f "$0")")"
6 # check to see if $1 is set and is not start of other cli set args
8 if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
9 # first argument exists and does not start with a "-" and is not "open"
14 JAVA="${APPDIR}/jre/bin/java"
15 GETDOWNTXT="${APPDIR}/getdown.txt"
17 if [ -e "${GETDOWNTXT}" ]; then
18 for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
19 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
20 CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
23 echo "Cannot find getdown.txt" >&2
27 if [ \! -e "${JAVA}" ]; then
28 echo "Cannot find bundled java, using system and hoping for the best!" >&2
32 declare -a ARGS=("${@}")
34 # change paths for Cygwin or Windows Subsystem for Linux (WSL)
35 if [ "$(uname -o)" = "Cygwin" ]; then
36 echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
37 CLASSPATH=$(cygpath -pw "${CLASSPATH}")
38 # now for some arg paths fun. only translating paths starting with './', '../' or '/'
41 if [ "${ARG}" != "${ARG#./}" -o "${ARG}" != "${ARG#/}" -o "${ARG}" != "${ARG#../}" ]; then
42 ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
44 ARGS=( "${ARGS[@]}" "${ARG}" )
48 elif uname -r | grep Microsoft >/dev/null; then
49 echo "When using relative paths in args within WSL. please start with './' or '../'" >&2
53 for JAR in $CLASSPATH; do
54 [ -n "${WCLASSPATH}" ] && WCLASSPATH="${WCLASSPATH};"
55 WCLASSPATH="${WCLASSPATH}$(wslpath -aw "${JAR}")"
57 CLASSPATH="${WCLASSPATH}"
61 if [ "${ARG}" != "${ARG#./}" -o "${ARG}" != "${ARG#/}" -o "${ARG}" != "${ARG#../}" ]; then
62 # annoyingly wslpath does not work if the file doesn't exist!
63 ARGBASENAME="$(basename "${ARG}")"
64 ARGDIRNAME="$(dirname "${ARG}")"
65 ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
67 ARGS=( "${ARGS[@]}" "${ARG}" )
74 "${JAVA}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"