#!/bin/bash
set -e

pkg="neobio"

if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi

cp -a /usr/lib/${pkg}/data/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP
gunzip -r *

echo "Test 1"
java -cp /usr/share/java/neobio.jar neobio.textui.NeoBio NW dna01a.txt dna02a.txt S 1 -1 -1
echo "PASS"

echo "Test 2"
java -cp /usr/share/java/neobio.jar neobio.textui.NeoBio CLZG dna01a.txt dna02a.txt M blosum62.txt
echo "PASS"
