3 declare -a ARGS=("${@}")
5 # this whole next part is because there's no readlink -f in Darwin
11 MAX=100 # just in case we end up in a loop
13 while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
15 FILE="$(readlink "${FILE}")"
16 if [ -z "${FILE}" ]; then
17 # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
18 FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
20 elif [ "${FILE#/}" = "${FILE}" ]; then
21 # FILE is not an absolute path link, we need to add the relative path to the previous dir
22 FILE="$(dirname "${PREVFILE}")/${FILE}"
26 if [ "${FOUND}" -ne 1 ]; then
27 echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
34 if [ "$( uname -s )" = "Darwin" ]; then
38 # check for headless mode
43 for RAWARG in "${@}"; do
46 --headless|--output|--image|--structureimage)
49 --help|--help-*|--version|-h)
60 if [ "${HELP}" = 1 ]; then
61 # --help takes precedence
64 elif [ "${GUI}" = 1 ]; then
65 # --gui takes precedence over --headless
72 # set vars for being inside the macos App Bundle
73 if [ "${ISMACOS}" = 1 ]; then
75 DIR="$(dirname "$(readlinkf "$0")")"
77 JAVA="${APPDIR}/jre/Contents/Home/bin/java"
78 JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
81 DIR="$(dirname "$(readlink -f "$0")")"
83 JAVA="${APPDIR}/jre/bin/java"
86 if [ "${HEADLESS}" = 1 ]; then
87 # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
88 if [ "${HELP}" = 1 ]; then
89 JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
91 # this suppresses the Java icon appearing in the macOS Dock
92 if [ "${ISMACOS}" = 1 ]; then
93 JVMARGS=( "${JVMARGS[@]}" "-Dapple.awt.UIElement=true" )
98 GETDOWNTXT="${APPDIR}/getdown.txt"
101 # save an array of JAR paths in case we're in WSL (see later)
102 declare -a JARPATHS=()
103 if [ -e "${GETDOWNTXT}" ]; then
104 # always check grep and sed regexes on macos -- they're not the same
105 for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
107 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
108 CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
109 JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
112 echo "Cannot find getdown.txt" >&2
116 # WINDOWS ONLY (Cygwin or WSL)
117 # change paths for Cygwin or Windows Subsystem for Linux (WSL)
118 if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
119 if [ "$(uname -o)" = "Cygwin" ]; then
121 CLASSPATH=$(cygpath -pw "${CLASSPATH}")
122 # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
124 for ARG in "${@}"; do
125 if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
126 ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
128 ARGS=( "${ARGS[@]}" "${ARG}" )
131 elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
134 for JARPATH in "${JARPATHS[@]}"; do
135 [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
136 CLASSPATH="${CLASSPATH}$(wslpath -aw "${JARPATH}")"
139 for ARG in "${@}"; do
140 if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
141 # annoyingly wslpath does not work if the file doesn't exist!
142 ARGBASENAME="$(basename "${ARG}")"
143 ARGDIRNAME="$(dirname "${ARG}")"
144 ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
146 ARGS=( "${ARGS[@]}" "${ARG}" )
154 # get console width -- three ways to try, just in case
155 if command -v tput 2>&1 >/dev/null; then
156 COLUMNS=$(tput cols) 2>/dev/null
157 elif command -v stty 2>&1 >/dev/null; then
158 COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
159 elif command -v resize 2>&1 >/dev/null; then
160 COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
162 JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
163 JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
165 # Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
166 if [ \! -e "${JAVA}" ]; then
168 echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
171 function quotearray() {
173 for VAL in "${@}"; do
174 if [ \! "$QUOTEDVALS" = "" ]; then
175 QUOTEDVALS="${QUOTEDVALS} "
177 QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
182 JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
183 ARGSSTR=$(quotearray "${ARGS[@]}")
185 if [ "${DEBUG}" = 1 ]; then
186 echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${CLASSPATH}"\" jalview.bin.Launcher ${ARGSSTR}
189 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"