reinit the tree, so we can have metadata

8 files changed, 337 insertions, 0 deletions

diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch
new file mode 100644
index 000000000000..ed5aa43e23c3
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-70_choose_tree.patch
@@ -0,0 +1,12 @@
+## 70_choose_tree.dpatch by William Alexander Grant <william.grant@ubuntu.com.au>
+--- tv-0.5.orig/tview.cpp
++++ tv-0.5/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);
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch
new file mode 100644
index 000000000000..c136539726a3
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-fix_loading_crash.patch
@@ -0,0 +1,40 @@
+Bug: http://code.google.com/p/treeviewx/issues/detail?id=1
+Description: fix crash on loading tree file.
+Author: Tim Booth
+--- tv-0.5.orig/tview.cpp
++++ tv-0.5/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();
+ }
+ 
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch
new file mode 100644
index 000000000000..33bd3b1741f6
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch
@@ -0,0 +1,77 @@
+diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp
+--- tv-0.5.1/TreeLib/Parse.cpp	2002-02-23 07:22:32.000000000 -0500
++++ tv-0.5.1.new/TreeLib/Parse.cpp	2008-06-17 06:08:24.000000000 -0400
+@@ -24,6 +24,11 @@
+ #include <ctype.h>
+ #include "Parse.h"
+ 
++
++
++
++#include <cstring>
++
+ // Return the next token in the string
+ tokentype Parser::NextToken ()
+ {
+diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp
+--- tv-0.5.1/TreeLib/TreeLib.cpp	2004-05-13 08:22:11.000000000 -0400
++++ tv-0.5.1.new/TreeLib/TreeLib.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -24,6 +24,8 @@
+ #include "TreeLib.h"
+ #include "Parse.h"
+ 
++
++#include <cstdlib>
+ #include <vector>
+ 
+ 
+diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp
+--- tv-0.5.1/TreeLib/treereader.cpp	2003-09-10 08:58:16.000000000 -0400
++++ tv-0.5.1.new/TreeLib/treereader.cpp	2008-06-17 06:07:15.000000000 -0400
+@@ -28,6 +28,9 @@
+ 	#include <stdlib.h>
+ #endif
+ 
++#include <cstring>
++#include <cstdlib>
++
+ //------------------------------------------------------------------------------
+ TreeReader::TreeReader (Tokeniser &p) : parser (p)
+ {
+diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp
+--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp	2002-12-10 06:35:49.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp
+--- tv-0.5.1/ncl-2.0/src/nexus.cpp	2002-12-10 06:35:50.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp
+--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp	2005-04-29 10:28:17.000000000 -0400
++++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp
+--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp	2001-02-02 07:55:40.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,6 @@
++
++#include <cstring>
++
+ #ifdef __BORLANDC__
+ 	// Undefine __MINMAX_DEFINED so that min and max are correctly defined
+ 	#ifdef __MINMAX_DEFINED
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch
new file mode 100644
index 000000000000..67a62179bb87
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-svg.patch
@@ -0,0 +1,30 @@
+Author: Olly Betts <olly@survex.com>
+Description: Update configure.in to match what it must have said when configure was generated.
+ One thing I should probably explain about the patch as my change may
+ seem odd otherwise - upstream's configure.in says "USE_SVG=0" but the
+ generated configure says "USE_SVG=1", so I've simply updated
+ configure.in to match what it must have said when configure was
+ generated.
