--- biococoa.app-1.6.0.orig/debian/changelog +++ biococoa.app-1.6.0/debian/changelog @@ -0,0 +1,87 @@ +biococoa.app (1.6.0-8build3) oneiric; urgency=low + + * Rebuild for gnustep-base 0.22 and gnustep-gui 0.20. + + -- Colin Watson Mon, 11 Jul 2011 11:08:52 +0100 + +biococoa.app (1.6.0-8build2) natty; urgency=low + + * Rebuild for the GNUstep transition. + + -- Luca Falavigna Fri, 29 Oct 2010 20:10:27 +0200 + +biococoa.app (1.6.0-8build1) karmic; urgency=low + + * Rebuild for the GNUstep transition. + + -- Luca Falavigna Sun, 24 May 2009 11:38:23 +0000 + +biococoa.app (1.6.0-8) unstable; urgency=low + + * Changed the description of the binary package `biococoa.app' to reflect + that this package does not contain the biococoa libraries, but the + SequenceConverter demo application. + * Added myself to the Uploaders. + + -- Charles Plessy Fri, 08 Aug 2008 13:45:58 +0900 + +biococoa.app (1.6.0-7) unstable; urgency=low + + * Added Build-Depends quilt + Closes: #471183 + + -- Andreas Tille Mon, 17 Mar 2008 08:57:12 +0100 + +biococoa.app (1.6.0-6) unstable; urgency=low + + * Put biococoa.app under group maintenance of Debian Med packaging + team (Closes: #454458) + * Standards-Version: 3.7.3 (no changes needed) + * Homepage moved to tags + * Deebhelper >= 5 + * Vcs-* fields + * Added remark about upstream support of GNUstep to long description + + -- Andreas Tille Mon, 10 Mar 2008 22:48:09 +0100 + +biococoa.app (1.6.0-5) unstable; urgency=low + + * Orphaning package, setting maintainer to the Debian QA Group. + + -- Ana Beatriz Guerrero Lopez Fri, 07 Dec 2007 02:05:38 +0100 + +biococoa.app (1.6.0-4) unstable; urgency=low + + * GNUstep transition. + + Updated debian/rules. + + Updated debian/dirs. + * Menu transition: Moved from Apps/Tools to Applications/Science/Biology. + * Added a desktop file. + + -- Gürkan Sengün Sat, 06 Oct 2007 16:02:26 +0200 + +biococoa.app (1.6.0-3) unstable; urgency=low + + * Rebuild against latest libgnustep-gui-dev. + * Bump standards version. + + -- Gürkan Sengün Mon, 18 Sep 2006 23:02:34 +0200 + +biococoa.app (1.6.0-2) unstable; urgency=low + + * Rebuild against latest libgnustep-gui. + * Update manual page. + * Bump standards version. + + -- Gürkan Sengün Fri, 20 Jan 2006 10:48:05 +0100 + +biococoa.app (1.6.0-1) unstable; urgency=low + + * Initial Release. (closes: #287312) + * Incorporated small changes sent in by upstream developer Peter Schols. + * Slightly modified source to let the application be consistent + with other GNUstep applications: + + default background color + + main menu enabled + + -- Gürkan Sengün Tue, 21 Dec 2004 00:30:09 +0100 --- biococoa.app-1.6.0.orig/debian/rules +++ biococoa.app-1.6.0/debian/rules @@ -0,0 +1,57 @@ +#!/usr/bin/make -f +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +include /usr/share/quilt/quilt.make + +include /usr/share/GNUstep/debian/config.mk +GNUSTEP_MAKEFILES=$(GS_MAKE_DIR) + +build: patch build-stamp + +build-stamp: + dh_testdir + gs_make + touch build-stamp + +clean: unpatch + dh_testdir + dh_testroot + rm -f build-stamp + gs_make distclean clean + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + gs_make install DESTDIR=$(CURDIR)/debian/biococoa.app GNUSTEP_INSTALLATION_DOMAIN=SYSTEM + find `pwd`/debian/biococoa.app -name "*.plist" -exec chmod -x {} \; + dh_install debian/*.desktop usr/share/applications/ + rm $(CURDIR)/debian/*.app/usr/lib/GNUstep/Applications/*.app/Resources/*.desktop + +# Build architecture-independent files here. +binary-indep: build install +# We have nothing to do by default. + +# Build architecture-dependent files here. +binary-arch: build install + dh_testdir + dh_testroot + dh_installchangelogs + install -m 644 debian/lintian-override $(CURDIR)/debian/biococoa.app/usr/share/lintian/overrides/biococoa.app + dh_installdocs + dh_installmenu + dh_installman + dh_strip + dh_compress + dh_fixperms + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install --- biococoa.app-1.6.0.orig/debian/menu +++ biococoa.app-1.6.0/debian/menu @@ -0,0 +1,2 @@ +?package(biococoa.app):needs="X11" section="Applications/Science/Biology"\ + title="BioCocoa" command="/usr/bin/BioCocoa" --- biococoa.app-1.6.0.orig/debian/compat +++ biococoa.app-1.6.0/debian/compat @@ -0,0 +1 @@ +5 --- biococoa.app-1.6.0.orig/debian/lintian-override +++ biococoa.app-1.6.0/debian/lintian-override @@ -0,0 +1 @@ +biococoa.app: image-file-in-usr-lib --- biococoa.app-1.6.0.orig/debian/manpages +++ biococoa.app-1.6.0/debian/manpages @@ -0,0 +1 @@ +debian/BioCocoa.1 --- biococoa.app-1.6.0.orig/debian/control +++ biococoa.app-1.6.0/debian/control @@ -0,0 +1,28 @@ +Source: biococoa.app +Section: science +Priority: optional +Maintainer: Debian-Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Andreas Tille , Charles Plessy +Build-Depends: debhelper (>= 5), gnustep-make, libgnustep-gui-dev (>= 0.12.0), quilt +Standards-Version: 3.7.3 +Homepage: http://bioinformatics.org/biococoa/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biococoa/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biococoa/trunk/ + +Package: biococoa.app +Architecture: any +Depends: ${shlibs:Depends} +Description: biological sequence file format conversion applet for GNUstep + Demo application to demonstrate the possibilities of the BioCocoa framework. + . + This package contains a GNUstep applet to convert between sequence file + formats. The BioCocoa framework provides developers with the opportunity to + add support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, + Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT + files by writing only three lines of code. The framework is written in Cocoa + (Objective-C). + . + Version 1.6 is the last upstream version that works with GNUstep. If + newer versions are needed to work under Linux try to convince upstream to + support GNUstep. --- biococoa.app-1.6.0.orig/debian/dirs +++ biococoa.app-1.6.0/debian/dirs @@ -0,0 +1,2 @@ +usr/bin +usr/share/lintian/overrides --- biococoa.app-1.6.0.orig/debian/copyright +++ biococoa.app-1.6.0/debian/copyright @@ -0,0 +1,27 @@ +This package was debianized by Gürkan Sengün on +Tue, 21 Dec 2004 00:30:09 +0100. + +It was downloaded from http://bioinformatics.org/biococoa/ + +Upstream Author: Peter Schols + +Copyright: + + Copyright (C) 2004 The BioCocoa team + + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Library General Public + License as published by the Free Software Foundation; either + version 2 of the License, or (at your option) any later version. + + This library 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 + Library General Public License for more details. + + You should have received a copy of the GNU Library General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA + +Released under the GNU Lesser General Public Library 2.0 +Please see /usr/share/common-licenses/LGPL-2 for the full license. --- biococoa.app-1.6.0.orig/debian/BioCocoa.desktop +++ biococoa.app-1.6.0/debian/BioCocoa.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Type=Application +Version=0.94 +Categories=Education;Science;Biology; +Name=BioCocoa +Comment=GNUstep BioCocoa +Icon=/usr/lib/GNUstep/Applications/BioCocoa.app/Resources/biococoa.tiff +Exec=BioCocoa --- biococoa.app-1.6.0.orig/debian/BioCocoa.1 +++ biococoa.app-1.6.0/debian/BioCocoa.1 @@ -0,0 +1,27 @@ +.TH BIOCOCOA 1 "December 21, 2004" +.SH NAME +BioCocoa \- Sequence file format conversion +.SH SYNOPSIS +.B BioCocoa +.SH DESCRIPTION +This manual page documents briefly the +.B BioCocoa +command. +This manual page was written for the Debian distribution +because the original program does not have a manual page. +.PP +\fBBioCocoa\fP provides developers with the opportunity to add +support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, +Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and +TNT files by writing only three lines of code. The framework is written in +Cocoa (Objective-C). +.SH OPTIONS +These programs follow the usual GNU command line syntax, with long +options starting with two dashes (`-'). +A summary of options is included below. +.SH SEE ALSO +.BR GNUstep (7). +.br +.SH AUTHOR +This manual page was written by G\[:u]rkan Seng\[:u]n , +for the Debian project (but may be used by others). --- biococoa.app-1.6.0.orig/debian/patches/05_main.patch +++ biococoa.app-1.6.0/debian/patches/05_main.patch @@ -0,0 +1,18 @@ +--- biococoa.orig/main.m ++++ biococoa/main.m +@@ -17,7 +17,6 @@ + app = [NSApplication sharedApplication]; + [app setApplicationIconImage: [NSImage imageNamed: @"Calculator.app.tiff"]]; + +- /* + mainMenu = [[NSMenu new]autorelease]; + // Info + [mainMenu addItemWithTitle: @"Info..." +@@ -44,7 +43,6 @@ + keyEquivalent: @"q"]; + + [app setMainMenu: mainMenu]; +- */ + + brain = [Controller new]; + face = [Interface new]; --- biococoa.app-1.6.0.orig/debian/patches/01_plist.patch +++ biococoa.app-1.6.0/debian/patches/01_plist.patch @@ -0,0 +1,13 @@ +--- biococoa.orig/BioCocoaInfo.plist ++++ biococoa/BioCocoaInfo.plist +@@ -1,7 +1,7 @@ + { +- ApplicationName = BioCocoa +- ApplicationDescription = "GNUstep BioCocoaDemo"; +- ApplicationRelease = BioCocoa 1.6"; ++ ApplicationName = "BioCocoa"; ++ ApplicationDescription = "GNUstep BioCocoa"; ++ ApplicationRelease = "BioCocoa 1.6"; + FullVersionID = "1.6.0 Nov 2004"; + Authors = ("Peter Schols "); + Copyright = "Copyright (C) 2004 The BioCocoa team."; --- biococoa.app-1.6.0.orig/debian/patches/02_Controller.patch +++ biococoa.app-1.6.0/debian/patches/02_Controller.patch @@ -0,0 +1,13 @@ +--- biococoa.orig/Controller.m ++++ biococoa/Controller.m +@@ -49,9 +49,7 @@ + [panel setCanChooseDirectories:NO]; + [panel setPrompt:@"Choose File"]; + [panel runModalForDirectory:nil file:nil types:nil]; +- if ([panel filename]) { +- [self readSequenceFile:[panel filename]]; +- } ++ [self readSequenceFile:[panel filename]]; + } + + --- biococoa.app-1.6.0.orig/debian/patches/04_Interface.patch +++ biococoa.app-1.6.0/debian/patches/04_Interface.patch @@ -0,0 +1,11 @@ +--- biococoa.orig/Interface.m ++++ biococoa/Interface.m +@@ -101,7 +101,7 @@ + backing: NSBackingStoreBuffered + defer: NO]; + +- [self setBackgroundColor:[NSColor colorWithCalibratedRed:0.9254 green:0.91372 blue:0.8470 alpha:1.0]]; ++/* [self setBackgroundColor:[NSColor colorWithCalibratedRed:0.9254 green:0.91372 blue:0.8470 alpha:1.0]]; */ + + [self setInitialFirstResponder: openButton]; + --- biococoa.app-1.6.0.orig/debian/patches/03_GNUmakefile.patch +++ biococoa.app-1.6.0/debian/patches/03_GNUmakefile.patch @@ -0,0 +1,27 @@ +--- biococoa.orig/GNUmakefile ++++ biococoa/GNUmakefile +@@ -1,12 +1,14 @@ + # GNUmakefile: makefile for Biococoa + # ++# Copyright (C) 1999 Free Software Foundation, Inc. ++# + # Author: Peter Schols + # Date: 2004 + # + # This file is part of GNUstep. + # + # This program is free software; you can redistribute it and/or modify +-# it under the terms of the GNU Lesser General Public License as published by ++# 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. + # +@@ -25,7 +27,7 @@ + BioCocoa_HEADERS = Controller.h Interface.h BCReader.h BCCreator.h StringAdditions.h + BioCocoa_OBJC_FILES = main.m Controller.m Interface.m BCReader.m BCCreator.m StringAdditions.m + BioCocoa_APPLICATION_ICON = biococoa.tiff +-BioCocoa_RESOURCE_FILES = biococoa.tiff ++BioCocoa_RESOURCE_FILES = biococoa.tiff BioCocoaInfo.plist + + include $(GNUSTEP_MAKEFILES)/application.make + --- biococoa.app-1.6.0.orig/debian/patches/series +++ biococoa.app-1.6.0/debian/patches/series @@ -0,0 +1,5 @@ +01_plist.patch +02_Controller.patch +03_GNUmakefile.patch +04_Interface.patch +05_main.patch