Merge lp:~ubuntu-branches/ubuntu/utopic/gentle/utopic-201408050405 into lp:ubuntu/utopic/gentle

[Ubuntu Package Importer]

The package importer has detected a possible inconsistency between the package history in the archive and the history in bzr. As the archive is authoritative the importer has made lp:ubuntu/utopic/gentle reflect what is in the archive and the old bzr branch has been pushed to lp:~ubuntu-branches/ubuntu/utopic/gentle/utopic-201408050405. This merge proposal was created so that an Ubuntu developer can review the situations and perform a merge/upload if necessary. There are three typical cases where this can happen.
  1. Where someone pushes a change to bzr and someone else uploads the package without that change. This is the reason that this check is done by the importer. If this appears to be the case then a merge/upload should be done if the changes that were in bzr are still desirable.
  2. The importer incorrectly detected the above situation when someone made a change in bzr and then uploaded it.
  3. The importer incorrectly detected the above situation when someone just uploaded a package and didn't touch bzr.

If this case doesn't appear to be the first situation then set the status of the merge proposal to "Rejected" and help avoid the problem in future by filing a bug at https://bugs.launchpad.net/udd linking to this merge proposal.

(this is an automatically generated message)

Unmerged revisions

8. By Luke Yelavich on 2014-08-05

Merge branch lp:~noskcaj/ubuntu/utopic/gentle/wxwidgets-3.0

=== renamed file '.pc/applied-patches' => '.pc/applied-patches.THIS'
=== removed directory '.pc/forward_slashes.patch'
=== removed file '.pc/forward_slashes.patch/MyFrame.cpp'
--- .pc/forward_slashes.patch/MyFrame.cpp	2011-06-03 21:12:05 +0000
+++ .pc/forward_slashes.patch/MyFrame.cpp	1970-01-01 00:00:00 +0000
@@ -1,2790 +0,0 @@
-#include "MyFrame.h"
-#include "SendHTTP.h"
-#include <wx/sysopt.h>
-#include "TEliteLaChromLogDialog.h"
-
-// ---------------------------------------------------------------------------
-// MyFrame
-// ---------------------------------------------------------------------------
-
-BEGIN_EVENT_TABLE(MyFrame, MyFrameType)
-EVT_MENU(MDI_ABOUT, MyFrame::OnAbout)
-EVT_MENU(MDI_HELP, MyFrame::OnHelp)
-EVT_MENU(MDI_ENZYME_EDITOR, MyFrame::OnEnzymeEditor)
-EVT_MENU(MDI_ALIGNMENT, MyFrame::OnAlignment)
-EVT_MENU(MDI_IMAGE_VIEWER, MyFrame::OnImageViewer)
-EVT_MENU(MDI_EXTERNAL_INTERFACE, MyFrame::OnExternalInterface)
-EVT_MENU(MDI_CALCULATOR, MyFrame::OnCalculator)
-EVT_MENU(MDI_GRAPH, MyFrame::OnGraph)
-EVT_MENU(MDI_FILE_OPEN, MyFrame::OnFileOpen)
-EVT_MENU(MDI_FILE_IMPORT, MyFrame::OnFileImport)
-EVT_MENU(MDI_FILE_SAVE_ALL, MyFrame::OnStoreAll)
-EVT_MENU(MDI_TEXT_IMPORT, MyFrame::OnTextImport)
-EVT_MENU(MDI_PROJECT_SAVE, MyFrame::OnProjectSave)
-EVT_MENU(MDI_PROJECT_LOAD, MyFrame::OnProjectLoad)
-EVT_MENU(MDI_PROJECT_CLOSE, MyFrame::OnProjectClose)
-EVT_MENU(MDI_QUIT, MyFrame::OnQuit)
-EVT_MENU(MDI_CLOSE, MyFrame::OnMDIClose)
-EVT_MENU(MDI_MANAGE_DATABASE, MyFrame::OnManageDatabase)
-EVT_MENU(PROGRAM_OPTIONS, MyFrame::OnProgramOptions)
-EVT_MENU(MDI_HOMEPAGE, MyFrame::OnHomepage)
-EVT_MENU(MDI_LIGATION, MyFrame::OnLigation)
-EVT_MENU(MDI_CLONING_ASSISTANT, MyFrame::OnCloningAssistant)
-EVT_MENU(MDI_SEQUENCING_ASSISTANT, MyFrame::OnSequencingAssistant)
-EVT_MENU(MDI_DOTPLOT, MyFrame::OnDotPlot)
-EVT_MENU(MDI_RESTRICTION_IDENTIFIER, MyFrame::OnRestrictionIdentifier)
-
-EVT_MENU(Y___, MyFrame::TestMenu)
-EVT_MENU(MDI_RESTRICTION, MyFrame::BollocksMenu)
-EVT_MENU(MDI_PRINT_REPORT, MyFrame::BollocksMenu)
-
-EVT_MENU(MDI_NEXT_WINDOW, MyFrame::BollocksMenu)
-EVT_MENU(MDI_PREV_WINDOW, MyFrame::BollocksMenu)
-
-EVT_MENU_RANGE(A___,Z___,MyFrame::RerouteMenu)
-EVT_MENU_RANGE(ONLINE_TOOLS_BEGIN,ONLINE_TOOLS_END,MyFrame::OnlineTools)
-
-
-EVT_SASH_DRAGGED_RANGE(FRAME_SASH_1, FRAME_SASH_TOP, MyFrame::OnSashDrag)
-
-EVT_CLOSE(MyFrame::OnClose)
-
