Clean java bits thanks to sera. General cleanup, fix linking order, fix building with gcc 4.6 wrt #360517. Drop old.

Package-Manager: portage-2.2.0_alpha27/cvs/Linux x86_64

1 files changed, 50 insertions, 0 deletions

diff --git a/sci-biology/amap/amap-2.2-r2.ebuild b/sci-biology/amap/amap-2.2-r2.ebuild
new file mode 100644
index 000000000000..5e47337e2554
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.2-r2.ebuild,v 1.1 2011/03/26 10:56:00 xarthisius Exp $
+
+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
+}