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# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI="2"
inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2
MY_P=${PN}.${PV}
DESCRIPTION="Protein multiple-alignment-based sequence annealing"
HOMEPAGE="http://bio.math.berkeley.edu/amap/"
SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
RDEPEND="java? ( >=virtual/jre-1.5 )"
DEPEND="java? ( >=virtual/jdk-1.5 )"
S=${WORKDIR}/${PN}-align
src_prepare() {
epatch "${FILESDIR}"/${P}-makefile.patch \
"${FILESDIR}"/${P}-includes.patch
}
src_compile() {
emake -C align CXX="$(tc-getCXX)" \
OPT_CXXFLAGS="${CXXFLAGS}" || die "make failed"
if use java; then
pushd "${S}"/display
eant -Ddisplay all || die
popd
fi
}
src_install() {
dobin align/${PN} || die
dodoc align/{README,PROBCONS.README} || die
insinto /usr/share/${PN}/examples
doins examples/* || die
if use java; then
java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar
java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
fi
}
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