-EVT_SIZE(MyFrame::OnSize)
-END_EVENT_TABLE()
-
-/// \brief Number of wxAcceleratorEntry entries
-#define ACC_ENT 43
-
-/** \brief Constructor
- 
- * - Initializes variables
- * - Sets the accelerator keys
- */
-MyFrame::MyFrame(wxWindow *parent,
-                 const wxWindowID id,
-                 const wxString& title,
-                 const wxPoint& pos,
-                 const wxSize& size,
-                 const long style)
-: MyFrameType(parent, id, title, pos, size, style)
-{
-    dying = false ;
-    activating = false ;
-    locked = 0 ;
-    update_child_list = false ;
-#ifdef MYTEST
-    test_suite = NULL ;
-#endif
-	
-#ifndef __WXMAC__
-    // Accelerators
-    wxAcceleratorEntry entries[ACC_ENT];
-    entries[ 0].Set(wxACCEL_CTRL, (int) 'X', MDI_CUT);
-    entries[ 1].Set(wxACCEL_CTRL, (int) 'C', MDI_COPY);
-    entries[ 2].Set(wxACCEL_CTRL, (int) 'V', MDI_PASTE);
-    entries[ 3].Set(wxACCEL_CTRL, (int) 'L', MDI_LIGATION);
-    entries[ 4].Set(wxACCEL_CTRL, (int) 'A', MDI_MARK_ALL);
-    entries[ 5].Set(wxACCEL_CTRL, (int) 'S', MDI_FILE_SAVE);
-    entries[ 6].Set(wxACCEL_CTRL, (int) 'E', MDI_EXPORT);
-    entries[ 7].Set(wxACCEL_NORMAL, WXK_F2, MDI_EDIT_MODE);
-    entries[ 8].Set(wxACCEL_CTRL, (int) '0', AA_NONE);
-    entries[ 9].Set(wxACCEL_CTRL, (int) '1', AA_THREE_1);
-    entries[10].Set(wxACCEL_CTRL, (int) '2', AA_THREE_2);
-    entries[11].Set(wxACCEL_CTRL, (int) '3', AA_THREE_3);
-    entries[12].Set(wxACCEL_CTRL, (int) '4', AA_THREE_M1);
-    entries[13].Set(wxACCEL_CTRL, (int) '5', AA_THREE_M2);
-    entries[14].Set(wxACCEL_CTRL, (int) '6', AA_THREE_M3); 
-    entries[15].Set(wxACCEL_CTRL, (int) '7', AA_ALL);
-    entries[16].Set(wxACCEL_CTRL, (int) '8', AA_KNOWN);
-    entries[17].Set(wxACCEL_CTRL, (int) 'G', MDI_ALIGNMENT);
-    entries[18].Set(wxACCEL_CTRL, (int) 'F', MDI_FIND);
-    entries[19].Set(wxACCEL_NORMAL, WXK_F1, MDI_HELP);
-    entries[20].Set(wxACCEL_CTRL, (int) 'Y', AA_ONE);
-    entries[21].Set(wxACCEL_CTRL, (int) 'W', AA_THREE);
-    entries[22].Set(wxACCEL_NORMAL, WXK_F11, MDI_PROJECT_LOAD);
-    entries[23].Set(wxACCEL_NORMAL, WXK_F12, MDI_PROJECT_SAVE);
-    entries[24].Set(wxACCEL_NORMAL, WXK_F4, MDI_ORFS);
-    entries[25].Set(wxACCEL_NORMAL, WXK_F5, MDI_CIRCULAR_LINEAR);
-    entries[26].Set(wxACCEL_NORMAL, WXK_F3, MDI_VIEW_MODE);
-    entries[27].Set(wxACCEL_NORMAL, WXK_F6, MDI_TOGGLE_FEATURES);
-    entries[28].Set(wxACCEL_NORMAL, WXK_F7, MDI_TOGGLE_RESTRICTION);
-    entries[29].Set(wxACCEL_CTRL, (int) 'O', MDI_FILE_OPEN);
-    entries[30].Set(wxACCEL_CTRL, (int) 'I', MDI_FILE_IMPORT);
-    entries[31].Set(wxACCEL_CTRL, (int) 'Z', MDI_UNDO);
-    entries[32].Set(wxACCEL_CTRL, (int) 'N', MDI_TEXT_IMPORT);
-    entries[33].Set(wxACCEL_CTRL, (int) 'D', MDI_EXTERNAL_INTERFACE);
-    entries[34].Set(wxACCEL_CTRL, WXK_F4, MDI_CLOSE);
-    entries[35].Set(wxACCEL_CTRL, WXK_TAB, MDI_NEXT_WINDOW);
-    entries[36].Set(wxACCEL_CTRL|wxACCEL_SHIFT, WXK_TAB, MDI_PREV_WINDOW);
-    entries[37].Set(wxACCEL_NORMAL, WXK_F8, MDI_TOGGLE_IDNA);
-    entries[38].Set(wxACCEL_CTRL|wxACCEL_SHIFT, WXK_F12, Y___);
-	//    entries[38].Set(wxACCEL_CTRL, WXK_F12, MDI_GRAPH);
-    entries[39].Set(wxACCEL_CTRL, WXK_F1, MDI_ABOUT);
-    entries[40].Set(wxACCEL_NORMAL, WXK_F9, MDI_AUTO_ANNOTATE);
-    entries[41].Set(wxACCEL_CTRL, (int) 'K', MDI_CLONING_ASSISTANT);
-    entries[42].Set(wxACCEL_CTRL|wxACCEL_SHIFT, (int) 'S', MDI_FILE_SAVE_ALL);
-	
-    wxAcceleratorTable accel(ACC_ENT, entries);
-    SetAcceleratorTable(accel);
-#endif
-    html_ep = NULL ;
-    lastChild = NULL ;
-    tb_mychild = NULL ;
-    online_tools = new TOnlineTools ;
-	push_help ( _T("GENtle") ) ;
-	
-    // Load DNA markers
-	wxString marker_file = myapp()->homedir + myapp()->slash + _T("marker.txt") ;
-	wxTextFile tf ( marker_file ) ;
-    if ( tf.Open ( wxConvUTF8 ) ) wxSafeShowMessage ( marker_file , marker_file ) ;
-    for ( unsigned int a = 0 ; a < tf.GetLineCount() ; a++ )
