3 declare -a ARGS=("${@}")
6 # this whole next part is because there's no readlink -f in Darwin
12 MAX=100 # just in case we end up in a loop
14 while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
16 FILE="$(readlink "${FILE}")"
17 if [ -z "${FILE}" ]; then
18 # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
19 FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
21 elif [ "${FILE#/}" = "${FILE}" ]; then
22 # FILE is not an absolute path link, we need to add the relative path to the previous dir
23 FILE="$(dirname "${PREVFILE}")/${FILE}"
27 if [ "${FOUND}" -ne 1 ]; then
28 echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
35 if [ "$( uname -s )" = "Darwin" ]; then
41 # set vars for being inside the macos App Bundle
42 if [ "${ISMACOS}" = 1 ]; then
44 DIR="$(dirname "$(readlinkf "$0")")"
45 APP="${DIR%.app/Contents/*}".app
46 if [ "${APP}" = "${APP%.app}" ]; then
47 echo "Could not find Jalview.app" >&2
50 APPDIR="${APP}/Contents/Resources/app"
51 JAVA="${APPDIR}/jre/Contents/Home/bin/java"
52 JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
55 DIR="$(dirname "$(readlink -f "$0")")"
57 JAVA="${APPDIR}/jre/bin/java"
61 GETDOWNTXT="${APPDIR}/getdown.txt"
64 # save an array of JAR paths in case we're in WSL (see later)
65 declare -a JARPATHS=()
66 if [ -e "${GETDOWNTXT}" ]; then
67 # always check grep and sed regexes on macos -- they're not the same
68 for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
69 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
70 CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
71 JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
74 echo "Cannot find getdown.txt" >&2
78 # WINDOWS ONLY (Cygwin or WSL)
79 # change paths for Cygwin or Windows Subsystem for Linux (WSL)
80 if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
81 if [ "$(uname -o)" = "Cygwin" ]; then
83 echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
84 CLASSPATH=$(cygpath -pw "${CLASSPATH}")
85 # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
88 if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
89 ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
91 ARGS=( "${ARGS[@]}" "${ARG}" )
94 elif uname -r | grep Microsoft >/dev/null; then
96 echo "When using relative paths in args within WSL, please start with './' or '../'" >&2
98 for JARPATH in "${JARPATHS[@]}"; do
99 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
100 CLASSPATH="${CLASSPATH}$(wslpath -aw "${JARPATH}")"
103 for ARG in "${@}"; do
104 if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
105 # annoyingly wslpath does not work if the file doesn't exist!
106 ARGBASENAME="$(basename "${ARG}")"
107 ARGDIRNAME="$(dirname "${ARG}")"
108 ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
110 ARGS=( "${ARGS[@]}" "${ARG}" )
118 # Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
119 if [ \! -e "${JAVA}" ]; then
121 echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
124 # check to see if $1 is set and is not start of other cli args
126 if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
127 # first argument exists and does not start with a "-" and is not "open"
131 # don't quote $OPEN (don't want it accidentally mistaken as an empty string arg!)
132 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"