Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...

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

diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index c1ad597..90d1558 100755 (executable)
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -1,7 +1,6 @@
 #!/usr/bin/env bash
 
 declare -a ARGS=("${@}")
-ARG1=$1
 
 # this whole next part is because there's no readlink -f in Darwin
 function readlinkf() {
@@ -38,10 +37,33 @@ 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 +73,7 @@ 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
@@ -67,8 +84,14 @@ else
 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" )
+  # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
+  if [ "${HELP}" = 1 ]; then
+    JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+  fi
+  # this suppresses the Java icon appearing in the macOS Dock
+  if [ "${ISMACOS}" = 1 ]; then
+    JVMARGS=( "${JVMARGS[@]}" "-Dapple.awt.UIElement=true" )
+  fi
 fi
 
 SYSJAVA=java
@@ -145,4 +168,22 @@ if [ \! -e "${JAVA}" ]; then
   echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
 fi
 
+function quotearray() {
+  QUOTEDVALS=""
+  for VAL in "${@}"; do
+    if [ \! "$QUOTEDVALS" = "" ]; then
+      QUOTEDVALS="${QUOTEDVALS} "
+    fi
+    QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
+  done
+  echo $QUOTEDVALS
+}
+
+JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
+ARGSSTR=$(quotearray "${ARGS[@]}")
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${CLASSPATH}"\" jalview.bin.Launcher ${ARGSSTR}
+fi
+
 "${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"