-    {
-		wxString s = tf.GetLine ( a ) ;
-		s = s.Trim().Trim(false) ;
-		if ( s.IsEmpty() ) continue ; // Skip blank lines
-		if ( s.Left ( 1 ) == _T("#") ) continue ; // Skip comments
-		dna_marker.Add ( s ) ;
-    }
-}
-
-/** \brief Destructor
- 
- * - Stores the last project used, so it can be reopened on the next program start
- * - Clears memory
- */
-MyFrame::~MyFrame ()
-{
-	pop_help () ;
-    if ( html_ep ) delete html_ep ;
-    rememberLastProject () ;
-    CLEAR_DELETE ( dbcache ) ;
-	//    delete LS ;
-}
-
-/** \brief Initializes the frame
- 
- * - Creates frame layout
- * - Accesses local database and imports enzyme list
- * - Sets options
- * - Loads language file
- * - Checks for updates online (Windows only)
- * - Menus
- * - Initialized drop target
- * - Loads bitmaps for user interface
- * - Loads last project
- * - Parses command line paramaters
- */
-void MyFrame::initme ()
-{
-//	myapp()->sw.Start() ;
-
-#ifdef __WXGTK__
-    SetFont ( *MYFONT ( 8 , wxSWISS , wxNORMAL , wxNORMAL ) ) ;    
-#endif
-	
-	int borders = wxNO_BORDER ;
-    wxFileSystem::AddHandler(new wxInternetFSHandler );
-	
-  	wxSashLayoutWindow* win ;
-  	m_leftWindow2 = m_topWindow = m_bottomWindow = NULL ;
-	
-    // A window to the left of the client window
-    // This contains the main tree
-    win = new wxSashLayoutWindow(this, FRAME_SASH_1,
-								 wxDefaultPosition, wxSize(200, 30),
-								 borders | wxSW_3D | wxCLIP_CHILDREN);
-    win->SetDefaultSize(wxSize(200, 1000));
-    win->SetOrientation(wxLAYOUT_VERTICAL);
-    win->SetAlignment(wxLAYOUT_LEFT);
-    win->SetSashVisible(wxSASH_RIGHT, TRUE);
-    mainTree = new TMainTree ( win , MAIN_TREE_DUMMY ) ;
-    
-	
-    m_leftWindow1 = win;
-	
-    // The client window
-    win = new wxSashLayoutWindow(this, FRAME_SASH_2,
-								 wxDefaultPosition, wxSize(500, 30),
-								 borders | wxSW_3D | wxCLIP_CHILDREN);
-    win->SetDefaultSize(wxSize(500, 1000));
-    win->SetOrientation(wxLAYOUT_VERTICAL);
-    win->SetAlignment(wxLAYOUT_LEFT);
-    win->SetSashVisible(wxSASH_RIGHT, TRUE);
-    m_leftWindow2 = win;
-	
-    // Database access
-    LS = new TStorage ( LOCAL_STORAGE ) ;
-    LS->createDatabase() ;
-    LS->startup () ;
-    LS->syncEnzymes () ;
-	//    LS->optimizeDatabase () ; // This will VACUUM sqlite databases
-	
-    // Synchronize enzymes in known databases
-    // Turned of temporarily
-	//    LS->synchronize () ;
-    
-    // Import enzymes from local database
-    LS->import() ;
-	
-#ifndef MISER_MODE
-    bool default_update = false ;
-#else
-    bool default_update = true ;
-#endif
-	
-#ifdef __WXMAC__
-    default_update = true ;
-#endif
-	
-    // Loading program options from database
-    showVectorTitle = LS->getOption ( _T("SHOWVECTORTITLE") , true ) ;
-    showVectorLength = LS->getOption ( _T("SHOWVECTORLENGTH") , true ) ;
-    enhancedRefresh = LS->getOption ( _T("ENHANCEDREFRESH") , true ) ;
-    loadLastProject = LS->getOption ( _T("LOADLASTPROJECT") , true ) ;
-    useMetafile = LS->getOption ( _T("USEMETAFILE") , false ) ;
-    showSplashScreen = LS->getOption ( _T("SHOWSPLASHSCREEN") , true ) ;
-    checkUpdate = LS->getOption ( _T("CHECKUPDATE") , default_update ) ;
-    lang_string = LS->getOption ( _T("LANGUAGE") , _T("en") ) ;
-    doRegisterStuff = LS->getOption ( _T("REGISTERSTUFF") , true ) ;
-    editFeatureMode = LS->getOption ( _T("EDITFEATUREMODE") , 0 ) ;
-    showStopCodon = LS->getOption ( _T("SHOWSTOPCODON") , 0 ) ;
-    useCoolCanvas = LS->getOption ( _T("USECOOLCANVAS") , false ) ; // Ignored
-    useInternalHelp = LS->getOption ( _T("USEINTERNALHELP") , false ) ;
-    useOnlineHelp = LS->getOption ( _T("USEONLINEHELP") , true ) ;
-    showEnzymePos = LS->getOption ( _T("SHOWENZYMEPOS") , true ) ;
-    showToolTips = LS->getOption ( _T("SHOWTOOLTIPS") , true ) ;
-    showLowercaseDNA = LS->getOption ( _T("SHOWLOWERCASEDNA") , false ) ;
