mirror of
https://github.com/Ponce/slackbuilds
synced 2024-10-15 20:43:39 +02:00
1797 lines
82 KiB
Diff
1797 lines
82 KiB
Diff
|
--- treeviewx-0.5.1.orig/debian/watch
|
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+++ treeviewx-0.5.1/debian/watch
|
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@@ -0,0 +1,2 @@
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+version=3
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+http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html download\/\d\.\d\/tv-(\d+)\.(\d+)\.(\d+)\.tar\.gz
|
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|
|
--- treeviewx-0.5.1.orig/debian/treeviewx.sharedmimeinfo
|
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|
|
+++ treeviewx-0.5.1/debian/treeviewx.sharedmimeinfo
|
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@@ -0,0 +1,13 @@
|
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+<?xml version="1.0"?>
|
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+<mime-info xmlns='http://www.freedesktop.org/standards/shared-mime-info'>
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+ <mime-type type="text/x-clustalw-tree">
|
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+ <comment>Phylogenetic tree in Clustal W format</comment>
|
|||
|
|
+ <comment xml:lang="fr">Arbre phylogénétique au format Clustal W</comment>
|
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+ <comment xml:lang="it">Albero filogenetico in formato Clustal W</comment>
|
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+ <magic priority="50">
|
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+ <match type="string" offset="0" value="(\n"/>
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+ </magic>
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+ <glob pattern="*.phb"/>
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+ <glob pattern="*.ph"/>
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+ </mime-type>
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+</mime-info>
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--- treeviewx-0.5.1.orig/debian/menu
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+++ treeviewx-0.5.1/debian/menu
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@@ -0,0 +1,8 @@
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+?package(treeviewx):\
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+ needs="X11"\
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+ section="Applications/Science/Biology"\
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+ title="TreeView X"\
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+ command="/usr/bin/tv"\
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+ icon="/usr/share/pixmaps/treeviewx.xpm" \
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+ hints="Phylogenetic tree drawing program"\
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+ longtitle="TreeView X: a phylogenetic tree viewer which can do SVG export"
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--- treeviewx-0.5.1.orig/debian/rules
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+++ treeviewx-0.5.1/debian/rules
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@@ -0,0 +1,8 @@
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+#!/usr/bin/make -f
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+
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+include /usr/share/cdbs/1/class/autotools.mk
|
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+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
|
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+include /usr/share/cdbs/1/rules/debhelper.mk
|
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+
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+install/treeviewx::
|
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+ install -m 644 bitmaps/treeview.xpm $(CURDIR)/debian/treeviewx/usr/share/pixmaps/treeviewx.xpm
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--- treeviewx-0.5.1.orig/debian/upstream-metadata.yaml
|
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+++ treeviewx-0.5.1/debian/upstream-metadata.yaml
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@@ -0,0 +1,14 @@
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+Contact: Roderic D. M. Page <r.page@bio.gla.ac.uk>
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+DOI: 10.1093/bioinformatics/12.4.357
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+Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/
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+Name: Treeview X
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+PMID: 8902363
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+Reference-Author: Page, Roderic D. M.
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+Reference-Journal: Comput. Appl. Biosci.
|
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|
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+Reference-Number: 4
|
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+Reference-Page: 357-8
|
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|
|
+Reference-Title: TreeView: an application to display phylogenetic trees on personal computers
|
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|
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+Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357
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+Reference-Volume: 12
|
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+Reference-Year: 1996
|
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+Watch: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download.html download\/\d\.\d\/tv-(\d+)\.(\d+)\.(\d+)\.tar\.gz
|
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--- treeviewx-0.5.1.orig/debian/control
|
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+++ treeviewx-0.5.1/debian/control
|
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@@ -0,0 +1,22 @@
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+Source: treeviewx
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+Section: science
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+Priority: optional
|
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+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
|
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+DM-Upload-Allowed: yes
|
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+Uploaders: Charles Plessy <plessy@debian.org>,
|
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|
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+ Andreas Tille <tille@debian.org>
|
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+Build-Depends: debhelper (>= 7.1), cdbs, autotools-dev, quilt, libwxgtk2.8-dev
|
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+Standards-Version: 3.8.4
|
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|
|
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/treeviewx/trunk/?rev=0&sc=0
|
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+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/treeviewx/trunk/
|
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+Homepage: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/
|
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+
|
|||
|
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+Package: treeviewx
|
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+Architecture: any
|
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+Depends: ${shlibs:Depends}, ${misc:Depends}
|
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+Description: Displays and prints phylogenetic trees
|
|||
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+ 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
|
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|
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+ (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It
|
|||
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+ allows to order the branches of the trees, and to export the trees in SVG
|
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+ format.
|
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|
|
--- treeviewx-0.5.1.orig/debian/copyright
|
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+++ treeviewx-0.5.1/debian/copyright
|
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@@ -0,0 +1,61 @@
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+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5’.
