debian/0000755000000000000000000000000012006473140007163 5ustar debian/upstream0000644000000000000000000000132011726145416010754 0ustar Archive: Google Code Contact: Roderic D. M. Page Download: http://code.google.com/p/treeviewx/downloads/ Homepage: http://code.google.com/p/treeviewx/ Name: Treeview X Reference: Author: Page, Roderic D. M. Journal: Comput. Appl. Biosci. Number: 4 Pages: 357-8 Title: > TreeView: an application to display phylogenetic trees on personal computers URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357 Volume: 12 Year: 1996 PMID: 8902363 DOI: 10.1093/bioinformatics/12.4.357 Repository: http://treeviewx.googlecode.com/svn/ Repository-Browse: http://code.google.com/p/treeviewx/source/browse/ Watch: http://googlecode.debian.net/p/treeviewx/tv.(\d+.*)\.tar\.gz debian/treeviewx.mime0000644000000000000000000000011711110210110012032 0ustar text/x-clustalw-tree; /usr/bin/tv '%s'; description=ClustalW Phylogenetic Tree debian/examples0000644000000000000000000000002011110210110010671 0ustar debian/tree.phb debian/source/0000755000000000000000000000000012006471476010475 5ustar debian/source/format0000644000000000000000000000001412006466054011677 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000073011601442101011333 0ustar This packages uses the quilt patch system. Please read /usr/share/doc/quilt/README.source for more information. -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 The original upstream source version 0.5 that were published on Google Code on the 23rd of August 2010, are a later than the version 0.5.1 on the homepage. I therefore use 0.5.1+20100823 as a version number for it. -- Charles Plessy Thu, 23 Jun 2011 08:22:10 +0900 debian/tv.1.xml0000644000000000000000000001340411601442101010470 0ustar Debian"> GNU"> GPL"> ]> &dhtitle; &dhproduct; &dhrelease; &dhucpackage; &dhsection; &dhpackage; displays and prints phylogenetic trees tv filename DESCRIPTION tv is the program that starts the TreeView X GUI. TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows one to order the branches of the trees, and to export the trees in SVG format. If started from the command line with filename as an argument, TreeView X will open the tree stored in filename. SEE ALSO At present there is is no documentation for TreeView X. In the meantime please see the online documentation for TreeView (remember that TreeView X has only a subset of the features of TreeView). http://taxonomy.zoology.gla.ac.uk/rod/treeview/treeview_manual.html REFERENCE Page, R. D. M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: 357-358. AUTHOR TreeView X was written by Rod Page (r.page@bio.gla.ac.uk) URL: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx. This manual page was written by &dhusername; (&dhemail;) for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify TreeView X and this document under the terms of the &gnu; General Public License, Version 2 or any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License version 2 can be found in /usr/share/common-licenses/GPL-2. debian/copyright0000644000000000000000000000523712006471670011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: TreeView X Upstream-Contact: Roderic D. M. Page Source: http://treeviewx.googlecode.com/files/tv-0.5.tar.gz Files: ncl-2.0/* Copyright: © 1999 Paul O. Lewis License: GPL-2+ Comment: TreeView X is statically linked to the Nexus Class Library. Files: TreeLib/* Copyright: © 2001 Roderic D. M. Page License: GPL-2+ Comment: The files under the TreeLib directory are part of TreeView X, as they have never been released as an independent library. Files: debian/tv.1.xml debian/tv.1 Copyright: © 2006-2008 Charles Plessy License: GPL-2+ Files: debian/* Copyright: © 2006–2010 Charles Plessy © 2007 David Paleino License: PD Please treat the packaging work as if it were in the public domain. License: GPL-2+ TreeView X is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . TreeView X is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . TreeView X has been released by its author under the GNU GPL (see COPYING), but most of its files use a header which places them under the GNU Library GPL (LGPL). The author of TreeView X confirmed to the maintainer of this package that his intention is to have TreeView X released under the GPL. Therefore, as permitted the clause 3 of the LGPL, the licence of these files is changed to the GPL through the patch in the following file: debian/patches/60_LGPLtoGPL.patch . 