-	orfLength = LS->getOption ( _T("ORFLENGTH") , 100 ) ;
-    nonstandard_translation_table = LS->getOption ( _T("nonstandard_translation_table") , -1 ) ;
-    proxy = LS->getOption ( _T("PROXY") , _T("") ) ;
-	//#ifdef __WXMAC__
-	useTwoToolbars = LS->getOption ( _T("use_two_toolbars") , true ) ;
-	/*#else
-	 useTwoToolbars = LS->getOption ( _T("use_two_toolbars") , false ) ;
-	 #endif*/
-	
-    
-    int aa_red = LS->getOption ( _T("AA_RED") , wxLIGHT_GREY->Red() ) ;
-    int aa_green = LS->getOption ( _T("AA_GREEN") , wxLIGHT_GREY->Green() ) ;
-    int aa_blue = LS->getOption ( _T("AA_BLUE") , wxLIGHT_GREY->Blue() ) ;
-    aa_color.Set ( aa_red , aa_green , aa_blue ) ;
-    
-	//    if ( !proxy.IsEmpty() ) wxURL::SetDefaultProxy ( proxy ) ;
-    
-    stopcodon = showStopCodon == 0 ? '|' : '*' ;
-	
-	myapp()->init_txt ( lang_string.c_str() , _T("variables.csv") ) ;
-	
-	
-    global_enzyme_rules = new TEnzymeRules ;
-    global_enzyme_rules->load_global_settings() ;
-	
-    // Set the DEBUGGING option in your local test database,
-    // so you won't be bothered with updates anymore :-)
-    if ( LS->getOption ( _T("DEBUGGING") , _T("") ) == _T("1") ) checkUpdate = false ;
-	
-#ifndef __WXMSW__
-#ifndef __WXMAC__
-	checkUpdate = false ;
-#endif
-#endif
-	
-    // Check for update online
-    if ( checkUpdate )
-	{
-//		wxMessageBox ( _T("A") , wxString::Format(_T("%d"),myapp()->sw.Time())); myapp()->sw.Start() ;
-        wxString cur_update = check4update () ;
-//		wxMessageBox ( _T("B") , wxString::Format(_T("%d"),myapp()->sw.Time())); myapp()->sw.Start() ;
-        if ( !cur_update.IsEmpty() )
-		{
-            update2version ( cur_update ) ;
-            return ;
-		}
-	}
-	
-    project.name = txt("project") ;
-    SetTitle ( txt("gentle") ) ;
-    mainTree->initme() ;
-    
-    // Give it an icon
-#ifdef __WXMSW__
-    SetIcon(wxIcon(_T("GENtle.ico"),wxBITMAP_TYPE_ICO));
-#elif __WXMAC__
-#else
-    SetIcon(wxIcon( mondrian_xpm ));
-#endif
-    
-    // Make a menubar
-    wxMenu *file_menu = new wxMenu;
-	
-    file_menu->Append(MDI_FILE_OPEN, txt("m_open") , txt("m_opentxt") );
-    file_menu->Append(MDI_FILE_IMPORT, txt("m_import") , txt("m_importtxt") );
-    file_menu->Append(MDI_TEXT_IMPORT, txt("m_text_import") , txt("m_text_importtxt") );
-    file_menu->AppendSeparator();
-    file_menu->Append(MDI_PROJECT_LOAD, txt("m_project_open") , txt("m_project_opentxt") );    
-    file_menu->Append(MDI_PROJECT_SAVE, txt("m_project_save") , txt("m_project_savetxt") );    
-    file_menu->Append(MDI_PROJECT_CLOSE, txt("m_project_close") , txt("m_project_closetxt") );    
-    file_menu->AppendSeparator();
-    file_menu->Append(MDI_QUIT, txt("m_exit") , txt("m_exittxt") ) ;
-	
-    wxMenu *tool_menu = getToolMenu ( false ) ;
-    wxMenu *help_menu = getHelpMenu () ;
-	
-    menu_bar = new wxMenuBar;
-	
-    menu_bar->Append(file_menu, txt("m_file") );
-    menu_bar->Append(tool_menu, txt("m_tools") );
-    menu_bar->Append(help_menu, txt("m_help") );
-	
-    // Associate the menu bar with the frame
-    SetMenuBar(menu_bar);
-    CreateStatusBar();
-    GetStatusBar()->SetFieldsCount ( 2 ) ;
-	
-    // Drag'n'drop    
-    MyFrameDropTarget *dt = new MyFrameDropTarget ;
-    SetDropTarget ( dt ) ;
-	
-    // Bitmap library
-    wxString icondir = myapp()->bmpdir + myapp()->slash ;
-    bitmaps.push_back ( wxBitmap (icondir + _T("document-new.png") , wxBITMAP_TYPE_PNG) ) ;  // 0
-    bitmaps.push_back ( wxBitmap (icondir + _T("document-open.png") , wxBITMAP_TYPE_PNG) ) ; // 1
-    bitmaps.push_back ( wxBitmap (icondir + _T("document-save.png") , wxBITMAP_TYPE_PNG) ) ; // 2
-    bitmaps.push_back ( wxBitmap (icondir + _T("edit-undo.png") , wxBITMAP_TYPE_PNG) ) ; // 3
-    bitmaps.push_back ( wxBitmap (icondir + _T("edit-cut.png") , wxBITMAP_TYPE_PNG) ) ;  // 4
-    bitmaps.push_back ( wxBitmap (icondir + _T("edit-copy.png") , wxBITMAP_TYPE_PNG) ) ; // 5
