Someone wasn't reading the upstream changelogs ... add an option to build the Java GUI.

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

4 files changed, 87 insertions, 7 deletions

diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog
index fcbb619bae1b..4f44c918c66a 100644
--- a/sci-biology/amap/ChangeLog
+++ b/sci-biology/amap/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/amap
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.4 2008/04/17 18:20:13 markusle Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.5 2009/07/27 05:52:01 dberkholz Exp $
+
+*amap-2.2-r1 (27 Jul 2009)
+
+  27 Jul 2009; Donnie Berkholz <dberkholz@gentoo.org>; +amap-2.2-r1.ebuild:
+  Someone wasn't reading the upstream changelogs ... add an option to build
+  the Java GUI.
 
 *amap-2.2 (17 Apr 2008)
 
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index 786b0a2f7e48..7401e09e5527 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 2.0-fix-cxxflags.patch 835 RMD160 d31c598e91e58ada05320f8c536a2b61c4d50f5d SHA1 42911d9882e4c359f68e318fe65efb9f877fb680 SHA256 fe3e568f785d1d4ee28deeb62cba28aa700066bab7d41828c84d9fcc612fff4e
 AUX 2.1-fix-cxxflags.patch 882 RMD160 003609b0c9ad3c74c28fa4f7be83ee24512b5722 SHA1 193671beb78a2ac6e7db037d782d7228dec1e23b SHA256 f2e9edef582eae51762703be4d34dcf6b760fecbcd338883efc926b120506a01
 AUX amap-2.2-cxxflags.patch 964 RMD160 e39ec71fbf1a65500037dd0d88aa7679f142d755 SHA1 63afb43ecb5f567a4ca81c7d7f17cf1c3ac2f3a4 SHA256 63f78e4384d7f00486097aea1c37ee1721c1bd3d3ddfc5f413849e959d6678bd
@@ -7,6 +10,14 @@ DIST amap.2.1.tar.gz 103301 RMD160 b8ade9699c0fa81100ebce8cbb3d0f812ba80824 SHA1
 DIST amap.2.2.tar.gz 102861 RMD160 6b47b66ab5095e35bcb14a599a25687fef8e799c SHA1 618e498581302e140270a0e029ab87d378c450ef SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4
 EBUILD amap-2.0.ebuild 802 RMD160 f18976169ccd0f9e9b3cf451bfb9050bd8cd1ad4 SHA1 307ff9955bcda4c041c147c43376d5b9d4d3523e SHA256 d579540cf8279214386ef0f0982d9a159d217ebe2a1ba0c14a3f27cead90a7e0
 EBUILD amap-2.1.ebuild 929 RMD160 2f3ccd91756e6c0257d1a3494dbab6568a5ddc6a SHA1 af196511bb2c04488f1010129c58c7acd75ab98c SHA256 844dba80f3ea12062dcfbbc4392e1991a4df752b82b773efc0f3645d4dae1c65
+EBUILD amap-2.2-r1.ebuild 1448 RMD160 efd711f93c8861d0938fbd96bd8b57b74aef869b SHA1 91392d7b837739573108b684ec1aea92bc4066e5 SHA256 fef2949a0b2b76cfac001029ed754db012a75783bdf830be9b1303cd28b73173
 EBUILD amap-2.2.ebuild 980 RMD160 ca076f2a81306b313c2861dbe5781a29c179f8f8 SHA1 bea1a904b24caab224c01159801fc572bb6b5ba5 SHA256 7172952f43000517cdb71065c594b38cd4fd6345b1c900f9c3ce1d16decb6b5e
-MISC ChangeLog 1063 RMD160 9ef1bbb7ac62ffe5f46d40a0a9ed02ff18e98dd3 SHA1 25fd10093515dc4509b6e930b090abfba9a57377 SHA256 9599d7a3172b5dc6ae9dcfa8435eacebc5f7f2dde5b6ef1cbc04fd88738af75b
+MISC ChangeLog 1261 RMD160 5514b8cf43edb3ed672ac86851750d1cf4c405d2 SHA1 a1caaa32a55e23ca44568feca24c532a908754be SHA256 25e04a32bcda6add908d3bc71a054864945126542fa421de068342d8fa1b9f72
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkptQIkACgkQXVaO67S1rttUAwCfe+hHm3OoFuKkAJkoI+u2JPyT
+ez0AoN2F7cOrwJ7blDVXGO9qQeyVQDkQ
+=Rwnc
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/amap/amap-2.2-r1.ebuild b/sci-biology/amap/amap-2.2-r1.ebuild
new file mode 100644
index 000000000000..bef78dab765f
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.2-r1.ebuild,v 1.1 2009/07/27 05:52:01 dberkholz Exp $
+
+# Java is optional, don't force an ant dependency
+JAVA_ANT_DISABLE_ANT_CORE_DEP="yes"
+
+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/amap/download/${MY_P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+RDEPEND="
+	java? (
+		>=virtual/jre-1.5
+	)"
+DEPEND="${RDEPEND}
+	java? (
+		>=dev-java/ant-core-1.7.0
+		>=dev-java/javatoolkit-0.3.0-r2
+		>=virtual/jdk-1.5
+	)"
+S="${WORKDIR}/${PN}-align"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-cxxflags.patch
+	epatch "${FILESDIR}"/${P}-gcc4.3.patch
+}
+
+src_compile() {
+	pushd "${S}"/align
+	emake \
+		CXX="$(tc-getCXX)" \
+		OPT_CXXFLAGS="${CXXFLAGS}" \
+		|| die "make failed"
+	popd
+
+	if use java; then
+		pushd "${S}"/display
+		eant all || die
+		popd
+	fi
+}
+
+src_install() {
+	dobin align/${PN}
+	dodoc align/README align/PROBCONS.README
+	insinto /usr/share/${PN}/examples
+	doins examples/* || die "Failed to install examples"
+	if use java; then
+		java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar
+		java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
+	fi
+}
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 58976b5791ab..095d25930c8d 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -3,13 +3,15 @@ Hash: SHA1
 
