diff --git a/academic/treeview/README b/academic/treeview/README new file mode 100644 index 0000000000..86281f2a43 --- /dev/null +++ b/academic/treeview/README @@ -0,0 +1,21 @@ +TreeView is a simple program for displaying phylogenies. Some of its +features include: + +- reads many different tree file formats (including NEXUS, PHYLIP, + Hennig86, NONA, MEGA, and ClustalW/X) +- supports standard the TrueType and Postscript fonts +- supports native graphics file format for copying pictures into + other applications, and for saving graphics files +- print preview +- can print multiple trees per page and/or one tree over more than + one page +- has drag-and-drop facility for easy opening of files +- Web-based online help +- tree editor + +For details and citation: +Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic +trees on personal computers. Computer Applications in the Biosciences +12: 357-358. + +This requires wxGTK or wxPython, available at SlackBuilds.org. diff --git a/academic/treeview/References b/academic/treeview/References new file mode 100644 index 0000000000..c5c8df7b7f --- /dev/null +++ b/academic/treeview/References @@ -0,0 +1 @@ +Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358. \ No newline at end of file diff --git a/academic/treeview/doinst.sh b/academic/treeview/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/treeview/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/treeview/slack-desc b/academic/treeview/slack-desc new file mode 100644 index 0000000000..1df5c90d4e --- /dev/null +++ b/academic/treeview/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +treeview: treeview (Program to display phylogenetic trees) +treeview: +treeview: TreeView provides a simple way to view the contents of a NEXUS, +treeview: PHYLIP, Hennig86, Clustal, or other format tree file. +treeview: +treeview: +treeview: +treeview: +treeview: +treeview: References: /usr/doc/treeview-$VERSION/References +treeview: Home: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ diff --git a/academic/treeview/treeview.SlackBuild b/academic/treeview/treeview.SlackBuild new file mode 100644 index 0000000000..2823c52761 --- /dev/null +++ b/academic/treeview/treeview.SlackBuild @@ -0,0 +1,109 @@ +#!/bin/sh + +# Slackware build script for treeview +# Written by Petar Petrov, and +# hereby submitted to the public domain + +# Based on the treeview PKGBUILD from Archlinux AUR +# (http://aur.archlinux.org/packages.php?ID=19489). +# PKGBUILD submitter is abhidg and PKGBUILD maintainer +# is Stunts. Thank you! + +# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING +# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ +# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. + +PRGNAM=treeview +VERSION=${VERSION:-0.5.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=tv + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) export ARCH=i486 ;; + arm*) export ARCH=arm ;; + *) export ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# The patch is from Archlinux AUR, as mentioned above. +# For AUR it has been taken from Debian. Thank you both! +patch -p1 < $CWD/treeviewx_0.5.1-7.diff +for i in ./debian/patches/*.diff; do +patch -p1 < $i +done + +# Disable SVG support. If you want it, you should build +# wxGTK or wxPython including svg from contrib/src/svg +# Then, of course comment the next line. +sed "s:USE_SVG=1:USE_SVG=0:" -i configure + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/tv.desktop $PKG/usr/share/applications +cp $CWD/tv.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING INSTALL \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/treeview/treeview.info b/academic/treeview/treeview.info new file mode 100644 index 0000000000..8fba131fb2 --- /dev/null +++ b/academic/treeview/treeview.info @@ -0,0 +1,10 @@ +PRGNAM="treeview" +VERSION="0.5.1" +HOMEPAGE="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html" +DOWNLOAD="http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/download/0.5/tv-0.5.1.tar.gz" +MD5SUM="07e1ed8873c5f19ded7294668233bae1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/treeview/treeviewx_0.5.1-7.diff b/academic/treeview/treeviewx_0.5.1-7.diff new file mode 100644 index 0000000000..dc9c12c204 --- /dev/null +++ b/academic/treeview/treeviewx_0.5.1-7.diff @@ -0,0 +1,1796 @@ +--- treeviewx-0.5.1.orig/debian/watch ++++ treeviewx-0.5.1/debian/watch +@@ -0,0 +1,2 @@ ++version=3 ++http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html download\/\d\.\d\/tv-(\d+)\.(\d+)\.