#!/bin/bash

cwd=$(pwd)
cwdmod=$(echo $cwd | sed -e "s/\//\\\\\//g")

procalign=$cwd/../align-4.0/lib/procalign.jar
echo $cwd
echo $cwdmod
echo $procalign

sed -i -e s/\\\(path=\"\\\).*lab4/\\1$cwdmod\\/../ "../Theme 5 Alignment API/.classpath"

java -jar $procalign file:///$cwd/$1 file:///$cwd/$2