-    bitmaps.push_back ( wxBitmap (icondir + _T("edit-paste.png") , wxBITMAP_TYPE_PNG) ) ;// 6
-    bitmaps.push_back ( wxBitmap (icondir + _T("display_circular_linear.png") , wxBITMAP_TYPE_PNG) ) ; // 7
-    bitmaps.push_back ( wxBitmap (icondir + _T("display_circular_linear.png") , wxBITMAP_TYPE_PNG) ) ;   // 8
-    bitmaps.push_back ( wxBitmap (icondir + _T("display_orfs.png") , wxBITMAP_TYPE_PNG) ) ; // 9
-    bitmaps.push_back ( wxBitmap (icondir + _T("display_features.png") , wxBITMAP_TYPE_PNG) ) ; // 10
-    bitmaps.push_back ( wxBitmap (icondir + _T("restriction_new.png") , wxBITMAP_TYPE_PNG) ) ; // 11
-    bitmaps.push_back ( wxBitmap (icondir + _T("view_new.png") , wxBITMAP_TYPE_PNG) ) ; // 12
-    bitmaps.push_back ( wxBitmap (icondir + _T("accessories-text-editor.png") , wxBITMAP_TYPE_PNG) ) ; // 13
-    bitmaps.push_back ( wxBitmap (icondir + _T("go-down.png") , wxBITMAP_TYPE_PNG) ) ; // 14
-    bitmaps.push_back ( wxBitmap (icondir + _T("go-up.png") , wxBITMAP_TYPE_PNG) ) ; // 15
-    bitmaps.push_back ( wxBitmap (icondir + _T("document-print.png") , wxBITMAP_TYPE_PNG) ) ; // 16
-    bitmaps.push_back ( wxBitmap (icondir + _T("alignments.png") , wxBITMAP_TYPE_PNG) ) ; // 17
-    bitmaps.push_back ( wxBitmap (icondir + _T("image_viewer.png") , wxBITMAP_TYPE_PNG) ) ; // 18
-    bitmaps.push_back ( wxBitmap (icondir + _T("applications-internet.png") , wxBITMAP_TYPE_PNG) ) ; // 19
-    bitmaps.push_back ( wxBitmap (icondir + _T("accessories-calculator.png") , wxBITMAP_TYPE_PNG) ) ; // 20
-    bitmaps.push_back ( wxBitmap (icondir + _T("preferences-desktop.png") , wxBITMAP_TYPE_PNG) ) ; // 21
-    bitmaps.push_back ( wxBitmap (icondir + _T("edit-find.png") , wxBITMAP_TYPE_PNG) ) ; // 22
-	
-    bitmaps.push_back ( to_grey ( bitmaps[ 4] ) ) ; // 23 - GREY Cut
-    bitmaps.push_back ( to_grey ( bitmaps[ 5] ) ) ; // 24 - GREY Copy
-    bitmaps.push_back ( to_grey ( bitmaps[ 6] ) ) ; // 25 - GREY Paste
-    bitmaps.push_back ( to_grey ( bitmaps[22] ) ) ; // 26 - GREY Find
-    bitmaps.push_back ( to_grey ( bitmaps[ 2] ) ) ; // 27 - GREY Save
-    bitmaps.push_back ( to_grey ( bitmaps[ 3] ) ) ; // 28 - GREY Undo
-    bitmaps.push_back ( to_grey ( bitmaps[16] ) ) ; // 29 - GREY Print sequence
-	
-	
-	if ( useTwoToolbars )
-	{
-		mainToolBar = CreateToolBar ( wxTB_HORIZONTAL ) ;
-		InitToolBar ( mainToolBar ) ;
-		addTool ( mainToolBar , MDI_TEXT_IMPORT ) ;
-		addTool ( mainToolBar , MDI_FILE_IMPORT ) ;
-		addTool ( mainToolBar , MDI_FILE_OPEN ) ;
-		addTool ( mainToolBar , MDI_FILE_SAVE ) ;
-		addTool ( mainToolBar , SEQ_PRINT ) ;
-		addTool ( mainToolBar , MDI_UNDO ) ;
-		addCCPFTools ( mainToolBar , true ) ;
-		addDefaultTools ( mainToolBar ) ;
-		mainToolBar->Realize() ;
-		updateCCP ( NULL ) ;
-	}
-	else
-	{
-		mainToolBar = NULL ;
-	}
-	
-#ifdef __WXGTK__
-    Show(TRUE);
-    int sw , sh ;
-    wxDisplaySize ( &sw , &sh ) ;
-    // SetSize ( sw/10 , sh/10 , sw*8/10 , sh*7/10 ) ;
-    SetSize ( 0 , 0 , sw , sh*9/10 ) ;
-#else
-    Show(TRUE);
-    Maximize() ;
-#endif
-	
-	
-    html_ep = new wxHtmlEasyPrinting ( _T("") , this ) ;
-    
-    wxBeginBusyCursor() ;
-#ifndef MISER_MODE
-    lockDisplay ( true ) ;
-#endif
-	
-    // Load last project?
-	//    loadLastProject = false ;
-    if ( loadLastProject )
-	{
-        wxString sql , n , d ;
-        TSQLresult r ;
-        sql = _T("SELECT s_value FROM stuff WHERE s_type='LASTPROJECT' AND s_name='NAME'") ;
-        r = LS->getObject ( sql ) ;
-        if ( r.rows() > 0 ) n = r[0][0] ;
-        sql = _T("SELECT s_value FROM stuff WHERE s_type='LASTPROJECT' AND s_name='DATABASE'") ;
-        r = LS->getObject ( sql ) ;
-        if ( r.rows() > 0 ) d = r[0][0] ;
-        if ( !n.IsEmpty() && !d.IsEmpty() )
-		{
-			TManageDatabaseDialog mdb ( this , _T("dummy") , ACTION_MODE_STARTUP ) ;
-			mdb.do_load_project ( n , d ) ;
-			mainTree->Refresh () ;
-		}
-	}
-	
-#ifndef MISER_MODE
-    lockDisplay ( false ) ;
-#endif
-	
-    // Command line parameters?