+Forwarded: no
+--- tv-0.5.orig/configure.in
++++ tv-0.5/configure.in
+@@ -66,7 +66,9 @@
+   case "$wx_version" in
+      2.4.*) WX_SVG_LIB=[`$WX_CONFIG --basename`_dcsvg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`]
+            ;;
+-     *)    WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`]
++     2.*)   WX_SVG_LIB=[`$WX_CONFIG --basename`_svg-`echo ${wx_version} | sed -e "s:\.[0-9]\{1,\}$::"`]
++           ;;
++     *)     WX_SVG_LIB=
+            ;;
+   esac
+ 
+@@ -76,7 +78,7 @@
+ 
+ if test "$USE_SVG" = 1 ; then
+    CXXFLAGS="$CXXFLAGS -DUSE_SVG"
+-   LIBS="$LIBS -l$WX_SVG_LIB"
++   test -n "$WX_SVG_LIB" && LIBS="$LIBS -l$WX_SVG_LIB"
+ fi
+ 
+ AC_OUTPUT(Makefile ncl-2.0/Makefile ncl-2.0/src/Makefile TreeLib/Makefile tv.spec)
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch
new file mode 100644
index 000000000000..a57ae19aaf26
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-treeview-xpm-not-xbm.patch
@@ -0,0 +1,16 @@
+Description: Fix the extension of the icon
+Author: Olly Betts <olly@survex.com>
+Last-Update: 2014-06-21
+Forwarded: http://code.google.com/p/treeviewx/issues/detail?id=4
+
+--- tv-0.5.orig/tv.cpp
++++ tv-0.5/tv.cpp
+@@ -215,7 +215,7 @@
+ 	frame->SetIcon(wxIcon("app")); // use the name of the icon in the resource file
+ #endif
+ #if defined(__WXGTK__) || defined(__WXMOTIF__)
+-	frame->SetIcon(wxIcon(wxT("bitmaps/treeview.xbm")));
++	frame->SetIcon(wxIcon(wxT("/usr/share/pixmaps/treeviewx.xpm")));
+ #endif
+ 
+ #ifdef __WXMAC__
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch
new file mode 100644
index 000000000000..b1db5749990c
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx30.patch
@@ -0,0 +1,78 @@
+ tv.cpp    |  4 ++--
+ tview.cpp | 12 ++++++++----
+ 2 files changed, 10 insertions(+), 6 deletions(-)
+
+diff --git a/tv.cpp b/tv.cpp
+old mode 100755
+new mode 100644
+index 1abe90b..0df45a8
+--- a/tv.cpp
++++ b/tv.cpp
+@@ -163,9 +163,9 @@ bool MyApp::OnInit(void)
+ {
+ 	// Optional command line argument is name of file to open
+ #if wxUSE_UNICODE
+-	wchar_t *InputFile = NULL;
++	const wchar_t *InputFile = NULL;
+ #else
+-	char *InputFile = NULL;
++	const char *InputFile = NULL;
+ #endif
+ 	// Read input/output files
+ 	if (argc > 1)
+diff --git a/tview.cpp b/tview.cpp
+old mode 100755
+new mode 100644
+index 93972c3..4b2d593
+--- a/tview.cpp
++++ b/tview.cpp
+@@ -62,9 +62,13 @@
+ #ifdef __WXMSW__
+ #else
+ #ifdef USE_SVG
++#if wxMAJOR_VERSION >= 3
++	#include <wx/dcsvg.h>
++#else
+ 	#include <wx/svg/dcsvg.h>
+ #endif
+ #endif
++#endif
+ 
+ // GUI interface
+ #include "tv.h"
+@@ -186,7 +190,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event))
+ 	wxFrame *f = GetMainFrame();
+ 	wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
+ 		pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"),
+-		wxSAVE|wxOVERWRITE_PROMPT);
++		wxFD_SAVE|wxFD_OVERWRITE_PROMPT);
+ 
+     if (dialog.ShowModal() == wxID_OK)
+     {
+@@ -206,7 +210,7 @@ void TView::OnSavePicture (wxCommandEvent& WXUNUSED(event))
+ 	#endif 
+ 	wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
+ 		pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"),
+-		wxSAVE|wxOVERWRITE_PROMPT);
++		wxFD_SAVE|wxFD_OVERWRITE_PROMPT);
+ 
+     if (dialog.ShowModal() == wxID_OK)
+     {
+@@ -361,7 +365,7 @@ bool TView::OnClose(bool deleteWindow)
+ 
+ 	// Clear the canvas in  case we're in single-window mode,
+ 	// and the canvas stays.
