add sci-biology/imagej

sci-biology/imagej/Manifest

@@ -0,0 +1,4 @@
+AUX fix_non-ascii_char.patch 593 SHA256 3f05ddf95c87587279e6f5a8404728daeab377d9b9de206c275240766ac1d9ed SHA512 7d4045664857336afeceaebb0a185a111ade58f2ee2cfbfab6f45d4916782b199b2ef0605cdbd19610e0a46305448572eac0c40bb639553db9436a46ba2fae31 WHIRLPOOL beffecd4dc34d75b9975f028f1b6ac6a5ce063a64fa03dbb2602b56e39b468ecfbb1694ad7c03bc3b2c4f84e0225e1bd0e62263b0f22efeff53a75a1b4a0d272
+DIST ImageJ.png 13012 SHA256 02b93e7614a2ab52ca5dbdc941dc99b4b461c91b28203d33e877746f97e12b86 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3 WHIRLPOOL c8f5328abd55b3ec23f0676d29bd47f91059f22de3ed6ad98c95670e504ffa3403bd91ee75d601b68034dd686d252163680b5fd57aaea8bb8b7b6d275ac9964f
+DIST ij149v-src.zip 1541887 SHA256 47518c5d1c4e68e9a84fee3909223d56b037339e86630cc422962b24861200a4 SHA512 c0cc6b66314a3a93d2dcfa6a7a6f98410a0cc14940c29f71d9e64285a8bed6213000bbcdc308b1727506af7ee02a17b8c82096a2259a64f8279fcc22ce3acf8f WHIRLPOOL 6dc4fb02aa3c8a9a3171461b57cfb65705665c7513cb513608a56508a61a0f81d3bd8baa74deaea104cb4325cf9902a4d8d13418abd4c14218a9d5d389285545
+EBUILD imagej-1.49v.ebuild 1166 SHA256 2821c9331467bee044f973ddc32da6d6c6740a0920b23051ff6542eeec92067b SHA512 023c1df963716c8114b965fded48c539c849b8438a303911fa899ebdffb40652fdce2e8368ef15e930c9b94a3a6a390b9372e3ec639569aff6eddb6f897c9cb4 WHIRLPOOL daee8b23edfe49462ad27b2d7a7371567af98b357ee44bca9ef44fd8e35cb283760beafacf9fefc8d9098fdd6ed85e8ada5d0603e32fbb55bae58dfdc961b9a8

sci-biology/imagej/files/fix_non-ascii_char.patch

@@ -0,0 +1,11 @@
+--- source/ij/process/AutoThresholder.java	2012-07-17 11:23:08.000000000 -0400
++++ source/ij/process/AutoThresholder.java.new	2012-09-28 10:15:29.997623832 -0400
+@@ -606,7 +606,7 @@
+ 		//
+ 		// Assumes a bimodal histogram. The histogram needs is smoothed (using a
+ 		// running average of size 3, iteratively) until there are only two local maxima.
+-		// Threshold t is such that yt−1 > yt <= yt+1.
++		// Threshold t is such that yt-1 > yt <= yt+1.
+ 		// Images with histograms having extremely unequal peaks or a broad and
+ 		// flat valleys are unsuitable for this method.
+ 		int iter =0;

sci-biology/imagej/imagej-1.49v.ebuild

@@ -0,0 +1,48 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+JAVA_PKG_IUSE="doc source examples"
+inherit java-pkg-2 java-ant-2
+
+ICON="ImageJ.png"
+
+DESCRIPTION="Image Processing and Analysis in Java"
+HOMEPAGE="http://rsb.info.nih.gov/ij/"
+SRC_URI="http://rsb.info.nih.gov/ij/download/src/ij${PV/./}-src.zip
+http://rsb.info.nih.gov/ij/images/${ICON}"
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="debug"
+
+RDEPEND=">=virtual/jre-1.6"
+DEPEND=">=virtual/jdk-1.6
+source? ( app-arch/zip )"
+
+S=${WORKDIR}/source
+
+pkg_setup() {
+	export EANT_BUILD_TARGET="build"
+	export EANT_DOCS_TARGET="javadocs"
+	export EANT_EXTRA_ARGS="
+-DImageJ.default=${EANT_BUILD_TARGET}
+-Djavac.debug=$(use debug && echo on || echo off)
+$(use_doc ${EANT_DOCS_TARGET})
+"
+}
+
+src_install() {
+	use doc && java-pkg_dojavadoc ../api/
+	use source && java-pkg_dosrc ij/
+	use examples && java-pkg_doexamples macros/ plugins/
+
+	doicon ${DISTDIR}/${ICON}
+	make_desktop_entry "${PN}" "ImageJ" ${ICON%\.*} \
+		"Graphics;Science;Biology"
+
+	java-pkg_dojar *.jar
+	java-pkg_dolauncher ${PN} --main ij.ImageJ --pwd /usr/share/imagej/lib
+}