#!/bin/sh
# ----------------------------------------------------------------------------
#  Copyright 2001-2006 The Apache Software Foundation.
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#       http://www.apache.org/licenses/LICENSE-2.0
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
# ----------------------------------------------------------------------------
#
#   Copyright (c) 2001-2006 The Apache Software Foundation.  All rights
#   reserved.


# resolve links - $0 may be a softlink
PRG="$0"

while [ -h "$PRG" ]; do
  ls=`ls -ld "$PRG"`
  link=`expr "$ls" : '.*-> \(.*\)$'`
  if expr "$link" : '/.*' > /dev/null; then
    PRG="$link"
  else
    PRG=`dirname "$PRG"`/"$link"
  fi
done

PRGDIR=`dirname "$PRG"`
BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`

# Reset the REPO variable. If you need to influence this use the environment setup file.
REPO=


# OS specific support.  $var _must_ be set to either true or false.
cygwin=false;
darwin=false;
case "`uname`" in
  CYGWIN*) cygwin=true ;;
  Darwin*) darwin=true
           if [ -z "$JAVA_VERSION" ] ; then
             JAVA_VERSION="CurrentJDK"
           else
             echo "Using Java version: $JAVA_VERSION"
           fi
		   if [ -z "$JAVA_HOME" ]; then
		      if [ -x "/usr/libexec/java_home" ]; then
			      JAVA_HOME=`/usr/libexec/java_home`
			  else
			      JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
			  fi
           fi       
           ;;
esac

if [ -z "$JAVA_HOME" ] ; then
  if [ -r /etc/gentoo-release ] ; then
    JAVA_HOME=`java-config --jre-home`
  fi
fi

# For Cygwin, ensure paths are in UNIX format before anything is touched
if $cygwin ; then
  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
fi

# If a specific java binary isn't specified search for the standard 'java' binary
if [ -z "$JAVACMD" ] ; then
  if [ -n "$JAVA_HOME"  ] ; then
    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
      # IBM's JDK on AIX uses strange locations for the executables
      JAVACMD="$JAVA_HOME/jre/sh/java"
    else
      JAVACMD="$JAVA_HOME/bin/java"
    fi
  else
    JAVACMD=`which java`
  fi
fi

if [ ! -x "$JAVACMD" ] ; then
  echo "Error: JAVA_HOME is not defined correctly." 1>&2
  echo "  We cannot execute $JAVACMD" 1>&2
  exit 1
fi

if [ -z "$REPO" ]
then
  REPO="$BASEDIR"/lib
fi

CLASSPATH="$BASEDIR"/etc:"$REPO"/rtree-0.4.1.jar:"$REPO"/rxjava-core-0.20.4.jar:"$REPO"/jsr305-3.0.2.jar:"$REPO"/guava-27.0.1-jre.jar:"$REPO"/failureaccess-1.0.1.jar:"$REPO"/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:"$REPO"/checker-qual-2.5.2.jar:"$REPO"/error_prone_annotations-2.2.0.jar:"$REPO"/j2objc-annotations-1.1.jar:"$REPO"/animal-sniffer-annotations-1.17.jar:"$REPO"/commons-io-2.6.jar:"$REPO"/commons-csv-1.6.jar:"$REPO"/commons-math3-3.6.1.jar:"$REPO"/alignment-1.9.3.jar:"$REPO"/core-1.9.3.jar:"$REPO"/bytecode-1.9.3.jar:"$REPO"/sequencing-1.9.3.jar:"$REPO"/dsh-commandline-1.1.jar:"$REPO"/commons-lang-2.6.jar:"$REPO"/dsh-compress-1.3.jar:"$REPO"/htsjdk-2.16.1.jar:"$REPO"/commons-jexl-2.1.1.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/snappy-java-1.1.4.jar:"$REPO"/xz-1.5.jar:"$REPO"/ngs-java-2.9.0.jar:"$REPO"/commons-compress-1.18.jar:"$REPO"/dsh-bio-align-1.1.jar:"$REPO"/dsh-bio-alignment-1.1.jar:"$REPO"/commons-codec-1.11.jar:"$REPO"/dsh-bio-assembly-1.1.jar:"$REPO"/dsh-bio-feature-1.1.jar:"$REPO"/dsh-bio-range-1.1.jar:"$REPO"/dsh-bio-read-1.1.jar:"$REPO"/dsh-bio-variant-1.1.jar:"$REPO"/dsh-graph-1.0.jar:"$REPO"/dsh-functor-1.0.jar:"$REPO"/dsh-bio-tools-1.1.jar

ENDORSED_DIR=
if [ -n "$ENDORSED_DIR" ] ; then
  CLASSPATH=$BASEDIR/$ENDORSED_DIR/*:$CLASSPATH
fi

if [ -n "$CLASSPATH_PREFIX" ] ; then
  CLASSPATH=$CLASSPATH_PREFIX:$CLASSPATH
fi

# For Cygwin, switch paths to Windows format before running java
if $cygwin; then
  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
  [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
  [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
  [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
fi

exec "$JAVACMD" $JAVA_OPTS  \
  -classpath "$CLASSPATH" \
  -Dapp.name="dsh-remap-phase-set" \
  -Dapp.pid="$$" \
  -Dapp.repo="$REPO" \
  -Dapp.home="$BASEDIR" \
  -Dbasedir="$BASEDIR" \
  org.dishevelled.bio.tools.RemapPhaseSet \
  "$@"