(\d+)\.tar\.gz +--- treeviewx-0.5.1.orig/debian/treeviewx.sharedmimeinfo ++++ treeviewx-0.5.1/debian/treeviewx.sharedmimeinfo +@@ -0,0 +1,13 @@ ++ ++ ++ ++ Phylogenetic tree in Clustal W format ++ Arbre phylogénétique au format Clustal W ++ Albero filogenetico in formato Clustal W ++ ++ ++ ++ ++ ++ ++ +--- treeviewx-0.5.1.orig/debian/menu ++++ treeviewx-0.5.1/debian/menu +@@ -0,0 +1,8 @@ ++?package(treeviewx):\ ++ needs="X11"\ ++ section="Applications/Science/Biology"\ ++ title="TreeView X"\ ++ command="/usr/bin/tv"\ ++ icon="/usr/share/pixmaps/treeviewx.xpm" \ ++ hints="Phylogenetic tree drawing program"\ ++ longtitle="TreeView X: a phylogenetic tree viewer which can do SVG export" +--- treeviewx-0.5.1.orig/debian/rules ++++ treeviewx-0.5.1/debian/rules +@@ -0,0 +1,8 @@ ++#!/usr/bin/make -f ++ ++include /usr/share/cdbs/1/class/autotools.mk ++include /usr/share/cdbs/1/rules/patchsys-quilt.mk ++include /usr/share/cdbs/1/rules/debhelper.mk ++ ++install/treeviewx:: ++ install -m 644 bitmaps/treeview.xpm $(CURDIR)/debian/treeviewx/usr/share/pixmaps/treeviewx.xpm +--- treeviewx-0.5.1.orig/debian/upstream-metadata.yaml ++++ treeviewx-0.5.1/debian/upstream-metadata.yaml +@@ -0,0 +1,14 @@ ++Contact: Roderic D. M. Page ++DOI: 10.1093/bioinformatics/12.4.357 ++Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ ++Name: Treeview X ++PMID: 8902363 ++Reference-Author: Page, Roderic D. M. ++Reference-Journal: Comput. Appl. Biosci. ++Reference-Number: 4 ++Reference-Page: 357-8 ++Reference-Title: TreeView: an application to display phylogenetic trees on personal computers ++Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357 ++Reference-Volume: 12 ++Reference-Year: 1996 ++Watch: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html download\/\d\.\d\/tv-(\d+)\.(\d+)\.(\d+)\.tar\.gz +--- treeviewx-0.5.1.orig/debian/control ++++ treeviewx-0.5.1/debian/control +@@ -0,0 +1,22 @@ ++Source: treeviewx ++Section: science ++Priority: optional ++Maintainer: Debian Med Packaging Team ++DM-Upload-Allowed: yes ++Uploaders: Charles Plessy , ++ Andreas Tille ++Build-Depends: debhelper (>= 7.1), cdbs, autotools-dev, quilt, libwxgtk2.8-dev ++Standards-Version: 3.8.4 ++Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/treeviewx/trunk/?rev=0&sc=0 ++Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/treeviewx/trunk/ ++Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ ++ ++Package: treeviewx ++Architecture: any ++Depends: ${shlibs:Depends}, ${misc:Depends} ++Description: Displays and prints phylogenetic trees ++ TreeView X is an open source and multi-platform program to display ++ phylogenetic trees. It can read and display NEXUS and Newick format tree files ++ (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It ++ allows to order the branches of the trees, and to export the trees in SVG ++ format. +--- treeviewx-0.5.1.orig/debian/copyright ++++ treeviewx-0.5.1/debian/copyright +@@ -0,0 +1,61 @@ ++Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5’. ++ ++Name : TreeView X ++Author : Roderic D. M. Page ++Source : http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz ++ ++License: GPL-2+ ++ ++ TreeView X 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. ++ ++ TreeView X 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 package; if not, write to the Free Software ++ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ ++TreeView X has been released by its author under the GNU GPL (see COPYING), but ++most of its files use a header which places them under the GNU Library GPL ++(LGPL). The author of TreeView X confirmed to the maintainer of this package ++that his intention is to have TreeView X released under the GPL. Therefore, as ++permitted the clause 3 of the LGPL, the licence of these files is changed to ++the GPL through the patch in the following file: ++debian/patches/60_LGPLtoGPL.dpatch ++ ++Some files which are part of TreeView X - namely ntree.h, ntree.cpp and ++lcaquery.cpp - have no copyright notice. The author of TreeView X confirmed to ++the maintainer of this package that he is the copyright holder for them. ++Therefore, they are distributed under the terms of the COPYING file, which is ++the GNU GPL. ++ ++On Debian systems, the complete text of the GNU Library General Public ++License can be found in ‘/usr/share/common-licenses/LGPL-2’ and the ++complete text of the GNU General Public License version 2 can be found ++in ‘/usr/share/common-licenses/GPL-2’. ++ ++Files: ncl-2.0/* ++Copyright: © 1999 Paul O. Lewis ++License: GPL-2+ ++Comment: TreeView X is statically linked to the Nexus Class Library. ++ ++Files: TreeLib/* ++Copyright: © 2001 Roderic D. M. Page ++License: GPL-2+ ++Comment: The files under the TreeLib directory are part of TreeView X, ++ as they have never been released as an independent library. ++ ++Files: debian/tv.1.xml debian/tv.1 ++Copyright: © 2006-2008 Charles Plessy ++License: Same as TreeView X ++ ++Files: debian/* ++Copyright: © 2006–2010 Charles Plessy ++ © 2007 David Paleino ++License: PD ++ Please treat the packaging work as if it were in the public domain. +--- treeviewx-0.5.1.orig/debian/treeviewx.mime ++++ treeviewx-0.5.1/debian/treeviewx.mime +@@ -0,0 +1 @@ ++text/x-clustalw-tree; /usr/bin/tv '%s'; description=ClustalW Phylogenetic Tree +--- treeviewx-0.5.1.orig/debian/manpages ++++ treeviewx-0.5.1/debian/manpages +@@ -0,0 +1 @@ ++debian/tv.1 +--- treeviewx-0.5.1.orig/debian/README.source ++++ treeviewx-0.5.1/debian/README.source +@@ -0,0 +1,4 @@ ++This packages uses the quilt patch system. Please read ++/usr/share/doc/quilt/README.source for more information. ++ ++ -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 +--- treeviewx-0.5.1.orig/debian/dirs ++++ treeviewx-0.5.1/debian/dirs +@@ -0,0 +1,2 @@ ++/usr/share/applications ++/usr/share/pixmaps +--- treeviewx-0.5.1.orig/debian/treeviewx.desktop ++++ treeviewx-0.5.1/debian/treeviewx.desktop +@@ -0,0 +1,19 @@ ++[Desktop Entry] ++Version=1.0 ++Terminal=false ++Icon=treeviewx ++Exec=tv %f ++Name=TreeView X ++GenericName=Tree Plotter ++GenericName[en]=Tree Plotter ++GenericName[fr]=Traceur d'arbres ++GenericName[pt_BR]=Plotador de árvores ++GenericName[it]=Plotter di Alberi ++Comment=Displays, modifies, prints and exports in SVG format phylogenetic trees ++Comment[en]=Displays, modifies, prints and exports in SVG format phylogenetic trees ++Comment[fr]=Affiche, modifie, imprime et exporte au format SVG des arbres phyolgénétiques ++Comment[pt_BR]=Exibe, modifica e exporta em formato SVG árvores filogenéticas ++Comment[it]=Mostra, modifica, stampa ed esporta in formato SVG alberi filogenetici ++Type=Application ++Categories=Biology;Science;Education; ++MimeType=text/x-clustalw-tree; +--- treeviewx-0.5.1.orig/debian/tv.1.xml ++++ treeviewx-0.5.1/debian/tv.1.xml +@@ -0,0 +1,109 @@ ++ ++ ++Charles"> ++ Plessy"> ++ 1"> ++ charles-debian-nospam@plessy.org"> ++ ++ TREEVIEW X"> ++ ++ Debian"> ++ GNU"> ++ GPL"> ++]> ++ ++ ++ ++
++ &dhemail; ++
++ ++ ++ 2006 ++ 2008 ++ &dhusername; ++ ++ ++ ++ &dhucpackage; ++ ++ &dhsection; ++ ++ ++ &dhpackage; ++ ++ displays and prints phylogenetic trees ++ ++ ++ ++ tv filename ++ ++ ++ ++ DESCRIPTION ++ ++ ++ tv is the program that starts the ++ TreeView X GUI. ++ ++ ++ TreeView X is an open source and multi-platform program to ++ display phylogenetic trees. It can read and display NEXUS and ++ Newick format tree files (such as those output by PAUP*, ++ ClustalX, TREE-PUZZLE, and other programs). It allows to order ++ the branches of the trees, and to export the trees in SVG ++ format. ++ ++ If started from the command line with ++ filename as an argument, TreeView X ++ will open the tree stored in filename. ++ ++ ++ ++ ++ ++ SEE ALSO ++ ++ ++ At present there is is no documentation for TreeView X. In the ++ meantime please see the online documentation for TreeView ++ (remember that TreeView X has only a subset of the features of ++ TreeView). http://taxonomy.zoology.gla.ac.uk/rod/treeview/treeview_manual.html ++ ++ ++ ++ ++ REFERENCE ++ Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358. ++ ++ ++ ++ AUTHOR ++ ++ TreeView X was written by Rod ++ Page (r.page@bio.gla.ac.uk) URL: ++ http://darwin.zoology.gla.ac.uk/~rpage/treeviewx. ++ ++ This manual page was written by &dhusername; (&dhemail;) for ++ the &debian; system (but may be used by others). ++ ++ ++ ++ ++ Permission is granted to copy, distribute and/or modify TreeView X and this document under the terms of the &gnu; General Public License, Version 2 or any later version published by the Free Software Foundation. ++ ++ ++ ++ On Debian systems, the complete text of the GNU General Public ++ License can be found in /usr/share/common-licenses/GPL. ++ ++ ++ ++ +--- treeviewx-0.5.1.orig/debian/tree.phb ++++ treeviewx-0.5.1/debian/tree.phb +@@ -0,0 +1,55 @@ ++( ++( ++( ++( ++( ++( ++( ++( ++( ++gi|6981382|ref|NP_037328.1|:0.01004, ++gi|53765|emb|CAA40856.1|:0.01133) ++100:0.04471, ++gi|3024415|sp|O35507|PPARA_CAV:0.06881) ++100:0.02177, ++gi|19401877|gb|AAL87699.1|AF48:0.07924) ++100:0.11628, ++( ++gi|50882280|gb|AAT85615.1|:0.13020, ++gi|14994035|gb|AAK76392.1|:-0.00248) ++100:0.11211) ++100:0.04510, ++( ++( ++gi|68303294|gb|AAY89587.1|:0.24273, ++gi|24666202|ref|NP_730322.1|:0.29207) ++100:0.05743, ++( ++( ++gi|32026|emb|CAA68398.1|:0.02054, ++gi|114585739|ref|XP_001164266.:0.00169) ++85:0.02207, ++gi|109502151|ref|XP_001059459.:0.04437) ++100:0.30861) ++100:0.14445) ++100:0.04138, ++( ++gi|85376346|gb|ABC70398.1|:0.14816, ++gi|16304880|emb|CAC95230.1|:0.21548) ++74:0.01669) ++100:0.08347, ++gi|13311191|emb|CAC34402.1|:0.08993) ++100:0.07117, ++( ++( ++( ++gi|6755138|ref|NP_035276.1|:0.00295, ++gi|454001|gb|AAC52134.1|:-0.00295) ++60:0.00339, ++gi|14627168|gb|AAG60685.2|:0.00503) ++85:0.00763, ++gi|22003526|gb|AAM88773.1|:0.01343) ++34:0.00198) ++22:0.00163, ++gi|66471842|emb|CAD91388.1|:0.06787, ++gi|47678881|dbj|BAD20642.1|:0.00789)TRICHOTOMY; +--- treeviewx-0.5.1.orig/debian/README.Debian ++++ treeviewx-0.5.1/debian/README.Debian +@@ -0,0 +1,7 @@ ++TreeView X for Debian ++--------------------- ++ ++The original source code was modified by wrapping some character chains with ++wxT(), in order to build it with wxGTK 2.6. ++ ++ -- Charles Plessy , Sat, 11 Feb 2006 17:27:26 +0900 +--- treeviewx-0.5.1.orig/debian/tv.1 ++++ treeviewx-0.5.1/debian/tv.1 +@@ -0,0 +1,51 @@ ++.