|
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+
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+Name : TreeView X
|
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|
|
+Author : Roderic D. M. Page <r.page@bio.gla.ac.uk>
|
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+Source : http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz
|
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+
|
|||
|
|
+License: GPL-2+
|
|||
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+
|
|||
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+ 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
|
|||
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|
+ the Free Software Foundation; either version 2 of the License, or
|
|||
|
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+ (at your option) any later version.
|
|||
|
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+
|
|||
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+ TreeView X is distributed in the hope that it will be useful,
|
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|
|
+ 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.
|
|||
|
|
+
|
|||
|
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+ You should have received a copy of the GNU General Public License
|
|||
|
|
+ along with this package; if not, write to the Free Software
|
|||
|
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+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
|
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+
|
|||
|
|
+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’.
|
|||
|
|
+
|
|||
|
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+Files: ncl-2.0/*
|
|||
|
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+Copyright: © 1999 Paul O. Lewis
|
|||
|
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+License: GPL-2+
|
|||
|
|
+Comment: TreeView X is statically linked to the Nexus Class Library.
|
|||
|
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+
|
|||
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+Files: TreeLib/*
|
|||
|
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+Copyright: © 2001 Roderic D. M. Page <r.page@bio.gla.ac.uk>
|
|||
|
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+License: GPL-2+
|
|||
|
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+Comment: The files under the TreeLib directory are part of TreeView X,
|
|||
|
|
+ as they have never been released as an independent library.
|
|||
|
|
+
|
|||
|
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+Files: debian/tv.1.xml debian/tv.1
|
|||
|
|
+Copyright: © 2006-2008 Charles Plessy <charles-debian-nospam@plessy.org>
|
|||
|
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+License: Same as TreeView X
|
|||
|
|
+
|
|||
|
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+Files: debian/*
|
|||
|
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+Copyright: © 2006–2010 Charles Plessy <plessy@debian.org>
|
|||
|
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+ © 2007 David Paleino <d.paleino@gmail.com>
|
|||
|
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+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
|
|||
|
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@@ -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 @@
|
|||
|
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+This packages uses the quilt patch system. Please read
|
|||
|
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+/usr/share/doc/quilt/README.source for more information.
|
|||
|
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+
|
|||
|
|
+ -- Andreas Tille <tille@debian.org> Mon, 31 Aug 2009 14:50:19 +0200
|
|||
|
|
--- treeviewx-0.5.1.orig/debian/dirs
|
|||
|
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+++ treeviewx-0.5.1/debian/dirs
|
|||
|
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@@ -0,0 +1,2 @@
|
|||
|
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+/usr/share/applications
|
|||
|
|
+/usr/share/pixmaps
|
|||
|
|
--- treeviewx-0.5.1.orig/debian/treeviewx.desktop
|
|||
|
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+++ treeviewx-0.5.1/debian/treeviewx.desktop
|
|||
|
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@@ -0,0 +1,19 @@
|
|||
|
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+[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 @@
|
|||
|
|
+<?xml version='1.0' encoding='UTF-8'?>
|
|||
|
|
+<?xml-stylesheet type="text/xsl"
|
|||
|
|
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
|
|||
|
|
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
|
|||
|
|
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
|
|||
|
|
+
|
|||
|
|
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
|
|||
|
|
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
|
|||
|
|
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
|
|||
|
|
+ <!ENTITY dhemail "<email>charles-debian-nospam@plessy.org</email>">
|
|||
|
|
+ <!ENTITY dhusername "Charles Plessy">
|
|||
|
|
+ <!ENTITY dhucpackage "<refentrytitle>TREEVIEW X</refentrytitle>">
|
|||
|
|
+ <!ENTITY dhpackage "tv">
|
|||
|
|
+ <!ENTITY debian "<productname>Debian</productname>">
|
|||
|
|
+ <!ENTITY gnu "<acronym>GNU</acronym>">
|
|||
|