-    if ( myapp()->argc > 1 )
-	{
-		int a ;
-		
-		// Pre-cache key-value pairs
-		for ( a = 1 ; a < myapp()->argc ; a++ )
-		{
-			wxString path = myapp()->argv[a] ;
-			if ( path.Left(1) != _T("-") ) continue ; // No key/value pair
-			while ( path.Left(1) == _T("-") ) path = path.Mid ( 1 ) ;
-			wxString key = path.BeforeFirst('=').Lower().Trim().Trim(false) ;
-			wxString value = path.AfterFirst('=').Trim().Trim(false) ;
-			if ( value.IsEmpty() ) value = _T("1") ;
-			myapp()->clp[key] = value ;
-		}
-		
-		// Try to import images
-		wxProgressDialog pd ( txt("t_loading") , _T("") , myapp()->argc-1 , NULL , wxPD_ALL ) ;
-		for ( a = 1 ; a < myapp()->argc ; a++ )
-		{
-			wxString path = myapp()->argv[a] ;
-			if ( !pd.Update ( a-1 , path ) ) break ;
-			if ( path.Left(1) == _T("-") ) continue ; // key/value pair, did these already
-			if ( path.Left(9).Upper() == _T("GENTLE://") )
-			{
-				path = path.Mid ( 9 ) ;
-				if ( path.GetChar ( path.length()-1 ) == '/' ) // Trailing '/'
-					path = path.Mid ( 0 , path.length() - 1 ) ;
-				wxString db = path.BeforeFirst ( ':' ) ;
-				wxString name = path.AfterFirst ( ':' ) ;
-				TManageDatabaseDialog mdb ( this , _T("dummy") , ACTION_MODE_STARTUP ) ;
-				if ( !mdb.do_load_DNA ( name , db ) ) wxMessageBox ( txt("t_not_all_files_imported") ) ;
-				mainTree->Refresh () ;
-			}
-			else
-			{
-				if ( !wxFileExists ( path ) ) continue ; // No such file
-				wxString file = path.AfterLast ( '/' ) ;
-				file = file.AfterLast ( '\\' ) ;
-				importFile ( file , path , -1 ) ;
-				wxSetWorkingDirectory ( myapp()->homedir ) ;
-			}   	
-		}
-	}
-	
-	
-    wxEndBusyCursor() ;
-    Raise () ;
-    mainTree->Refresh () ;
-    
-    SetSizeHints ( 600 , 400 ) ;
-    Show(TRUE);
-    m_leftWindow2->SetFocus () ;
-}
-
-wxBitmap MyFrame::to_grey ( wxBitmap &bmp1 )
-{
-	/*#ifndef __WXMSW__
-     return wxNullBitmap ;
-	 #endif*/
-	wxImage i = bmp1.ConvertToImage () ;
-#ifdef __WXMSW__
-	wxImage i2 ( i.GetWidth() , i.GetHeight() ) ;
-#endif
-	for ( int x = 0 ; x < i.GetWidth() ; x++ )
-	{
-		for ( int y = 0 ; y < i.GetHeight() ; y++ )
-		{
-			int z = ( i.GetRed(x,y) + i.GetGreen(x,y) + i.GetBlue(x,y) ) / 3 ;
-#ifndef __WXMSW__
-			z /= 2 ;
-			i.SetRGB ( x , y , z , z , z ) ;
-#else
-			if ( i.GetAlpha ( x , y ) < 255 ) z = 200 ;
-			else z /= 2 ;
-			i2.SetRGB ( x , y , z , z , z ) ;
-#endif
-		}
-	}
-#ifdef __WXMSW__
-	return wxBitmap ( i2 ) ;
-#else
-	return wxBitmap ( i ) ;
-#endif
-}
-
-
-/** \brief Handles close event
- 
- Scans through all the children; if any one is changed, ask the user the
- darn "are you sure" question, unless in debugging mode
- */
-void MyFrame::OnClose(wxCloseEvent& event)
-{
-    bool canclose = true ;
-    for ( unsigned int a = 0 ; canclose && a < children.GetCount() ; a++ )
-        canclose = ! ( children[a]->vec && children[a]->vec->isChanged() ) ;
-    if ( LS->getOption ( _T("DEBUGGING") , _T("") ) == _T("1") ) canclose = true ; // For debugging
-    if ( !canclose )
-	{
-        if ( wxYES == wxMessageBox ( txt("t_some_changed") , txt("msg_box") , wxICON_QUESTION | wxYES | wxNO ) )
-			canclose = true ;
-	}
-    if ( canclose )
-	{    
-        dying = true ;
-        event.Skip();
-	}    
-    else event.Veto() ;
-}
-
-/** \brief Handles the Quit command, closes
- */
-void MyFrame::OnQuit(wxCommandEvent& event)
-{
-    Close();
-}
-
-/** \brief Displays "About" text
- */
-void MyFrame::OnAbout(wxCommandEvent& event )
-{
-	wxString text = txt("t_about_txt") ;
-    (void)wxMessageBox(text + _T("\n\nV ") + myapp()->get_GENtle_version(), txt("t_about") );
-}
-
-/** \brief Invokes homepage
- */
-void MyFrame::OnHomepage(wxCommandEvent& event )
-{
-	wxExecute ( myapp()->getHTMLCommand ( _T("http://gentle.magnusmanske.de") ) ) ;
-}
-
-/** \brief Invokes help
- */
-void MyFrame::OnHelp(wxCommandEvent& event )
-{
-	wxString helpfile ;
-    if ( useInternalHelp )
-	{
-        wxHtmlHelpController *hc = new wxHtmlHelpController ( wxHF_DEFAULT_STYLE|wxHF_OPEN_FILES ) ;
-        helpfile += myapp()->homedir ;
-        helpfile += _T("\\help\\") ;
-        helpfile += lang_string ;
-        helpfile += _T(".hhp") ;
-        hc->AddBook ( helpfile ) ;
-        hc->DisplayContents () ;
-	}
-    else
-	{
-		helpfile = get_help() ;
-		if ( useOnlineHelp && !helpfile.IsEmpty() )
-		{
-			helpfile = _T("http://en.wikibooks.org/wiki/") + helpfile ;
-		}
-		else helpfile.Clear() ;
-		
-		if ( helpfile.IsEmpty() )
-		{
-#ifdef __WXMAC__