\" Title: TREEVIEW X ++.\" Author: ++.\" Generator: DocBook XSL Stylesheets v1.73.2 ++.\" Date: 01/12/2008 ++.\" Manual: ++.\" Source: ++.\" ++.TH "TREEVIEW X" "1" "01/12/2008" "" "" ++.\" disable hyphenation ++.nh ++.\" disable justification (adjust text to left margin only) ++.ad l ++.SH "NAME" ++tv - displays and prints phylogenetic trees ++.SH "SYNOPSIS" ++.HP 3 ++\fBtv\fR [\fIfilename\fR] ++.SH "DESCRIPTION" ++.PP ++\fBtv\fR ++is the program that starts the TreeView X GUI\. ++.PP ++TreeView X is an open source and multi\-platform program to display phylogenetic trees\. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE\-PUZZLE, and other programs)\. It allows to order the branches of the trees, and to export the trees in SVG format\. ++.PP ++If started from the command line with ++\fIfilename\fR ++as an argument, TreeView X will open the tree stored in ++\fIfilename\fR\. ++.SH "SEE ALSO" ++.PP ++At present there is is no documentation for TreeView X\. In the meantime please see the online documentation for TreeView (remember that TreeView X has only a subset of the features of TreeView)\. http://taxonomy\.zoology\.gla\.ac\.uk/rod/treeview/treeview_manual\.html ++.SH "REFERENCE" ++.PP ++Page, R\. D\. M\. 1996\. TREEVIEW: An application to display phylogenetic trees on personal computers\. Computer Applications in the Biosciences 12: 357\-358\. ++.SH "AUTHOR" ++.PP ++TreeView X ++was written by Rod Page (r\.page@bio\.gla\.ac\.uk) URL: http://darwin\.zoology\.gla\.ac\.uk/~rpage/treeviewx\. ++.PP ++This manual page was written by Charles Plessy () for the ++Debian(TM) ++system (but may be used by others)\. ++.PP ++Permission is granted to copy, distribute and/or modify TreeView\ X and this document under the terms of the ++GNU ++General Public License, Version 2 or any later version published by the Free Software Foundation\. ++.PP ++On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\. ++.SH "COPYRIGHT" ++Copyright \(co 2006, 2008 Charles Plessy ++.br +--- treeviewx-0.5.1.orig/debian/changelog ++++ treeviewx-0.5.1/debian/changelog +@@ -0,0 +1,96 @@ ++treeviewx (0.5.1-7) unstable; urgency=low ++ ++ * Refreshed debian/copyright according to latest developments ++ of the machine-readable format. ++ * Collected upstream information in debian/upstream-metadata.yaml ++ and removed bibliographic information from the long description ++ (debian/control). ++ * Added in ‘debian/patches/90_fix_for_wx2.8.diff’ Ryan Niebur's patch ++ to build TreeView X with wxWidgets 2.8 (Closes: #567238, thanks!). ++ * Build against libwxgtk2.8-dev (debian/control). ++ * Checked conformance with Policy 3.8.4 and incremented Standards-Version ++ to reflect this (debian/control, no changes needed). ++ ++ -- Charles Plessy Thu, 28 Jan 2010 18:52:23 +0900 ++ ++treeviewx (0.5.1-6) unstable; urgency=low ++ ++ [ Charles Plessy ] ++ * Updated my email address. ++ ++ [ David Paleino ] ++ * Removed myself from Uploaders ++ ++ [ Andreas Tille ] ++ * Standards-Version: 3.8.3 (Added README.source) ++ * debhelper 7 ++ * Added myself to uploaders ++ * Tested whether package also build against libwxgtk2.8-dev but failed ++ -> Upstream should be contacted about wxgtk upgrade to be safe for ++ the future ++ * Removed explicit dependency from libgnomeprintui2.2-0 ++ Closes: #542579 ++ ++ -- Andreas Tille Tue, 01 Sep 2009 11:18:11 +0200 ++ ++treeviewx (0.5.1-5) unstable; urgency=low ++ ++ [ Charles Plessy ] ++ * Debian Menu transition: Apps/Science becomes Applications/Science/Biology. ++ * debian/control: ++ - Moved the Homepage: field out from the package's description. ++ - Checked conformance with policy 3.7.3 ++ - Allowed upload by Debian Maintainers. ++ * MIME support: ++ - debian/treeviewx.sharedmimeinfo declares that .phb and .ph files are ++ Clustal W phylogenetic trees. ++ - debian/treeviewx.mime and debian/treeviewx.desktop declare that ++ TreeView X can open Clustal W phylogenetic trees. ++ - debian/rules calls dh_installmime. ++ * debian/copyright: made machine-parsable. ++ * Relicensed the manpage under "same as TreeView X" terms. ++ * Switched to CDBS and quilt. ++ ++ [ David Paleino ] ++ * Added support for MIME types (.phb is now associated to treeviewx) ++ * fixed FTBFS with GCC 4.3: missing #includes (Closes: #455177) ++ * Added statically generated tv.1 (to save buildd time) ++ * Other minor fixes ++ * Added Italian to the .desktop file ++ ++ -- Charles Plessy Sat, 26 Jan 2008 22:32:36 +0900 ++ ++treeviewx (0.5.1-4) unstable; urgency=low ++ ++ * Add Subversion repository URL to debian/control. ++ * Including /usr/share/dpatch/dpatch.make in debian/rules. ++ * Including