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’. debian/compat0000644000000000000000000000000212006472717010372 0ustar 9 debian/tree.phb0000644000000000000000000000175211110210110010577 0ustar ( ( ( ( ( ( ( ( ( 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; debian/treeviewx.desktop0000644000000000000000000000135711110210110012563 0ustar [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; debian/treeviewx.sharedmimeinfo0000644000000000000000000000102511110210110014074 0ustar Phylogenetic tree in Clustal W format Arbre phylogénétique au format Clustal W Albero filogenetico in formato Clustal W debian/install0000644000000000000000000000006211110210110010527 0ustar debian/treeviewx.desktop /usr/share/applications/ debian/control0000644000000000000000000000171112006472731010573 0ustar Source: treeviewx Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 9), libwxgtk2.8-dev Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/treeviewx/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/treeviewx/trunk/ Homepage: http://code.google.com/p/treeviewx/ Package: treeviewx Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Displays and prints phylogenetic trees TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows one to order the branches of the trees, and to export the trees in SVG format. debian/patches/0000755000000000000000000000000012006467667010633 5ustar debian/patches/70_choose_tree.patch0000644000000000000000000000073312006467356014457 0ustar ## 70_choose_tree.dpatch by William Alexander Grant --- treeviewx-0.5.1+20100823.orig/tview.cpp +++ treeviewx-0.5.1+20100823/tview.cpp @@ -209,7 +209,7 @@ wxT("SVG vector picture files (*.svg)|*.svg"), wxSAVE|wxOVERWRITE_PROMPT); - if (dialog.ShowModal() == wxID_OK) + if ((dialog.ShowModal() == wxID_OK) && (p.GetNumTrees() != 0)) { wxSVGFileDC pictureDC (dialog.GetPath(), 600, 650) ; OnDraw (&pictureDC); debian/patches/series0000644000000000000000000000010012006467614012027 0ustar 60_LGPLtoGPL.patch 70_choose_tree.patch fix_loading_crash.patch debian/patches/fix_loading_crash.patch0000644000000000000000000000162612006466054015311 0ustar # Patch from http://code.google.com/p/treeviewx/issues/detail?id=1 # to fix crash on loading tree file. --- a/tview.cpp +++ b/tview.cpp @@ -278,7 +278,7 @@ char buf[256]; strcpy (buf, p->GetLabel().c_str()); wchar_t wbuf[256]; - mbstowcs (wbuf, buf, size_t(wbuf)); + mbstowcs (wbuf, buf, 256); s << wbuf; #else s << p->GetLabel().c_str(); @@ -563,7 +563,7 @@ char buf[256]; strcpy (buf, t.GetName().c_str()); wchar_t wbuf[256]; - mbstowcs (wbuf, buf, size_t(wbuf)); + mbstowcs (wbuf, buf, 256); txt << wbuf; #else txt << t.GetName().c_str(); @@ -712,7 +712,7 @@ char buf[256]; strcpy (buf, p.GetIthTreeName(i).c_str()); wchar_t wbuf[256]; - mbstowcs (wbuf, buf, size_t(wbuf)); + mbstowcs (wbuf, buf, 256); std::wstring tname = wbuf; @@ -1046,6 +1046,7 @@ void MyCanvas::OnSize(wxSizeEvent& event) { Resize (); + Refresh(); event.Skip(); } debian/patches/60_LGPLtoGPL.patch0000644000000000000000000014733012006467347013630 0ustar Converts LGPL statements to GPL, updates FSF's adress. --- treeviewx-0.5.1+20100823.orig/COPYING +++ treeviewx-0.5.1+20100823/COPYING @@ -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. --- /dev/null +++ treeviewx-0.5.1+20100823/LGPLtoGPL.diff @@ -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. --- treeviewx-0.5.1+20100823.orig/tdoc.cpp +++ treeviewx-0.5.1+20100823/tdoc.cpp @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tdoc.cpp,v 1.6 2001/07/25 10:37:06 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/tdoc.h +++ treeviewx-0.5.1+20100823/tdoc.h @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tdoc.h,v 1.4 2001/07/24 10:49:48 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/tproject.h +++ treeviewx-0.5.1+20100823/tproject.h @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tproject.h,v 1.9 2005/08/31 08:55:25 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/lcaquery.h +++ treeviewx-0.5.1+20100823/TreeLib/lcaquery.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: lcaquery.h,v 1.1 2002/03/14 14:11:42 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/mast.cpp +++ treeviewx-0.5.1+20100823/TreeLib/mast.