X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=utils%2Fgetdown%2Fbin%2Fjalview.sh;h=849d71a9a1ea99ea112c8c8897bd88935732b23c;hb=cb31e23d9138e481479623374aed7767bf8934d2;hp=c1ad597874788156386dd23e1d1c34dbfc5420e7;hpb=5e462885d21193706d23e42cd5e21e88763788cb;p=jalview.git

diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index c1ad597..849d71a 100755
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -38,10 +38,33 @@ fi
 
 # check for headless mode
 HEADLESS=0
-for ARG in ARGS; do
-  if [ "${ARG}" = "--headless" ]; then
+GUI=0
+HELP=0
+DEBUG=0
+for RAWARG in "${@}"; 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 [ "${HELP}" = 1 ]; then
+    # --help takes precedence
     HEADLESS=1
-    break
+    GUI=0
+  elif [ "${GUI}" = 1 ]; then
+    # --gui takes precedence over --headless
+    HEADLESS=0
   fi
 done
 
@@ -51,12 +74,7 @@ declare -a JVMARGS=()
 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=${APPDIR}/resource/jalview_logo.png" )
 else
@@ -145,4 +163,8 @@ if [ \! -e "${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[@]}"