# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

inherit versionator java-pkg-2 java-ant-2 eutils

EANT_ANT_TASKS="jaxb-tools"

MY_PV=$(replace_all_version_separators '_')

DESCRIPTION="A visualization platform for molecular interaction networks"
HOMEPAGE="http://www.cytoscape.org/"
SRC_URI="http://chianti.ucsd.edu/Cyto-${MY_PV}/cytoscapeSource-v${PV}.tar.gz"

LICENSE="LGPL-2.1"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"

DEPEND=">=virtual/jdk-1.6"
RDEPEND=">=virtual/jre-1.6"

S="${WORKDIR}"

src_unpack() {
	unpack ${A}
#	java-ant_remove-taskdefs
#	find -name '*.jar' -print -delete
	# Skip the jalopy ant build target (produces access violations)
	perl -i -ne 'print unless /taskdef.*name="jalopy"/../<\/target>/' "${S}/build.xml" || die
}

src_install() {
	java-pkg_dojar cytoscape.jar
	dobin resources/bin/cytoscape.sh
	make_desktop_entry cytoscape.sh Cytoscape
	dodoc docs/pdf/manual.pdf
}