Add new alignment package, probalign.

4 files changed, 96 insertions, 0 deletions

diff --git a/sci-biology/probalign/Manifest b/sci-biology/probalign/Manifest
new file mode 100644
index 0000000..3658d66
--- /dev/null
+++ b/sci-biology/probalign/Manifest
@@ -0,0 +1,5 @@
+AUX 1.3-look-in-usr-bin-for-probalign.patch 584 RMD160 16b0112df505052f003e94e1ae9b691c3b98ff00 SHA1 fbcb633fa5c57c61d6d9a1c7e8df2f8c0b6a60e1 SHA256 312e2f0ae50ae66e3c384c2d3e73d5d360c2366a8659d35b0e5d19674fb0a47f
+AUX gcc-4.3.patch 438 RMD160 7cf8e4661e2f973ba95e450a20f21807c4838b8f SHA1 cfa326205d497ae7156627e67a0a097ae08acbc3 SHA256 fd382a6cc25050b4fae74a6e3047cba5a31e73c623f31898b0fcbdefedaebad5
+DIST probaligngui_beta_1.3.tar.gz 1794865 RMD160 bb20fe4fd50015b839df78c4f179c21e6d0e041f SHA1 3456aa2d17c2ad42323e49f7530476679708210d SHA256 7343024dc7c2ae5fa415697bc1e1fe8accf93e515f093dea09ed1fc256c4f2a0
+EBUILD probalign-1.3_beta.ebuild 1507 RMD160 0b2515f3e93e91f3a9923500f4bd6b344c9b821a SHA1 a01ace6e7960427d008b1b68d1c8fd75fd9ba379 SHA256 518a0f1dbce897f171e95a5be9a9659525beb7fb738066692f4242f946ba22ac
+MISC ., 584 RMD160 16b0112df505052f003e94e1ae9b691c3b98ff00 SHA1 fbcb633fa5c57c61d6d9a1c7e8df2f8c0b6a60e1 SHA256 312e2f0ae50ae66e3c384c2d3e73d5d360c2366a8659d35b0e5d19674fb0a47f
diff --git a/sci-biology/probalign/files/1.3-look-in-usr-bin-for-probalign.patch b/sci-biology/probalign/files/1.3-look-in-usr-bin-for-probalign.patch
new file mode 100644
index 0000000..57d1e02
--- /dev/null
+++ b/sci-biology/probalign/files/1.3-look-in-usr-bin-for-probalign.patch
@@ -0,0 +1,12 @@
+diff -ur probaligngui_beta_1.3.orig/javagui/src/Frame1.java probaligngui_beta_1.3/javagui/src/Frame1.java
+--- probaligngui_beta_1.3.orig/javagui/src/Frame1.java	2008-04-08 19:26:11.000000000 -0700
++++ probaligngui_beta_1.3/javagui/src/Frame1.java	2008-04-08 19:26:57.000000000 -0700
+@@ -1042,7 +1042,7 @@
+     //System.getenv("PROBALIGN_HOME");
+ 
+     //unix code
+-    String command = new String(basedir+"/probalign/bin/probalign "); 
++    String command = new String("/usr/bin/probalign "); 
+     command = command + filename;
+ 
+     GapOpen = Float.parseFloat(jGapOpen.getText());
diff --git a/sci-biology/probalign/files/gcc-4.3.patch b/sci-biology/probalign/files/gcc-4.3.patch
new file mode 100644
index 0000000..3803dcc
--- /dev/null
+++ b/sci-biology/probalign/files/gcc-4.3.patch
@@ -0,0 +1,12 @@
+diff -ur probaligngui_beta_1.3.orig/probalign/src/Main.cc probaligngui_beta_1.3/probalign/src/Main.cc
+--- probaligngui_beta_1.3.orig/probalign/src/Main.cc	2006-11-25 12:34:24.000000000 -0800
++++ probaligngui_beta_1.3/probalign/src/Main.cc	2008-04-08 19:26:12.000000000 -0700
+@@ -14,6 +14,8 @@
+ #include <iomanip>

+ #include <iostream>

+ #include <cerrno>

++#include <climits>

++#include <cstring>

+ 

+ //struct for column reliability

+ 

diff --git a/sci-biology/probalign/probalign-1.3_beta.ebuild b/sci-biology/probalign/probalign-1.3_beta.ebuild
new file mode 100644
index 0000000..609a9b5
--- /dev/null
+++ b/sci-biology/probalign/probalign-1.3_beta.ebuild
@@ -0,0 +1,67 @@
+# 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
+	java-pkg_jar-from itext
+	ejavac \
+		-d classes \
+		-classpath iText.jar \
+		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
+}