-			helpfile = _T("\"") ;
-			helpfile += myapp()->homedir ;
-			helpfile += _T("/") ;
-			helpfile += txt("f_help").AfterFirst ( '/' ) ;
-			helpfile += _T("\"") ;
-#endif
-			
-#ifdef __WXMSW__
-			helpfile = _T("\"") ;
-			helpfile += myapp()->homedir ;
-			helpfile += _T("\\") ;
-			helpfile += txt("f_help") ;
-			helpfile += _T("\"") ;
-            
-			for ( int a = 0 ; a < helpfile.length() ; a++ )
-				if ( helpfile.GetChar(a) == '/' ) helpfile.SetChar ( a , '\\' ) ;
-#endif
-		}
-		
-		if ( !helpfile.IsEmpty() )
-		{
-			wxString command = myapp()->getHTMLCommand ( helpfile ) ;
-			wxExecute ( command ) ;
-		}
-	}
-}
-
-/** \brief Returns pointer to last (active) child
- */
-ChildBase *MyFrame::GetActiveChild() //SDI
-{
-    return lastChild ;
-}
-
-/** \brief Invokes the enzyme editor
- */
-void MyFrame::OnEnzymeEditor(wxCommandEvent& event )
-{   
-    TVectorEditor ee ( this , txt("t_enzymeeditor") , NULL ) ;
-    ee.ShowModal () ;
-}
-
-/** \brief Invokes the "open from database" dialog
- */
-void MyFrame::OnFileOpen(wxCommandEvent& event )
-{
-	unsigned int i = children.GetCount() ;
-    TManageDatabaseDialog dbd ( this , txt("t_open") , ACTION_MODE_LOAD ) ;
-    dbd.ShowModal () ;
-    if ( i != children.GetCount() )
-		setActiveChild ( children[children.GetCount()-1] ) ;
-    if ( GetActiveChild() ) GetActiveChild()->SetFocus() ;
-}
-
-/** \brief Invokes the "enter sequence manually" dialog and calls the appropriate creation function
- */
-void MyFrame::OnTextImport(wxCommandEvent& event )
-{
-    TextImportDialog d ( this , txt("m_text_importtxt") ) ;
-    
-    ChildBase *c = (ChildBase*) GetActiveChild() ;
-    if ( c && c->def == _T("PrimerDesign") ) d.type->SetSelection ( 4 ) ;
-    
-    if ( d.ShowModal () != wxID_OK ) return ;
-	
-    int type = d.type->GetSelection () ;
-	
-    if ( type == 0 ) // DNA
-	{
-        TVector *v = new TVector ;
-        v->setName ( d.sName ) ;
-        v->setSequence ( d.sSequence ) ;
-        v->setDescription ( txt("manually_entered_sequence") + wxString ( _T("\n") + wxGetUserName() ) ) ;
-        newFromVector ( v ) ;
-	}
-    else if ( type == 1 ) // Amino Acids 
-	{
-        newAminoAcids ( d.sSequence , d.sName ) ;
-	}
-    else if ( type == 2 ) // GenBank
-	{
-        TGenBank gb ;
-        gb.paste ( d.sequence->GetValue() ) ;
-        newGB ( gb , d.sName ) ;
-	}        
-    else if ( type == 3 ) // XML
-	{
-        // Trying XML formats
-        TXMLfile xml ;
-        xml.parse ( d.sequence->GetValue().c_str() ) ;
-        if ( xml.success() )
-		{
-			newXML ( xml , d.sName ) ;
-			return ;
-		}
-	}
-    else if ( type == 4 ) // Primer
-	{
-        TVector *v = new TVector ;
-        v->setName ( d.sName ) ;
-        v->setSequence ( d.sSequence ) ;
-        v->setType ( TYPE_PRIMER ) ;
-        v->setDescription ( txt("manually_entered_sequence") + _T("\n") + wxGetUserName() ) ;
-        newFromVector ( v , TYPE_PRIMER ) ;
-	}
-}
-
-/** \brief Saves an image (actually, a wxBitmap) to a file, with "save as" dialog
- */
-void MyFrame::saveImage ( wxBitmap *bmp , wxString name )
-{
-    wxString wildcard ;
-    wildcard += _T("PNG (*.png)|*.png") ;
-	//    wildcard += _T("|TIF (*.tif)|*.tif") ;
-    wildcard += _T("|Bitmap (*.bmp)|*.bmp") ;
-    wildcard += _T("|JPEG (*.jpg)|*.jpg") ;
-    
-    name.Replace ( _T("*") , _T("") , TRUE ) ;
-    name.Replace ( _T(":") , _T("_") , TRUE ) ;
-    name.Replace ( _T("/") , _T("_") , TRUE ) ;
-    name.Replace ( _T("\\") , _T("_") , TRUE ) ;
-	
-    wxString lastdir = LS->getOption ( _T("LAST_IMPORT_DIR") , _T("C:") ) ;
-    wxFileDialog d ( this , txt("t_save_image") , lastdir , name , wildcard , wxSAVE|wxOVERWRITE_PROMPT ) ;
-    if ( d.ShowModal() != wxID_OK ) return ;
-    wxString filename = d.GetPath() ;
-    
-    wxBeginBusyCursor () ;
-    wxString type = filename.AfterLast('.').Upper() ;
-    if ( type == _T("BMP") ) bmp->SaveFile ( filename , wxBITMAP_TYPE_BMP ) ;
-    if ( type == _T("PNG") ) bmp->SaveFile ( filename , wxBITMAP_TYPE_PNG ) ;
-    if ( type == _T("JPG") ) bmp->SaveFile ( filename , wxBITMAP_TYPE_JPEG ) ;
-    if ( type == _T("TIF") ) bmp->SaveFile ( filename , wxBITMAP_TYPE_TIF ) ;
-    wxEndBusyCursor () ;
-}    
-
-/** \brief Handles the "import from file" dialog, then calls MyFrame::importFile 
- */
-void MyFrame::OnFileImport(wxCommandEvent& event )
-{
-    wxString wcAutomatic = txt("format_filter_auto") ;
-    wxString wcClone = txt("format_filter_clone") ;