a patch from Martin Michlmayr to build TreeView X ++ with gcc 4.3 (Closes: #417729). ++ ++ -- Charles Plessy Mon, 9 Apr 2007 10:03:14 +0900 ++ ++treeviewx (0.5.1-3) unstable; urgency=low ++ ++ [ William Alexander Grant ] ++ * Added 70_choose_tree.dpatch, prevents segfault when choosing no tree. ++ ++ [ Charles Plessy ] ++ * Tested and imported the patch from Ubuntu. Thanks William ! ++ ++ -- Charles Plessy Tue, 13 Feb 2007 23:38:33 +0900 ++ ++treeviewx (0.5.1-2) unstable; urgency=low ++ ++ * Added a transitional dependency on libgnomeprintui2.2-0, thanks to Roger ++ Leigh for understanding the problem. Closes: #392219 ++ * Fixed the debian/watch file. ++ * Added an example tree (courtesy of Roger Leigh). ++ ++ -- Charles Plessy Sat, 14 Oct 2006 12:16:21 +0900 ++ ++treeviewx (0.5.1-1) unstable; urgency=low ++ ++ * Initial release Closes: #352506 ++ ++ -- Charles Plessy Thu, 16 Mar 2006 11:30:23 +0900 ++ +--- treeviewx-0.5.1.orig/debian/compat ++++ treeviewx-0.5.1/debian/compat +@@ -0,0 +1 @@ ++7 +--- treeviewx-0.5.1.orig/debian/examples ++++ treeviewx-0.5.1/debian/examples +@@ -0,0 +1 @@ ++debian/tree.phb +--- treeviewx-0.5.1.orig/debian/install ++++ treeviewx-0.5.1/debian/install +@@ -0,0 +1 @@ ++debian/treeviewx.desktop /usr/share/applications/ +--- treeviewx-0.5.1.orig/debian/patches/series ++++ treeviewx-0.5.1/debian/patches/series +@@ -0,0 +1,7 @@ ++45_gcc4.3.diff ++50_wxT_tv.cpp.diff ++51_wxT_tview.cpp.diff ++60_LGPLtoGPL.diff ++70_choose_tree.diff ++80_missing_includes.diff ++90_fix_for_wx2.8.diff +--- treeviewx-0.5.1.orig/debian/patches/51_wxT_tview.cpp.diff ++++ treeviewx-0.5.1/debian/patches/51_wxT_tview.cpp.diff +@@ -0,0 +1,25 @@ ++Adding wxT escapes in the tview.cpp file ++--- tv-0.5.1-old/tview.cpp 2005-08-31 17:55:13.000000000 +0900 +++++ tv-0.5.1/tview.cpp 2006-03-13 09:35:50.000000000 +0900 ++@@ -184,8 +184,8 @@ ++ wxString pictureFileName = GetFrame()->GetTitle(); ++ pictureFileName += wxT(".emf"); ++ wxFrame *f = GetMainFrame(); ++- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, ++- "Enhanced metafile (*.emf)|*.emf", +++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName, +++ wxT("Enhanced metafile (*.emf)|*.emf"), ++ wxSAVE|wxOVERWRITE_PROMPT); ++ ++ if (dialog.ShowModal() == wxID_OK) ++@@ -204,8 +204,8 @@ ++ #else ++ wxFrame *f = GetMainFrame(); ++ #endif ++- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, ++- "SVG vector picture files (*.svg)|*.svg", +++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), pictureFileName, +++ wxT("SVG vector picture files (*.svg)|*.svg"), ++ wxSAVE|wxOVERWRITE_PROMPT); ++ ++ if (dialog.ShowModal() == wxID_OK) +--- treeviewx-0.5.1.orig/debian/patches/90_fix_for_wx2.8.diff ++++ treeviewx-0.5.1/debian/patches/90_fix_for_wx2.8.diff +@@ -0,0 +1,15 @@ ++Author: Ryan Niebur ++Bug-Debian: http://bugs.debian.org/567238 ++Description: To build with wxwidgets 2.8 ++Forwarded: Roderic Page ++--- treeviewx-0.5.1.orig/tview.cpp +++++ treeviewx-0.5.1/tview.cpp ++@@ -994,7 +994,7 @@ ++ MyCanvas::MyCanvas(wxView *v, wxMDIChildFrame *frame, const wxPoint& pos, const wxSize& size, long style): ++ wxScrolledWindow(frame, -1, pos, size, style) ++ { ++- SetBackgroundColour(wxColour("WHITE")); +++ SetBackgroundColour(wxColour(wxT("WHITE"))); ++ view = v; ++ magnification = 1; ++ } +--- treeviewx-0.5.1.orig/debian/patches/80_missing_includes.diff ++++ treeviewx-0.5.1/debian/patches/80_missing_includes.diff +@@ -0,0 +1,71 @@ ++80_strlen_charactersblock.cpp.dpatch by David Paleino ++Fixes "error: ‘strlen’ was not declared in this scope" during compilation ++diff -urNad trunk~/TreeLib/Parse.cpp trunk/TreeLib/Parse.cpp ++--- trunk~/TreeLib/Parse.cpp 2007-11-18 14:39:17.000000000 +0100 +++++ trunk/TreeLib/Parse.cpp 2007-11-18 14:39:18.000000000 +0100 ++@@ -19,8 +19,9 @@ ++ */ ++ ++ // $Id: Parse.cpp,v 1.9 2002/02/23 12:22:32 rdmp1c Exp $ ++- +++ ++ #include +++#include ++ #include "Parse.h" ++ ++ // Return the next token in the string ++diff -urNad trunk~/TreeLib/treereader.cpp trunk/TreeLib/treereader.cpp ++--- trunk~/TreeLib/treereader.cpp 2007-11-18 14:39:17.000000000 +0100 +++++ trunk/TreeLib/treereader.cpp 2007-11-18 14:39:36.000000000 +0100 ++@@ -22,6 +22,7 @@ ++ ++ #include "treereader.h" ++ #include +++#include ++ ++ #if __MWERKS__ ++ #include ++diff -urNad trunk~/ncl-2.0/src/charactersblock.cpp trunk/ncl-2.0/src/charactersblock.cpp ++--- trunk~/ncl-2.0/src/charactersblock.cpp 2007-11-18 14:14:43.000000000 +0100 +++++ trunk/ncl-2.0/src/charactersblock.cpp 2007-11-18 14:39:18.000000000 +0100 ++@@ -8,6 +8,7 @@ ++ #include "discretematrix.h" ++ #include "assumptionsblock.h" ++ #include "charactersblock.h" +++#include ++ ++ using namespace std; ++ ++diff -urNad trunk~/ncl-2.0/src/nexus.cpp trunk/ncl-2.0/src/nexus.cpp ++--- trunk~/ncl-2.0/src/nexus.cpp 2007-10-02 09:51:43.000000000 +0200 +++++ trunk/ncl-2.0/src/nexus.cpp 2007-11-18 