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 [ "$( uname -s )" = "Darwin" ]; then
39 # check for headless mode
44 for RAWARG in "${@}"; do
47 --headless|--output|--image|--structureimage)
50 --help|--help-*|--version|-h)
61 if [ "${HELP}" = 1 ]; then
62 # --help takes precedence
65 elif [ "${GUI}" = 1 ]; then
66 # --gui takes precedence over --headless
73 # set vars for being inside the macos App Bundle
74 if [ "${ISMACOS}" = 1 ]; then
76 DIR="$(dirname "$(readlinkf "$0")")"
78 JAVA="${APPDIR}/jre/Contents/Home/bin/java"
79 JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
82 DIR="$(dirname "$(readlink -f "$0")")"
84 JAVA="${APPDIR}/jre/bin/java"
87 if [ "${HEADLESS}" = 1 ]; then
88 # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes
89 JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
93 GETDOWNTXT="${APPDIR}/getdown.txt"
96 # save an array of JAR paths in case we're in WSL (see later)
97 declare -a JARPATHS=()
98 if [ -e "${GETDOWNTXT}" ]; then
99 # always check grep and sed regexes on macos -- they're not the same
100 for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
102 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
103 CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
104 JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
107 echo "Cannot find getdown.txt" >&2
111 # WINDOWS ONLY (Cygwin or WSL)
112 # change paths for Cygwin or Windows Subsystem for Linux (WSL)
113 if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
114 if [ "$(uname -o)" = "Cygwin" ]; then
116 CLASSPATH=$(cygpath -pw "${CLASSPATH}")
117 # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
119 for ARG in "${@}"; do
120 if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
121 ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
123 ARGS=( "${ARGS[@]}" "${ARG}" )
126 elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
129 for JARPATH in "${JARPATHS[@]}"; do
130 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
131 CLASSPATH="${CLASSPATH}$(wslpath -aw "${JARPATH}")"
134 for ARG in "${@}"; do
135 if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
136 # annoyingly wslpath does not work if the file doesn't exist!
137 ARGBASENAME="$(basename "${ARG}")"
138 ARGDIRNAME="$(dirname "${ARG}")"
139 ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
141 ARGS=( "${ARGS[@]}" "${ARG}" )
149 # get console width -- three ways to try, just in case
150 if command -v tput 2>&1 >/dev/null; then
151 COLUMNS=$(tput cols) 2>/dev/null
152 elif command -v stty 2>&1 >/dev/null; then
153 COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
154 elif command -v resize 2>&1 >/dev/null; then
155 COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
157 JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
158 JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
160 # Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
161 if [ \! -e "${JAVA}" ]; then
163 echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
166 if [ "${DEBUG}" = 1 ]; then
167 echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -cp \""${CLASSPATH}"\" jalview.bin.Launcher "${ARGS[@]}"
170 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"