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: mast.cpp,v 1.5 2005/05/24 22:55:16 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/mast.h +++ treeviewx-0.5.1+20100823/TreeLib/mast.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: mast.h,v 1.1 2002/05/16 16:07:32 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/nodeiterator.h +++ treeviewx-0.5.1+20100823/TreeLib/nodeiterator.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: nodeiterator.h,v 1.5 2005/03/29 16:48:52 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/Parse.cpp +++ treeviewx-0.5.1+20100823/TreeLib/Parse.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: Parse.cpp,v 1.9 2002/02/23 12:22:32 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/Parse.h +++ treeviewx-0.5.1+20100823/TreeLib/Parse.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: Parse.h,v 1.7 2004/03/04 23:22:42 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/profile.h +++ treeviewx-0.5.1+20100823/TreeLib/profile.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: profile.h,v 1.31 2007/06/05 13:26:17 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/quartet.cpp +++ treeviewx-0.5.1+20100823/TreeLib/quartet.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: quartet.cpp,v 1.2 2002/03/14 16:37:13 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/quartet.h +++ treeviewx-0.5.1+20100823/TreeLib/quartet.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: quartet.h,v 1.2 2005/09/08 12:58:29 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/tokeniser.cpp +++ treeviewx-0.5.1+20100823/TreeLib/tokeniser.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tokeniser.cpp,v 1.14 2005/09/05 07:44:48 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/tokeniser.h +++ treeviewx-0.5.1+20100823/TreeLib/tokeniser.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tokeniser.h,v 1.14 2003/09/17 13:05:57 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treedrawer.cpp +++ treeviewx-0.5.1+20100823/TreeLib/treedrawer.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treedrawer.cpp,v 1.20 2007/06/07 15:48:02 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treedrawer.h +++ treeviewx-0.5.1+20100823/TreeLib/treedrawer.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treedrawer.h,v 1.10 2007/06/07 15:48:02 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/TreeLib.cpp +++ treeviewx-0.5.1+20100823/TreeLib/TreeLib.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: TreeLib.cpp,v 1.30 2007/08/04 21:41:55 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/TreeLib.h +++ treeviewx-0.5.1+20100823/TreeLib/TreeLib.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: TreeLib.h,v 1.30 2007/08/04 21:41:57 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treeorder.cpp +++ treeviewx-0.5.1+20100823/TreeLib/treeorder.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treeorder.cpp,v 1.2 2005/02/23 14:19:00 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treeorder.h +++ treeviewx-0.5.1+20100823/TreeLib/treeorder.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treeorder.h,v 1.4 2005/02/23 14:19:00 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treereader.cpp +++ treeviewx-0.5.1+20100823/TreeLib/treereader.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treereader.cpp,v 1.5 2003/09/10 12:58:16 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treereader.h +++ treeviewx-0.5.1+20100823/TreeLib/treereader.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treereader.h,v 1.4 2003/10/21 10:58:45 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treewriter.cpp +++ treeviewx-0.5.1+20100823/TreeLib/treewriter.cpp @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treewriter.cpp,v 1.4 2005/02/23 14:32:44 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/TreeLib/treewriter.h +++ treeviewx-0.5.1+20100823/TreeLib/treewriter.h @@ -3,20 +3,19 @@ * A library for manipulating phylogenetic trees. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treewriter.h,v 1.5 2005/02/23 14:36:08 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/treeorder_dialog.cpp +++ treeviewx-0.5.1+20100823/treeorder_dialog.cpp @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treeorder_dialog.cpp,v 1.2 2005/02/21 19:41:24 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/treeorder_dialog.h +++ treeviewx-0.5.1+20100823/treeorder_dialog.h @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: treeorder_dialog.h,v 1.2 2003/10/22 16:46:26 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/tv.cpp +++ treeviewx-0.5.1+20100823/tv.cpp @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tv.cpp,v 1.43 2007/03/09 13:58:19 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/tv.h +++ treeviewx-0.5.1+20100823/tv.h @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tv.h,v 1.4 2004/08/05 15:55:26 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/tview.cpp +++ treeviewx-0.5.1+20100823/tview.cpp @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tview.cpp,v 1.40 2007/03/09 13:59:19 rdmp1c Exp $ --- treeviewx-0.5.1+20100823.orig/tview.h +++ treeviewx-0.5.1+20100823/tview.h @@ -3,20 +3,19 @@ * A phylogenetic tree viewer. * Copyright (C) 2001 Roderic D. M. Page * - * This library is free software; you can redistribute it and/or - * modify it under the terms of the GNU Library General Public - * License as published by the Free Software Foundation; either - * version 2 of the License, or (at your option) any later version. + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. * - * This library is distributed in the hope that it will be useful, + * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Library General Public License for more details. + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. * - * You should have received a copy of the GNU Library General Public - * License along with this library; if not, write to the Free - * Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, - * MA 02111-1307, USA. + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ // $Id: tview.h,v 1.21 2005/08/31 08:55:01 rdmp1c Exp $ debian/manpages0000644000000000000000000000001411110210110010651 0ustar debian/tv.1 debian/watch0000644000000000000000000000057412006466054010230 0ustar version=3 # http://googlecode.debian.net/p/treeviewx/tv.(\d+.*)\.tar\.gz #add version mangle to reflect the decision noted in README.source #This is nasty but then this watchfile is nigh-on useless without it. opts="uversionmangle=s/^0.5$/0.5.1+20100823/" \ http://code.google.com/p/treeviewx/downloads/list?can=1 \ .*/tv-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip) debian/tv.10000644000000000000000000000564511601442101007701 0ustar '\" t .\" Title: TREEVIEW X .\" Author: [see the "AUTHOR" section] .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 06/23/2011 .\" Manual: User Manuals .\" Source: TreeView X 0.5 .\" Language: English .\" .TH "TREEVIEW X" "1" "06/23/2011" "TreeView X 0.5" "User Manuals" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" TreeView_X \- displays and prints phylogenetic trees .SH "SYNOPSIS" .HP \w'\fBtv\fR\ 'u \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 one to order the branches of the trees, and to export the trees in SVG format\&. .PP If started from the command line with filename as an argument, TreeView X will open the tree stored in filename\&. .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 (plessy@debian\&.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 version 2 can be found in /usr/share/common\-licenses/GPL\-2\&. debian/dirs0000644000000000000000000000005311110210110010022 0ustar /usr/share/applications /usr/share/pixmaps debian/menu0000644000000000000000000000043511110210110010031 0ustar ?package(treeviewx):\ needs="X11"\ section="Applications/Science/Biology"\ title="TreeView X"\ command="/usr/bin/tv"\ icon="/usr/share/pixmaps/treeviewx.xpm" \ hints="Phylogenetic tree drawing program"\ longtitle="TreeView X: a phylogenetic tree viewer which can do SVG export" debian/changelog0000644000000000000000000001163112006472750011045 0ustar treeviewx (0.5.1+20100823-2) unstable; urgency=low * debian/watch: Fixed after Google code redirector stopped working * debian/upstream: Fix typo (s/Pages/Page/) * debian/patches: refreshed * debian/control: - Do not Build-Depend from quilt any more since we have source format 3.0 (quilt) * debian/copyright: DEP5 * debhelper 9 (control+compat) -- Andreas Tille Thu, 02 Aug 2012 14:42:29 +0200 treeviewx (0.5.1+20100823-2precise3) precise; urgency=low * Fudge watchfile to renumber version as in README.source * Apply patch from