+-#if (wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated
++#if (wxMAJOR_VERSION >= 3 || wxMINOR_VERSION > 4) // from 2.5 Clear is deprecated
+ 	canvas->ClearBackground();
+ #else
+ 	canvas->Clear();
+@@ -686,7 +690,7 @@ void TView::OnLeafFont (wxCommandEvent& WXUNUSED(event))
+ 	wxFontData data;
+ 	data.SetInitialFont (LeafFont);
+ 
+-#ifdef __WXMAC__
++#if wxMAJOR_VERSION >= 3 || defined __WXMAC__
+ 	wxFontDialog dialog((wxWindow *)GetFrame(), data);
+ #else
+ 	wxFontDialog dialog((wxWindow *)GetMainFrame(), &data);
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch
new file mode 100644
index 000000000000..2c5179f778ca
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wxstring-maxlen.patch
@@ -0,0 +1,34 @@
+Description: Remove wxSTRING_MAXLEN (removed in wx3.0) and incomp. definition.
+ The definition wxSTRING_MAXLEN was removed from the public API of wxWidgets.
+ Its meaning was basically "take all the string", whenever a string length was
+ expected. The missing definition didn't raise a compilation error because
+ TreeLib's treedrawer.h contained a fall-back definition, which is however
+ incompatible with the original definition of wxWidgets and therefore is
+ interpreted by wxWidgets as a number representing the real string length.
+ This patch gets rid of the dangerous fall-back definition and of all of its
+ uses by using alternative wxString constructors that achieve the same
+ behavior.
+Author: Martin Steghöfer <martin@steghoefer.eu>
+Last-Update: Sun, 10 Aug 2014 14:06:42 +0200
+Bug-Debian: http://bugs.debian.org/751255
+
+--- tv-0.5.orig/TreeLib/treedrawer.cpp
++++ tv-0.5/TreeLib/treedrawer.cpp
+@@ -245,7 +245,7 @@
+ 	// error in gcc, which is probably a gcc bug
+ 	{
+ 		wxCoord w, h, descent;
+-		wxString s (formatedString.c_str(), wxSTRING_MAXLEN);
++		wxString s (formatedString.c_str());
+ 		pt.x += dc->GetCharWidth();
+ 		pt.y -= dc->GetCharHeight()/2;
+ 		dc->DrawText (s, (int)pt.x, (int)pt.y);
+@@ -566,7 +566,7 @@
+ 
+ #if USE_WXWINDOWS
+         wxCoord w, h;
+-        wxString s (buf, wxSTRING_MAXLEN);
++        wxString s (buf);
+         dc->GetTextExtent (s, &w, &h);
+         int x = (int)pt2.x;
+         int y = (int)pt2.y;
diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch
new file mode 100644
index 000000000000..b1c03bbb39f9
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch
@@ -0,0 +1,50 @@
+--- tv.cpp~	2005-10-01 16:47:35.000000000 -0400
++++ tv.cpp	2005-10-01 16:52:30.000000000 -0400
+@@ -312,11 +312,15 @@
+ 	{
+ #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();
+--- tview.cpp~	2005-10-01 16:47:45.000000000 -0400
++++ tview.cpp	2005-10-01 16:50:42.000000000 -0400
+@@ -184,10 +184,10 @@
+ 	wxString pictureFileName = GetFrame()->GetTitle();
+ 	pictureFileName += wxT(".emf");
+ 	wxFrame *f = GetMainFrame();
+-   	wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
+-        "Enhanced metafile (*.emf)|*.emf",
+-        wxSAVE|wxOVERWRITE_PROMPT);
+-    
++	wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
++		pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"),
++		wxSAVE|wxOVERWRITE_PROMPT);
++
+     if (dialog.ShowModal() == wxID_OK)
+     {
+ 		wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ;
+@@ -204,9 +204,9 @@
+ 	#else
+ 	wxFrame *f = GetMainFrame();
+ 	#endif 
+-    wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
+-        "SVG vector picture files (*.svg)|*.svg",
+-        wxSAVE|wxOVERWRITE_PROMPT);
++	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)
+     {