X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=utils%2Fgetdown%2Fbin%2Fjalview.sh;h=849d71a9a1ea99ea112c8c8897bd88935732b23c;hb=cb31e23d9138e481479623374aed7767bf8934d2;hp=912f1adcd3dae7f996ad2fdc1c33bbe6fa239849;hpb=810d16f4bf7bd2db5c38d66ff0f529e4f769102b;p=jalview.git

diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index 912f1ad..849d71a 100755
--- 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}/${JAR}" )
@@ -80,7 +113,6 @@ fi
 if [ "${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 # older macos doesn't like uname -o, best to avoi
         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="${CLASSPATH};"
@@ -124,6 +155,7 @@ elif command -v resize 2>&1 >/dev/null; then
   COLUMNS=$(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 "${JAVA}" ]; then
@@ -131,4 +163,8 @@ if [ \! -e "${JAVA}" ]; then
   echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
 fi
 
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -cp \""${CLASSPATH}"\" jalview.bin.Launcher "${ARGS[@]}"
+fi
+
 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"