14:39:18.000000000 +0100 ++@@ -2,6 +2,7 @@ ++ #include "xnexus.h" ++ #include "nexustoken.h" ++ #include "nexus.h" +++#include ++ ++ #define NCL_NAME_AND_VERSION "NCL version 2.01" ++ #define NCL_COPYRIGHT "Copyright (c) 2000 by Paul O. Lewis" ++diff -urNad trunk~/ncl-2.0/src/nexustoken.cpp trunk/ncl-2.0/src/nexustoken.cpp ++--- trunk~/ncl-2.0/src/nexustoken.cpp 2007-10-02 09:51:43.000000000 +0200 +++++ trunk/ncl-2.0/src/nexustoken.cpp 2007-11-18 14:39:18.000000000 +0100 ++@@ -1,6 +1,7 @@ ++ #include "nexusdefs.h" ++ #include "xnexus.h" ++ #include "nexustoken.h" +++#include ++ ++ using namespace std; ++ ++diff -urNad trunk~/ncl-2.0/src/nxsstring.cpp trunk/ncl-2.0/src/nxsstring.cpp ++--- trunk~/ncl-2.0/src/nxsstring.cpp 2007-10-02 09:51:43.000000000 +0200 +++++ trunk/ncl-2.0/src/nxsstring.cpp 2007-11-18 14:39:18.000000000 +0100 ++@@ -20,6 +20,7 @@ ++ #include ++ #include ++ #include +++#include ++ #include "nxsstring.h" ++ ++ nxsstring& nxsstring::operator+=( const double d ) +--- treeviewx-0.5.1.orig/debian/patches/70_choose_tree.diff ++++ treeviewx-0.5.1/debian/patches/70_choose_tree.diff +@@ -0,0 +1,13 @@ ++## 70_choose_tree.dpatch by William Alexander Grant ++diff -urNad treeviewx-0.5.1~/tview.cpp treeviewx-0.5.1/tview.cpp ++--- treeviewx-0.5.1~/tview.cpp 2006-12-17 10:33:21.000000000 +1100 +++++ treeviewx-0.5.1/tview.cpp 2006-12-17 10:33:53.000000000 +1100 ++@@ -742,7 +742,7 @@ ++ ++ dialog.SetSelection(p.GetCurrentTreeNumber()); ++ ++- if (dialog.ShowModal() == wxID_OK) +++ if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) ++ { ++ int j = dialog.GetSelection (); ++ #ifdef __WXMAC__ +--- treeviewx-0.5.1.orig/debian/patches/60_LGPLtoGPL.diff ++++ treeviewx-0.5.1/debian/patches/60_LGPLtoGPL.diff +@@ -0,0 +1,1067 @@ ++Converts LGPL statements to GPL, updates FSF's adress. ++diff -ruN tv.orig/COPYING tv/COPYING ++--- tv.orig/COPYING 2006-06-12 21:11:38.000000000 +0900 +++++ tv/COPYING 2006-06-28 20:39:19.000000000 +0900 ++@@ -2,7 +2,7 @@ ++ Version 2, June 1991 ++ ++ Copyright (C) 1989, 1991 Free Software Foundation, Inc. ++- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +++ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ Everyone is permitted to copy and distribute verbatim copies ++ of this license document, but changing it is not allowed. ++ ++@@ -305,7 +305,7 @@ ++ ++ You should have received a copy of the GNU General Public License ++ along with this program; if not, write to the Free Software ++- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +++ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ ++ ++ Also add information on how to contact you by electronic and paper mail. ++diff -ruN tv.orig/LGPLtoGPL.diff tv/LGPLtoGPL.diff ++--- tv.orig/LGPLtoGPL.diff 1970-01-01 09:00:00.000000000 +0900 +++++ tv/LGPLtoGPL.diff 2006-06-28 20:48:52.000000000 +0900 ++@@ -0,0 +1,21 @@ +++diff -ruN tv.orig/COPYING tv/COPYING +++--- tv.orig/COPYING 2006-06-12 21:11:38.000000000 +0900 ++++++ tv/COPYING 2006-06-28 20:39:19.000000000 +0900 +++@@ -2,7 +2,7 @@ +++ Version 2, June 1991 +++ +++ Copyright (C) 1989, 1991 Free Software Foundation, Inc. +++- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ++++ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA +++ Everyone is permitted to copy and distribute verbatim copies +++ of this license document, but changing it is not allowed. +++ +++@@ -305,7 +305,7 @@ +++ +++ You should have received a copy of the GNU General Public License +++ along with this program; if not, write to the Free Software +++- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ++++ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA +++ +++ +++ Also add information on how to contact you by electronic and paper mail. ++diff -ruN tv.orig/tdoc.cpp tv/tdoc.cpp ++--- tv.orig/tdoc.cpp 2006-06-12 21:11:38.000000000 +0900 +++++ tv/tdoc.cpp 2006-06-28 20:30:56.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tdoc.cpp,v 1.6 2001/07/25 10:37:06 rdmp1c Exp $ ++diff -ruN tv.orig/tdoc.h tv/tdoc.h ++--- tv.orig/tdoc.h 2006-06-28 20:26:50.000000000 +0900 +++++ tv/tdoc.h 2006-06-28 20:24:07.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tdoc.h,v 1.4 2001/07/24 10:49:48 rdmp1c Exp $ ++diff -ruN tv.orig/tproject.h tv/tproject.h ++--- tv.orig/tproject.h 2006-06-12 21:11:38.000000000 +0900 +++++ tv/tproject.h 2006-06-28 20:30:40.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tproject.h,v 1.9 2005/08/31 08:55:25 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/lcaquery.h tv/TreeLib/lcaquery.h ++--- tv.orig/TreeLib/lcaquery.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/lcaquery.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: lcaquery.h,v 1.1 2002/03/14 14:11:42 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/mast.cpp tv/TreeLib/mast.cpp ++--- tv.orig/TreeLib/mast.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/mast.cpp 2006-06-28 20:31:07.