 AUX mafft-6.240-mktemp.patch 6497 RMD160 ffa5d5889315614fd065e72425b1db3e8272f7b2 SHA1 5584719991e7b5c7d014c8cb1b59391f71f24668 SHA256 783f6f5678781dff1fafece92f37688698052fe1e0bfa13850443a0f8cc91533
 DIST mafft-6.240-src.tgz 657197 RMD160 1cb77af7a5a6b9ab818560d9626e746fb7a3b839 SHA1 8fc05350d9dcf8a9f56bdeed20790a4e1f21ceba SHA256 d0183ab1d6a5e0d1132b95cb917fedb3b6dc16c38d3fde35d7140ecdca555e8f
+DIST mafft-6.707-without-extensions-src.tgz 455884 RMD160 6676133b9f50c2037f13f50ea86e9543022028ce SHA1 1dd955255e5572b8c4a0b23c65cea832383b6a97 SHA256 08789aa9351128e32b0003cb524668c3f2e35aec7ea9f834047f0780851989a0
 EBUILD mafft-6.240-r1.ebuild 910 RMD160 c09e76a79148cd64c8c931e33a9dbf4fdee086b7 SHA1 3de8b46a86dd83496ae1520893a576179b77ddf0 SHA256 45ebb273c1f05c1012a16b79305916792a8dedb42020d1ada18244ea5ea2d6aa
-MISC ChangeLog 1243 RMD160 9a2941a4ee2fca396974a0c03c9ef039c2ab54ef SHA1 c7a2b07e8d8f594efec2710eba7317a79a23a00a SHA256 c72af12ced5f1108e7edc01ed34ba5bbf7663522f871b0dbf14739f1cc3c198d
+EBUILD mafft-6.707.ebuild 873 RMD160 5551f700c2d01ea25d1b0074273db8292d22157f SHA1 6d1d10296e13df14ed3db9ae9ded77adbad10ed4 SHA256 fd2c6d4be6a8eb56fed19bfd0fecba8ad41beff499189bd0e0f982eaebe173eb
+MISC ChangeLog 1514 RMD160 6f172ceb02ccf3feedc704091c8e714a87721aeb SHA1 4b96fdce6c2bea0513c8a225154b05426872fb21 SHA256 8ec35ebab8941b0556090eb5eae3d22179dbeb8c14269f786cd8145a5c2372c2
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
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