#!/usr/bin/env bash

ARG1="$1"

# this whole next part is because there's no readlink -f in Darwin
function readlinkf() {
  FINDFILE="$1"
  FILE="${FINDFILE}"
  PREVFILE=""
  C=0
  MAX=100 # just in case we end up in a loop
  FOUND=0
  while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
    PREVFILE="${FILE}"
    FILE="$(readlink "${FILE}")"
    if [ -z "${FILE}" ]; then
      # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
      FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
      FOUND=1
    elif [ "${FILE#/}" = "${FILE}" ]; then
      # FILE is not an absolute path link, we need to add the relative path to the previous dir
      FILE="$(dirname "${PREVFILE}")/${FILE}"
    fi
    C=$((C+1))
  done
  if [ "${FOUND}" -ne 1 ]; then
    echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
    exit 1
  fi
  echo "${FILE}"
}

DIR="$(dirname "$(readlinkf "$0")")"
APP="${DIR%.app/Contents/*}".app

if [ "${APP}" = "${APP%.app}" ]; then
  echo "Could not find Jalview.app dir" >&2
  exit 2
fi

# check to see if $1 is set and is not start of other cli set args
OPEN=""
if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
 # first argument exists and does not start with a "-" and is not "open"
 OPEN="-open"
fi

APPDIR="${APP}/Contents/Resources/app"
JAVA="${APPDIR}/jre/Contents/Home/bin/java"
GETDOWNTXT="${APPDIR}/getdown.txt"
CLASSPATH=""
if [ -e "${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
    [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
    CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
  done
else
  echo "Cannot find getdown.txt" >&2
  exit 3
fi

if [ \! -e "${JAVA}" ]; then
  echo "Cannot find bundled java, using system and hoping for the best!" >&2
  JAVA=java
fi

# don't quote $OPEN
"${JAVA}" -Xdock:icon="${APPDIR}"/resource/jalview_logo.png -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "$@"