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: mast.cpp,v 1.5 2005/05/24 22:55:16 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/mast.h tv/TreeLib/mast.h ++--- tv.orig/TreeLib/mast.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/mast.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: mast.h,v 1.1 2002/05/16 16:07:32 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/nodeiterator.h tv/TreeLib/nodeiterator.h ++--- tv.orig/TreeLib/nodeiterator.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/nodeiterator.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: nodeiterator.h,v 1.5 2005/03/29 16:48:52 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/Parse.cpp tv/TreeLib/Parse.cpp ++--- tv.orig/TreeLib/Parse.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/Parse.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: Parse.cpp,v 1.9 2002/02/23 12:22:32 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/Parse.h tv/TreeLib/Parse.h ++--- tv.orig/TreeLib/Parse.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/Parse.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: Parse.h,v 1.7 2004/03/04 23:22:42 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/profile.h tv/TreeLib/profile.h ++--- tv.orig/TreeLib/profile.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/profile.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: profile.h,v 1.30 2005/08/31 08:55:59 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/quartet.cpp tv/TreeLib/quartet.cpp ++--- tv.orig/TreeLib/quartet.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/quartet.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: quartet.cpp,v 1.2 2002/03/14 16:37:13 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/quartet.h tv/TreeLib/quartet.h ++--- tv.orig/TreeLib/quartet.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/quartet.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: quartet.h,v 1.1 2002/03/14 14:11:42 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/tokeniser.cpp tv/TreeLib/tokeniser.cpp ++--- tv.orig/TreeLib/tokeniser.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/tokeniser.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tokeniser.cpp,v 1.14 2005/09/05 07:44:48 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/tokeniser.h tv/TreeLib/tokeniser.h ++--- tv.orig/TreeLib/tokeniser.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/tokeniser.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tokeniser.h,v 1.14 2003/09/17 13:05:57 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treedrawer.cpp tv/TreeLib/treedrawer.cpp ++--- tv.orig/TreeLib/treedrawer.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treedrawer.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treedrawer.cpp,v 1.18 2005/09/06 13:00:14 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treedrawer.h tv/TreeLib/treedrawer.h ++--- tv.orig/TreeLib/treedrawer.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treedrawer.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treedrawer.h,v 1.8 2004/03/16 07:07:40 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/TreeLib.cpp tv/TreeLib/TreeLib.cpp ++--- tv.orig/TreeLib/TreeLib.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/TreeLib.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: TreeLib.cpp,v 1.26 2004/05/13 12:22:11 jcotton Exp $ ++diff -ruN tv.orig/TreeLib/TreeLib.h tv/TreeLib/TreeLib.h ++--- tv.orig/TreeLib/TreeLib.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/TreeLib.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: TreeLib.h,v 1.26 2004/05/13 12:22:11 jcotton Exp $ ++diff -ruN tv.orig/TreeLib/treeorder.cpp tv/TreeLib/treeorder.cpp ++--- tv.orig/TreeLib/treeorder.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treeorder.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treeorder.cpp,v 1.2 2005/02/23 14:19:00 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treeorder.h tv/TreeLib/treeorder.h ++--- tv.orig/TreeLib/treeorder.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treeorder.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treeorder.h,v 1.4 2005/02/23 14:19:00 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treereader.cpp tv/TreeLib/treereader.cpp ++--- tv.orig/TreeLib/treereader.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treereader.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treereader.h tv/TreeLib/treereader.h ++--- tv.orig/TreeLib/treereader.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treereader.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treereader.h,v 1.4 2003/10/21 10:58:45 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treewriter.cpp tv/TreeLib/treewriter.cpp ++--- tv.orig/TreeLib/treewriter.cpp 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treewriter.cpp 2006-06-28 20:31:08.