debian/0000755000000000000000000000000012147174300007165 5ustar debian/rules0000755000000000000000000000103212147174167010254 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 VERSION := $(shell dpkg-parsechangelog | grep '^Version:' | sed 's/^Version: \(.*\)-1/\1/') %: dh $@ --with javahelper override_dh_auto_build: mkdir -p classes javac -cp src -source 1.5 -target 1.5 -d classes $(shell find src -name "*.java") jar -cf neobio-$(VERSION).jar -C classes neobio -C bin neobio/gui/icons override_dh_clean: rm -f neobio*.jar rm -rf classes dh_clean get-orig-source: . debian/get-orig-source debian/control0000644000000000000000000000166412147174235010606 0ustar Source: neobio Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Christoph Gille , Andreas Tille Build-Depends: debhelper (>= 8), default-jdk (>= 1:1.6), javahelper (>=0.25) Standards-Version: 3.9.3 Homepage: http://neobio.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/neobio/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/neobio/trunk/ Package: neobio Architecture: all Depends: default-jre | java6-runtime, java-wrappers, ${misc:Depends}, ${java:Depends} Suggests: strap Enhances: strap Description: computes alignments of amino acid and nucleotide sequences Library and graphical user interface for pairwise sequence alignments. Implementation of the dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment). debian/neobio.10000644000000000000000000000137711761352071010536 0ustar .TH NEOBIO 1 "October 30, 2011" .SH NAME neobio \- Pairwise Amino acid sequence and nucleotide sequence alignment in Java .SH SYNOPSIS .B neobio .br .SH DESCRIPTION A graphical user interface is opened. Two amino acid or nucleotide sequences are entered by the user. The program aligns them automatically. .SH SEE ALSO .BR M Crochemore, G Laundau and M Ziv-Ukelson (2002): "A sub-quadratic sequence alignment algorithm for unrestricted cost matrices." http://www.arnetminer.org/viewpub.do?pid=610321 .BR clustalw (1) .BR mafft (1) .BR strap (1) .BR seaview (1) .SH AUTHOR neobio was written by Sergio Anibal de Carvalho Junior. .PP This manual page was written by Christoph Gille , for the Debian project and may be used by others. debian/source/0000755000000000000000000000000012147174300010465 5ustar debian/source/format0000644000000000000000000000001411655325304011700 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000142712147174027011051 0ustar neobio (0.0.20030929-1.1) unstable; urgency=low [ Andreas Tille ] * Enhanced short description [ gregor herrmann ] * Non-maintainer upload. * Fix "Transition package to default java implementation": apply patch from Ubuntu / James Page: * Transition package to default java implementation: - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency to default-jre | java6-runtime. - d/rules: Specify source/target = 1.5 to ensure that backwards compatible bytecode is built. (Closes: #684162) -- gregor herrmann Wed, 22 May 2013 18:53:39 +0200 neobio (0.0.20030929-1) unstable; urgency=low * Initial release (Closes: #647543) -- Christoph Gille Wed, 30 May 2012 11:21:18 +0200 debian/neobio.manpages0000644000000000000000000000001211655325304012153 0ustar debian/*1 debian/compat0000644000000000000000000000000211655371767010406 0ustar 8 debian/neobio.install0000644000000000000000000000023511661450224012032 0ustar data usr/lib/neobio debian/bin/neobio usr/bin neobio-*.jar usr/share/java/ debian/neobio.desktop usr/share/applications doc/* usr/share/doc/neobio/html debian/copyright0000644000000000000000000000402711761350767011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://sourceforge.net/projects/neobio/files/neobio/pre-alpha/neobio.zip Comment: Some files were removed, see the get-orig-source target in ‘debian/rules’. Files: * Copyright: © 2003 Sergio Anibal de Carvalho Junior License: GPL-2+ NeoBio is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . NeoBio is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with NeoBio; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. . Proper attribution of the author as the source of the software would be appreciated. Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’ Files: debian/* Copyright: © 2011 Christoph Gille License: GPL-3 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . Comment: On Debian systems, the complete text of the GNU General Public License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’ debian/doc-base0000644000000000000000000000053211661450224010567 0ustar Document: neobio Title: NeoBio class library API Author: Sergio A. de Carvalho Jr. Abstract: NeoBio class library API This document is the API specification for the NeoBio class library of computational biology algorithms. Section: Science/Medicine Format: HTML Index: /usr/share/doc/neobio/html/index.html Files: /usr/share/doc/neobio/html/* debian/menu0000644000000000000000000000036211761352071010061 0ustar ?package(neobio):\ needs="X11"\ section="Applications/Science/Biology"\ hints="Sequence alignment"\ longtitle="Neobio: sequence alignment computation"\ title="Neobio"\ command="/usr/bin/neobio" debian/get-orig-source0000644000000000000000000000130711761351256012134 0ustar #!/bin/sh set -x VERSION=`dpkg-parsechangelog | grep '^Version:' | sed 's/^Version: \(.*\)-1/\1/'` ZIPF=neobio_${VERSION}.zip REPACKED=neobio-${VERSION} TARBALLS=`pwd`/../tarballs mkdir -p ${TARBALLS} cd ${TARBALLS} [ -f ${ZIPF} ] || wget -q -O ${ZIPF} http://sourceforge.net/projects/neobio/files/neobio/pre-alpha/neobio.zip rm -rf ${REPACKED} mkdir ${REPACKED} cd ${REPACKED} unzip -q ../${ZIPF} find . -name "*.class" -delete find . -name "Thumbs.db" -delete find . -name "*.ps" -delete find . -name "*.pdf" -delete find . -empty -type d -delete cd .. GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf neobio_${VERSION}.orig.tar.gz ${REPACKED} rm -rf ${REPACKED} cd .. debian/neobio.jlibs0000644000000000000000000000001411761363523011470 0ustar neobio*.jar debian/bin/0000755000000000000000000000000012147174300007735 5ustar debian/bin/neobio0000755000000000000000000000023211761365134011143 0ustar #!/bin/sh . /usr/lib/java-wrappers/java-wrappers.sh find_java_runtime java6 exec $JAVA_HOME/bin/java -cp /usr/share/java/neobio.jar neobio.gui.NeoBio $* debian/upstream0000644000000000000000000000053311761352071010755 0ustar Reference: Author: Maxime Crochemore and Gad M. Landau and Michal Ziv-Ukelson Title: A sub-quadratic sequence alignment algorithm for unrestricted cost matrices Booktitle: "SODA'02" Year: 2002 Pages: 679-688 URL: http://arnetminer.org/publication/a-sub-quadratic-sequence-alignment-algorithm-for-unrestricted-cost-matrices-610321.html debian/neobio.desktop0000644000000000000000000000026611655325304012044 0ustar [Desktop Entry] Version=1.0 Name=Sequence alignments neobio Exec=/usr/bin/neobio Terminal=false Type=Application Categories=Education;Science;Chemistry; GenericName=neobio Comment=