|
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
|
|||
|
|
+]>
|
|||
|
|
+
|
|||
|
|
+<refentry>
|
|||
|
|
+ <refentryinfo>
|
|||
|
|
+ <address>
|
|||
|
|
+ &dhemail;
|
|||
|
|
+ </address>
|
|||
|
|
+<!-- <author>
|
|||
|
|
+ &dhfirstname;
|
|||
|
|
+ &dhsurname;
|
|||
|
|
+ </author> -->
|
|||
|
|
+ <copyright>
|
|||
|
|
+ <year>2006</year>
|
|||
|
|
+ <year>2008</year>
|
|||
|
|
+ <holder>&dhusername;</holder>
|
|||
|
|
+ </copyright>
|
|||
|
|
+ </refentryinfo>
|
|||
|
|
+ <refmeta>
|
|||
|
|
+ &dhucpackage;
|
|||
|
|
+
|
|||
|
|
+ &dhsection;
|
|||
|
|
+ </refmeta>
|
|||
|
|
+ <refnamediv>
|
|||
|
|
+ <refname>&dhpackage;</refname>
|
|||
|
|
+
|
|||
|
|
+ <refpurpose>displays and prints phylogenetic trees</refpurpose>
|
|||
|
|
+ </refnamediv>
|
|||
|
|
+ <refsynopsisdiv>
|
|||
|
|
+ <cmdsynopsis>
|
|||
|
|
+ <command>tv</command> <arg choice="opt"><replaceable>filename</replaceable></arg>
|
|||
|
|
+ </cmdsynopsis>
|
|||
|
|
+ </refsynopsisdiv>
|
|||
|
|
+ <refsect1>
|
|||
|
|
+ <title>DESCRIPTION</title>
|
|||
|
|
+
|
|||
|
|
+
|
|||
|
|
+ <para><command>tv</command> is the program that starts the
|
|||
|
|
+ TreeView X GUI.</para>
|
|||
|
|
+
|
|||
|
|
+
|
|||
|
|
+ <para>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.</para>
|
|||
|
|
+
|
|||
|
|
+ <para>If started from the command line with
|
|||
|
|
+ <filename>filename</filename> as an argument, TreeView X
|
|||
|
|
+ will open the tree stored in <filename>filename</filename>.</para>
|
|||
|
|
+
|
|||
|
|
+
|
|||
|
|
+ </refsect1>
|
|||
|
|
+
|
|||
|
|
+ <refsect1>
|
|||
|
|
+ <title>SEE ALSO</title>
|
|||
|
|
+
|
|||
|
|
+ <para>
|
|||
|
|
+ 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
|
|||
|
|
+ </para>
|
|||
|
|
+ </refsect1>
|
|||
|
|
+
|
|||
|
|
+ <refsect1>
|
|||
|
|
+ <title>REFERENCE</title>
|
|||
|
|
+ <para>Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358.</para>
|
|||
|
|
+ </refsect1>
|
|||
|
|
+
|
|||
|
|
+ <refsect1>
|
|||
|
|
+ <title>AUTHOR</title>
|
|||
|
|
+
|
|||
|
|
+ <para><application>TreeView X</application> was written by Rod
|
|||
|
|
+ Page (r.page@bio.gla.ac.uk) URL:
|
|||
|
|
+ http://darwin.zoology.gla.ac.uk/~rpage/treeviewx.</para>
|
|||
|
|
+
|
|||
|
|
+ <para>This manual page was written by &dhusername; (&dhemail;) for
|
|||
|
|
+ the &debian; system (but may be used by others).</para>
|
|||
|
|
+
|
|||
|
|
+ <!-- You can copy, distribute and/or modify this document under the same terms as TreeView X itself. -->
|
|||
|
|
+
|
|||
|
|
+ <para>
|
|||
|
|
+ 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.
|
|||
|
|
+ </para>
|
|||
|
|
+
|
|||
|
|
+ <para>
|
|||
|
|
+ On Debian systems, the complete text of the GNU General Public
|
|||
|
|
+ License can be found in /usr/share/common-licenses/GPL.
|
|||
|
|
+ </para>
|
|||
|
|
+
|
|||
|
|
+ </refsect1>
|
|||
|
|
+</refentry>
|
|||
|
|
--- 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 <charles-debian-nospam@plessy.org>, 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 <http://docbook.sf.net/>
|
|||
|
|
+.\" 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 (<charles\-debian\-nospam@plessy\.org>) 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 <plessy@debian.org> 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 <tille@debian.org> 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 <charles-debian-nospam@plessy.org> 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 <charles-debian-nospam@plessy.org> 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 <charles-debian-nospam@plessy.org> 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 <charles-debian-nospam@plessy.org> Sat, 14 Oct 2006 12:16:21 +0900
|
|||
|
|
+
|
|||
|
|
+treeviewx (0.5.1-1) unstable; urgency=low
|
|||
|
|
+
|
|||
|
|
+ * Initial release Closes: #352506
|
|||
|
|
+
|
|||
|
|
+ -- Charles Plessy <charles-debian-nospam@plessy.org> 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+--- 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 <d.paleino@gmail.com>
|
|||
|
|
+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 <ctype.h>
|
|||
|
|
++#include <cstring>
|
|||
|
|
+ #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 <cstdlib>
|
|||
|
|
++#include <cstring>
|
|||
|
|
+
|
|||
|
|
+ #if __MWERKS__
|
|||
|
|
+ #include <string.h>
|
|||
|
|
+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 <cstring>
|
|||
|
|
+
|
|||
|
|
+ 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 <cstring>
|
|||
|
|
+
|
|||
|
|
+ #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 <cstring>
|
|||
|
|
+
|
|||
|
|
+ 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 <stdio.h>
|
|||
|
|
+ #include <assert.h>
|
|||
|
|
+ #include <math.h>
|
|||
|
|
++#include <cstring>
|
|||
|
|
+ #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 <william.grant@ubuntu.com.au>
|
|||
|
|
+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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <r.page@bio.gla.ac.uk>
|
|||
|
|
+ *
|
|||
|
|
+- * 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 <cstdlib>
|
|||
|
|
+ #include <vector>
|
|||
|
|
+
|
|||
|
|
+
|
|||
|
|
+--- ./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 <cstdlib>
|
|||
|
|
+
|
|||
|
|
+ #if __MWERKS__
|
|||
|
|
+ #include <string.h>
|