Add biojava for bug #231333. Bump dev-java/bytecode to latest revision.

svn path=/java-overlay/; revision=7056

4 files changed, 80 insertions, 3 deletions

diff --git a/dev-java/biojava/Manifest b/dev-java/biojava/Manifest
new file mode 100644
index 00000000..642550fb
--- /dev/null
+++ b/dev-java/biojava/Manifest
@@ -0,0 +1,2 @@
+DIST biojava-1.6-all.jar 24571007 RMD160 b3e64f00406d8d075c0074273fb1420f28eea024 SHA1 16b01300e56189ad3ce8a5dfc74ecae70b195174 SHA256 2d10334fe6022d1b64219505ba4d2a32027ab7218d775878506d3e7c00f6ce7e
+EBUILD biojava-1.6.ebuild 2034 RMD160 de1a477d8d70a743c0e746e15a91cfa6da730867 SHA1 7332016c135fc67376038e3e74d14f5d00ee6fde SHA256 a27e656ec261230bbc4991787af3c36b2823477076dd4fa6d05032c58ba9a38d
diff --git a/dev-java/biojava/biojava-1.6.ebuild b/dev-java/biojava/biojava-1.6.ebuild
new file mode 100644
index 00000000..19be364e
--- /dev/null
+++ b/dev-java/biojava/biojava-1.6.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# TODO:
+# -Fix javadoc generation OutOfMemoryError
+# -Add launchers for 2 apps in biojava-apps.jar
+# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag)
+
+EAPI=2
+
+#JAVA_PKG_IUSE="doc source test"
+JAVA_PKG_IUSE="source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="Biojava bytecode manipulation library"
+HOMEPAGE="http://biojava.org"
+SRC_URI="http://www.biojava.org/download/bj${PN/./}/all/${P}-all.jar"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jgrapht:0
+	dev-java/commons-cli:1
+	dev-java/commons-collections:0
+	dev-java/commons-dbcp:0
+	dev-java/commons-pool:0
+	dev-java/bytecode:0"
+
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEPEND}"
+DEPEND=">=virtual/jdk-1.5
+	app-arch/unzip
+	${COMMON_DEPEND}
+	test?
+	(
+		dev-java/junit:4
+		dev-java/ant-junit4
+	)"
+
+S="${WORKDIR}/biojava-live_${PV}"
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+
+src_prepare() {
+	einfo "Removing budled jars."
+	find . -name "*.jar" -print -delete
+	rm -r doc/*
+	java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar
+	java-pkg_jar-from commons-cli-1
+	#java-pkg_jar-from commons-collections commons-collections.jar commons-collections-2.1.jar
+	java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar
+	java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar
+	java-pkg_jar-from bytecode
+	java-pkg_jar-from --build-only junit-4 junit.jar junit-4.4.jar
+}
+
+src_compile() {
+	#ANT_OPTS="${ANT_OPTS} -Xmx512m"
+	eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all)
+}
+
+src_install() {
+	java-pkg_newjar ant-build/biojava.jar ${PN}.jar
+	java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar
+	java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar
+	#use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos}
+	use source && java-pkg_dosrc {src,apps,demos}/org
+}
+
+src_test() {
+	ANT_TASKS="ant-junit4" eant runtests
+}
diff --git a/dev-java/bytecode/Manifest b/dev-java/bytecode/Manifest
index 4b320947..25beb75b 100644
--- a/dev-java/bytecode/Manifest
+++ b/dev-java/bytecode/Manifest
@@ -1,2 +1,2 @@
-DIST bytecode-0.92.tar.bz2 27711 RMD160 86914c77f9f0136d42c2c21cbfb28842fda73e7e SHA1 01a44de64fe9467e363fd41ac04a3f601b000f70 SHA256 65153dd67dbb3c785305f2830d7232f83e1fa6e014560804c1ca46f55c8cf954
-EBUILD bytecode-0.92.ebuild 828 RMD160 02f096dc5168c72af2c6f044503b7c9ce16da4a0 SHA1 135531c6b73c2727e7c0dc88f8d9fd5e42b86d19 SHA256 b10fb964af59a150440830b5572258c4a2a21d88b8084e18c64c89a305192d33
+DIST bytecode-20081007.tar.bz2 29112 RMD160 6f9a651fa5a9d655c0087fdae8ce3086d424936c SHA1 86e46eb96889d77309b632d6dbe33b270cdaeedd SHA256 fbcbecc957675128d1ae5d34288ecab8d8086cc2949b503ac1800b64e2ed556a
+EBUILD bytecode-20081007.ebuild 814 RMD160 77a33f03e35f61470bb45b649fd70beb8cb91b0d SHA1 7e869c4b1924f1de16495beb5ffadda87046b597 SHA256 8cd906e589c229eb72b95188bcb39db586413fadd28f2e1b2a54fb0374857a34
diff --git a/dev-java/bytecode/bytecode-0.92.ebuild b/dev-java/bytecode/bytecode-20081007.ebuild
index 56f25f55..0b48bfb0 100644
--- a/dev-java/bytecode/bytecode-0.92.ebuild
+++ b/dev-java/bytecode/bytecode-20081007.ebuild
@@ -11,7 +11,7 @@ inherit eutils java-pkg-2 java-ant-2
 DESCRIPTION="Biojava bytecode manipulation library"
 HOMEPAGE="http://biojava.org"
 SRC_URI="http://dev.gentoo.org/~serkan/distfiles/${P}.tar.bz2"
-# svn export svn://code.open-bio.org/biojava/bytecode/tags/bytecode-0_92/ bytecode-0.92
+# svn export svn://code.open-bio.org/biojava/bytecode/trunk -r {20081007}
 LICENSE="LGPL-2.1"
 SLOT="0"
 KEYWORDS="~amd64"