#!/usr/bin/env bash

program_dir() {
 local p l
 if [ "${0:0:1}" = "/" ]
 then
   p=$0
 else
   p=$PWD/$0
 fi
 if [ -L "$p" ]
 then
   l=$(find $p -printf '%l')
   if [ "${l:0:1}" = "/" ]
   then
     p=$l
   else
     p=$(dirname $p)/$l
   fi
 fi
 echo $(dirname $p)
} 


dir=$(program_dir)
dir=${dir%"/."}

dir=${dir%"/bin"}

export SARSE_HOME=$dir

if [ $PERL5LIB ]; then
	PERL5LIB=$PERL5LIB:$dir/programs/rnadbtools/perl/perl_modules
else
  	export PERL5LIB=$dir/programs/rnadbtools/perl/perl_modules
fi

PATH=$dir/programs/rnadbtools/bin:$PATH
PATH=$dir/programs/pipes:$PATH
PATH=$dir/programs/pfold/bin:$PATH
PATH=$dir/programs/pcluster/bin:$PATH
PATH=$dir/programs/foldalignm/src:$PATH
PATH=$dir/programs/foldalignm:$PATH

ver_pat='[a-z"](1\.[5-9])'
if java -version 2>&1 | grep -qE $ver_pat
then
  java=java
else
  java=$(ls -1 /usr/java/*/bin/java \
         | grep -E $ver_pat \
         | sort -r | head -n 1)
  [ -x "$java" ] || {
      echo "Cannot find usable Java version in /usr/java/" 1>&2
      echo "Please install SUN Java 1.5 or 6" 1>&2
      exit 1
  }
fi 

CLASSPATH=$dir/lib/biojava-1.4.jar:$dir/lib/editor.jar:$dir/lib/xercesImpl.jar:$dir/lib/xml-apis.jar
export CLASSPATH=$CLASSPATH:$dir/programs/foldalignm:$dir/programs/foldalignm/src

$java -cp $CLASSPATH -Xmx512m -DSARSE_HOME=$dir -jar $dir/lib/editor.jar $*
