Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / utils / getdown / bin / jalview.sh

diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index 112c3e6..849d71a 100755 (executable)
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -36,18 +36,45 @@ if [ "$( uname -s )" = "Darwin" ]; then
   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=${APPDIR}/resource/jalview_logo.png" )
 else
@@ -57,6 +84,11 @@ else
   JAVA="${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"
 
@@ -65,7 +97,8 @@ CLASSPATH=""
 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}" )
@@ -77,10 +110,9 @@ fi
 
 # WINDOWS ONLY (Cygwin or WSL)
 # change paths for Cygwin or Windows Subsystem for Linux (WSL)
-if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
+if [ "${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 "${CLASSPATH}")
     # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
     ARGS=()
@@ -91,9 +123,8 @@ if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
         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="${CLASSPATH};"
@@ -115,18 +146,25 @@ if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
   fi
 fi
 
+# get console width -- three ways to try, just in case
+if command -v tput 2>&1 >/dev/null; then
+  COLUMNS=$(tput cols) 2>/dev/null
+elif command -v stty 2>&1 >/dev/null; then
+  COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
+elif command -v resize 2>&1 >/dev/null; then
+  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
   JAVA=$SYSJAVA
   echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
 fi
 
-# check to see if $1 is set and is not start of other cli args
-OPEN=""
-if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
- # first argument exists and does not start with a "-" and is not "open"
- OPEN="-open"
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -cp \""${CLASSPATH}"\" jalview.bin.Launcher "${ARGS[@]}"
 fi
 
-# don't quote $OPEN (don't want it accidentally mistaken as an empty string arg!)
-"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"
+"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"