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# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
inherit toolchain-funcs java-pkg-2
PV_TYPE="${PV##*_}"
PV_NUM="${PV%%_*}"
MY_PV="${PV_TYPE}_${PV_NUM}"
MY_PN="${PN}gui"
MY_P="${MY_PN}_${MY_PV}"
DESCRIPTION="Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments"
HOMEPAGE="http://www.cs.njit.edu/usman/probalign/"
SRC_URI="http://www.cs.njit.edu/usman/probalign/${MY_P}.tar.gz"
LICENSE=""
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
RDEPEND=">=virtual/jre-1.4
dev-java/itext"
DEPEND=">=virtual/jdk-1.4
dev-java/itext"
S=${WORKDIR}/${MY_P}
src_unpack() {
unpack ${A}
cd "${S}"
epatch "${FILESDIR}"/1.3-look-in-usr-bin-for-probalign.patch
epatch "${FILESDIR}"/gcc-4.3.patch
}
src_compile() {
pushd probalign/src
emake \
CXX=$(tc-getCXX) \
CXXFLAGS="${CXXFLAGS} ${LDFLAGS}" \
|| die "emake failed"
popd
pushd javagui
ejavac \
-d classes \
-classpath $(java-pkg_getjars itext) \
src/*.java \
|| die
pushd classes
jar cvf \
probaligngui.jar \
probalign/*.class -C ../ images/about.png -C ../ images/a.gif \
|| die
popd
popd
}
src_install() {
dobin probalign/bin/probalign || die
java-pkg_dojar javagui/classes/probaligngui.jar
java-pkg_dolauncher probaligngui --main probalign.gui
newdoc probalign/README README.probalign
newdoc probalign/RELEASE_NOTES RELEASE_NOTES.probalign
newdoc README README.probaligngui
}
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