http://code.google.com/p/treeviewx/issues/detail?id=1 to fix crash loading trees. * Moved to DH build system (fairly trivial) * Refresh patches -- Tim Booth Wed, 01 Aug 2012 18:01:41 +0100 treeviewx (0.5.1+20100823-1) unstable; urgency=low * New upstream version, hosted on Google Code. * Deleted debian/patches 45_gcc4.3.diff, 50_wxT_tv.cpp.diff, 51_wxT_tview.cpp.diff, 80_missing_includes.diff, 90_fix_for_wx2.8.diff, applied upstream, and debian/README.Debian, that only mentioned these patches. * Corrected Vcs-* URLs in debian/control. * Using Debhelper 8 (debian/control, debian/compat). * Incremented Standards-Version to reflect conformance with Policy 3.9.2. (debian/control, no changes needed) -- Charles Plessy Fri, 24 Jun 2011 08:34:48 +0900 treeviewx (0.5.1-7) unstable; urgency=low * Refreshed debian/copyright according to latest developments of the machine-readable format. * Collected upstream information in debian/upstream-metadata.yaml and removed bibliographic information from the long description (debian/control). * Added in ‘debian/patches/90_fix_for_wx2.8.diff’ Ryan Niebur's patch to build TreeView X with wxWidgets 2.8 (Closes: #567238, thanks!). * Build against libwxgtk2.8-dev (debian/control). * Checked conformance with Policy 3.8.4 and incremented Standards-Version to reflect this (debian/control, no changes needed). -- Charles Plessy Thu, 28 Jan 2010 18:52:23 +0900 treeviewx (0.5.1-6) unstable; urgency=low [ Charles Plessy ] * Updated my email address. [ David Paleino ] * Removed myself from Uploaders [ Andreas Tille ] * Standards-Version: 3.8.3 (Added README.source) * debhelper 7 * Added myself to uploaders * Tested whether package also build against libwxgtk2.8-dev but failed -> Upstream should be contacted about wxgtk upgrade to be safe for the future * Removed explicit dependency from libgnomeprintui2.2-0 Closes: #542579 -- Andreas Tille Tue, 01 Sep 2009 11:18:11 +0200 treeviewx (0.5.1-5) unstable; urgency=low [ Charles Plessy ] * Debian Menu transition: Apps/Science becomes Applications/Science/Biology. * debian/control: - Moved the Homepage: field out from the package's description. - Checked conformance with policy 3.7.3 - Allowed upload by Debian Maintainers. * MIME support: - debian/treeviewx.sharedmimeinfo declares that .phb and .ph files are Clustal W phylogenetic trees. - debian/treeviewx.mime and debian/treeviewx.desktop declare that TreeView X can open Clustal W phylogenetic trees. - debian/rules calls dh_installmime. * debian/copyright: made machine-parsable. * Relicensed the manpage under "same as TreeView X" terms. * Switched to CDBS and quilt. [ David Paleino ] * Added support for MIME types (.phb is now associated to treeviewx) * fixed FTBFS with GCC 4.3: missing #includes (Closes: #455177) * Added statically generated tv.1 (to save buildd time) * Other minor fixes * Added Italian to the .desktop file -- Charles Plessy Sat, 26 Jan 2008 22:32:36 +0900 treeviewx (0.5.1-4) unstable; urgency=low * Add Subversion repository URL to debian/control. * Including /usr/share/dpatch/dpatch.make in debian/rules. * Including a patch from Martin Michlmayr to build TreeView X with gcc 4.3 (Closes: #417729). -- Charles Plessy Mon, 9 Apr 2007 10:03:14 +0900 treeviewx (0.5.1-3) unstable; urgency=low [ William Alexander Grant ] * Added 70_choose_tree.dpatch, prevents segfault when choosing no tree. [ Charles Plessy ] * Tested and imported the patch from Ubuntu. Thanks William ! -- Charles Plessy Tue, 13 Feb 2007 23:38:33 +0900 treeviewx (0.5.1-2) unstable; urgency=low * Added a transitional dependency on libgnomeprintui2.2-0, thanks to Roger Leigh for understanding the problem. Closes: #392219 * Fixed the debian/watch file. * Added an example tree (courtesy of Roger Leigh). -- Charles Plessy Sat, 14 Oct 2006 12:16:21 +0900 treeviewx (0.5.1-1) unstable; urgency=low * Initial release Closes: #352506 -- Charles Plessy Thu, 16 Mar 2006 11:30:23 +0900 debian/rules0000755000000000000000000000057512006466054010260 0ustar #!/usr/bin/make -f # -*- makefile -*- # # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ #Installation is simply a matter of copying the files, without extensions override_dh_install: dh_install install -m 644 bitmaps/treeview.xpm $(CURDIR)/debian/treeviewx/usr/share/pixmaps/treeviewx.xpm override_dh_auto_clean: dh_auto_clean rm -f debian/stamp-*