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treewriter.cpp,v 1.4 2005/02/23 14:32:44 rdmp1c Exp $ ++diff -ruN tv.orig/TreeLib/treewriter.h tv/TreeLib/treewriter.h ++--- tv.orig/TreeLib/treewriter.h 2006-06-12 21:11:34.000000000 +0900 +++++ tv/TreeLib/treewriter.h 2006-06-28 20:31:23.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A library for manipulating phylogenetic trees. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treewriter.h,v 1.5 2005/02/23 14:36:08 rdmp1c Exp $ ++diff -ruN tv.orig/treeorder_dialog.cpp tv/treeorder_dialog.cpp ++--- tv.orig/treeorder_dialog.cpp 2006-06-12 21:11:38.000000000 +0900 +++++ tv/treeorder_dialog.cpp 2006-06-28 20:30:56.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treeorder_dialog.cpp,v 1.2 2005/02/21 19:41:24 rdmp1c Exp $ ++diff -ruN tv.orig/treeorder_dialog.h tv/treeorder_dialog.h ++--- tv.orig/treeorder_dialog.h 2006-06-12 21:11:38.000000000 +0900 +++++ tv/treeorder_dialog.h 2006-06-28 20:30:40.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: treeorder_dialog.h,v 1.2 2003/10/22 16:46:26 rdmp1c Exp $ ++diff -ruN tv.orig/tv.cpp tv/tv.cpp ++--- tv.orig/tv.cpp 2006-06-12 21:11:38.000000000 +0900 +++++ tv/tv.cpp 2006-06-28 20:30:56.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tv.cpp,v 1.41 2005/03/23 13:30:32 rdmp1c Exp $ ++diff -ruN tv.orig/tv.h tv/tv.h ++--- tv.orig/tv.h 2006-06-12 21:11:38.000000000 +0900 +++++ tv/tv.h 2006-06-28 20:29:26.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tv.h,v 1.4 2004/08/05 15:55:26 rdmp1c Exp $ ++diff -ruN tv.orig/tview.cpp tv/tview.cpp ++--- tv.orig/tview.cpp 2006-06-12 21:11:38.000000000 +0900 +++++ tv/tview.cpp 2006-06-28 20:30:56.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tview.cpp,v 1.37 2005/08/31 08:55:13 rdmp1c Exp $ ++diff -ruN tv.orig/tview.h tv/tview.h ++--- tv.orig/tview.h 2006-06-12 21:11:38.000000000 +0900 +++++ tv/tview.h 2006-06-28 20:30:43.000000000 +0900 ++@@ -3,20 +3,19 @@ ++ * A phylogenetic tree viewer. ++ * Copyright (C) 2001 Roderic D. M. Page ++ * ++- * 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 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 2 of the License, or +++ * (at your option) any later version. ++ * ++- * This library is distributed in the hope that it will be useful, +++ * 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 ++- * Library General Public License for more details. +++ * 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 Library General Public ++- * License along with this library; if not, write to the Free ++- * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, ++- * MA 02111-1307, USA. +++ * You should have received a copy of the GNU General Public License +++ * along with this program; if not, write to the Free Software +++ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA ++ */ ++ ++ // $Id: tview.h,v 1.21 2005/08/31 08:55:01 rdmp1c Exp $ +--- treeviewx-0.5.1.orig/debian/patches/50_wxT_tv.cpp.diff ++++ treeviewx-0.5.1/debian/patches/50_wxT_tv.cpp.diff +@@ -0,0 +1,17 @@ ++Adding wxT escapes in the tv.cpp file ++--- tv-0.5.1-old/tv.cpp 2005-03-23 22:30:32.000000000 +0900 +++++ tv-0.5.1/tv.cpp 2006-03-13 09:35:38.000000000 +0900 ++@@ -312,11 +312,11 @@ ++ { ++ #ifdef __WXMSW__ ++ file_menu->AppendSeparator(); ++- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile"); +++ file_menu->Append(SAVEAS_PICTURE_CMD, wxT("Save As Picture...")), wxT("Save picture of tree to metafile"); ++ #else ++ #ifdef USE_SVG ++ file_menu->AppendSeparator(); ++- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file"); +++ file_menu->Append(SAVEAS_PICTURE_CMD, wxT("Save As Picture...")), wxT("Save picture of tree to SVG file"); ++ #endif ++ #endif ++ file_menu->AppendSeparator(); +--- treeviewx-0.5.1.orig/debian/patches/45_gcc4.3.diff ++++ treeviewx-0.5.1/debian/patches/45_gcc4.3.diff +@@ -0,0 +1,21 @@ ++Makes TreeView X buildable with gcc 4.3 ++--- ./TreeLib/TreeLib.cpp~ 2007-04-04 12:30:13.000000000 +0000 +++++ ./TreeLib/TreeLib.cpp 2007-04-04 12:30:19.000000000 +0000 ++@@ -23,6 +23,7 @@ ++ #include "TreeLib.h" ++ #include "Parse.h" ++ +++#include ++ #include ++ ++ ++--- ./TreeLib/treereader.cpp~ 2007-04-04 12:33:15.000000000 +0000 +++++ ./TreeLib/treereader.cpp 2007-04-04 12:33:27.000000000 +0000 ++@@ -21,6 +21,7 @@ ++ // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $ ++ ++ #include "treereader.h" +++#include ++ ++ #if __MWERKS__ ++ #include diff --git a/academic/treeview/tv.desktop b/academic/treeview/tv.desktop new file mode 100644 index 0000000000..b2bdefa44c --- /dev/null +++ b/academic/treeview/tv.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=tv +Icon=tv.png +Name=TreeView +StartupNotify=false +Type=Application diff --git a/academic/treeview/tv.png b/academic/treeview/tv.png new file mode 100644 index 0000000000..fbdf9d2fcc Binary files /dev/null and b/academic/treeview/tv.png differ