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# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
JAVA_PKG_IUSE="doc source"
inherit java-pkg-opt-2 java-pkg-simple toolchain-funcs
DESCRIPTION="Protein multiple-alignment-based sequence annealing"
HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
SRC_URI="http://baboon.math.berkeley.edu/amap/download/${P/-/.}.tar.gz"
S="${WORKDIR}/amap-align"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
DEPEND="java? ( >=virtual/jdk-1.8:* )"
RDEPEND="java? ( >=virtual/jre-1.8:* )"
DOCS=( align/{README,PROBCONS.README} )
PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
"${FILESDIR}"/${P}-includes.patch
)
src_prepare() {
default
use java && java-pkg-opt-2_src_prepare && java-pkg_clean
}
src_configure() {
tc-export CXX
}
src_compile() {
emake -C align
if use java; then
JAVA_JAR_FILENAME="amapdisplay.jar"
JAVA_SRC_DIR="display/src"
java-pkg-simple_src_compile
fi
}
src_install() {
dobin align/${PN}
insinto /usr/share/${PN}
doins -r examples
use java && java-pkg-simple_src_install
}
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