dnaplotter

#!/bin/bash -

#
# This script will start the Artemis circular plot on a UNIX system.
#

QUIET=no

usage () {
    echo "SYNOPSIS"
    echo "        DNA Plotter: DNA Image Generation Tool"
    echo "USAGE"
    echo "        $0 [options]"
    echo "OPTIONS"
    echo "        -t FILE      Read a template file"
    echo
    echo "EXAMPLES"
    echo "        % dnaplotter" 
    echo "        % dnaplotter -t <template file>" 
    echo
    echo "HOMEPAGE"
    echo "        http://www.sanger.ac.uk/science/tools/dnaplotter/"
    echo   
    
    exit 0
}

add_proxy_properties() {

	if [[ "$http_proxy" = "" ]]
	then
		http_proxy=$HTTP_PROXY
	fi
	
	if [[ "$http_proxy" = "" ]]
	then
	 	http_proxy=$HTTP_proxy
	fi
	
	if [[ "$http_proxy" != "" ]]
	then
		APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
	fi
}


#
# Resolve script path (inc symlinks)
#
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
    SOURCE="$(readlink "$SOURCE")"
    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script


#
# Parse arguments.
#
TEMPLATE_FILE_ARG=
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
while test $# != 0
do
    case $1 in
	    -t)   	    TEMPLATE_FILE_ARG="$1 $2"; shift ;;
	    -D*)        APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES $1" ;;
	    -quiet)     QUIET=yes ; APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Drun_quietly=true" ;;
	    -help)      usage ;;
	    --help)     usage ;;
	    -h)         usage ;;
	    *)          usage ;;
    esac
    shift
done


JAR_NAME=dnaplotter.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED

#
# Use a custom Java version if necessary
#
if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
then
	JAVA=`which java`
else
	JAVA_HOME=$ARTEMIS_JAVA_JRE
	JAVA=$ARTEMIS_JAVA_JRE/bin/java
fi

#
# Allow URLs to work from behind firewalls.
#
add_proxy_properties

#
# "-mx2g" sets the maximum amount of memory to use. 
# This may need to be increased when dealing with large files
#
if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
then
    FLAGS="-mx2g -ms100m -noverify"
else
    FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
fi

PLATTMP=`uname`
if [[ "$PLATTMP" = "Darwin" ]]
then
  	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Circular-Plot"
  	JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
  	ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
fi

if [[ "$QUIET" = "no" ]]
then
    echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
fi

$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
result=$?

exit $result

exit $?