-    wxString wcGenBank = txt("format_filter_genbank") ;
-    wxString wcSequencing = txt("format_filter_fasta") ;
-    wxString wcPlainTextDNA = txt("format_filter_plain_dna") ;
-    wxString wcPlainTextAA = txt("format_filter_plain_aa") ;
-    wxString wcABIformat = txt("format_filter_abi") ;
-    wxString wcCSVformat = txt("format_filter_csv") ;
-    wxString wcCM5format = txt("format_filter_cm5") ;
-    wxString wildcard = wcAutomatic +
-	_T("|") + wcClone +
-	_T("|") + wcGenBank +
-	_T("|") + wcSequencing +
-	_T("|") + wcPlainTextDNA +
-	_T("|") + wcPlainTextAA +
-	_T("|") + wcABIformat +
-	_T("|") + wcCSVformat +
-	_T("|") + wcCM5format ;
-    wxString lastdir = LS->getOption ( _T("LAST_IMPORT_DIR") , _T("C:") ) ;
-    wxFileDialog d ( this , txt("import_file") , lastdir , 
-					_T("") , wildcard , wxOPEN | wxMULTIPLE ) ;
-    int x = d.ShowModal() ;
-    if ( x != wxID_OK ) return ;
-    
-    LS->setOption ( _T("LAST_IMPORT_DIR") , d.GetDirectory() ) ;
-	
-    int filter = d.GetFilterIndex () - 1 ;
-    wxArrayString files , paths ;
-    d.GetFilenames ( files ) ;
-    d.GetPaths ( paths ) ;
-    wxBeginBusyCursor();
-    wxSafeYield() ;
-    wxProgressDialog pd ( txt("t_loading") , _T("") , files.GetCount() , NULL , wxPD_ALL ) ;
-	//    lockDisplay ( true ) ;
-    wxString unknown ;
-    unsigned int a ;
-    for ( a = 0 ; a < files.GetCount() ; a++ )
-	{
-		if ( !pd.Update ( a , files[a] ) ) break ;
-		if ( !importFile ( files[a] , paths[a] , filter ) )
-		{
-   		    if ( !unknown.IsEmpty() ) unknown += _T("\n ") ;
-            unknown += files[a] ;
-		}    
-	}
-    if ( a == files.GetCount() ) pd.Update ( a ) ; // Hide progress dialog
-    if ( !unknown.IsEmpty() )
-    	wxMessageBox ( unknown , txt("t_unable_to_detect_file_type") ) ;
-	//    lockDisplay ( false ) ;
-    SetFocus () ;
-    wxEndBusyCursor();
-    mainTree->Refresh () ;
-    Refresh () ;
-    activateChild ( getChildIndex ( lastChild ) ) ;
-}
-
-/** \brief Imports a file
- 
- If a "filter" number is given, only the matching file type is tried.
- If "filter" is not given (-1), it tries to detect the type
- by opening it with all import modules until there is a match.
- */
-bool MyFrame::importFile ( wxString file , wxString path , int filter )
-{
-    wxString end = path.AfterLast('.').Lower() ;
-    
-    // Trying Elite LaChrom chromatogram software
-    if ( filter == -1 && ( end == _T("apex") || end == _T("area") || end == _T("estdconc") ) )
-    {
-		TEliteLaChromLogDialog *eld = new TEliteLaChromLogDialog ( this , txt("t_eld_dialog_title") , path ) ;
-		eld->Show ( TRUE ) ;
-		//eld.ShowModal() ;
-		return true ;
-    }
-	
-	
-    // Trying XML formats
-    if ( filter == -1 )
-	{
-        TXMLfile xml ;
-        xml.load ( path ) ;
-        if ( xml.success() )
-		{
-			newXML ( xml ) ;
-			return true ;
-		}
-	}
-	
-    // Trying GenBank format
-    if ( filter == 1 || filter == -1 )
-	{
-//		wxStartTimer () ;
-		TGenBank gb ;
-		gb.load ( path ) ;
-		mylog ( "GenBank import" , "loaded" ) ;
-		if ( gb.success )
-		{
-			newGB ( gb , file ) ;
-			return true ;
-		}
-	}
-	
-    // Trying ABI format
-    if ( filter == 5 || filter == -1 )
-	{
-        ABItype dummy ;
-        dummy.parse ( path ) ;
-        if ( dummy.vf.size() > 0 ) // Success
-		{
-			newABI ( path , file ) ;
-			return true ;
-		}
-	}
-	
-    // Trying SCF format
-    if ( filter == 5 || filter == -1 )
-	{
-        SCFtype dummy ;
-        if ( dummy.parse ( path ) ) // Success
-		{
-			newABI ( path , file ) ;
-			return true ;
-		}
-	}
-	
-    // Trying Clone Manager 5 format
-    if ( filter == -1 || filter == 7 )
-	{
-        TCloneManager cm ;
-        cm.load ( path ) ;
-        if ( cm.success() )
-		{
-			for ( int a = 0 ; a < cm.countVectors() ; a++ )
-				newFromVector ( cm.getVector ( a ) ) ;
-			return true ;
-		}
-	}
-	
-    // Trying PDB format
-    if ( filter == -1 )
-	{
-        TPDB pdb ;
-        pdb.load ( path ) ;
-        if ( pdb.success )
-		{
-			newPDB ( pdb , file ) ;
-			return true ;
-		}
-	}
-	
-	
-    // Trying spectra
-    if ( filter == 6 || filter == -1 )
-	{
-	    wxEndBusyCursor();
-        TGraph *g = RunGraph() ;
-        if ( filter == -1 && g->gd && g->gd->tryall ( path ) == _T("") )
-		{
-        	wxBeginBusyCursor();
-   		    g->Close () ;
-		}    
-        else if ( g->gd->SetupFromFile ( path ) )
-		{
-        	wxBeginBusyCursor();
-           	g->gd->AutoScale () ;
-           	g->gd->UpdateDisplay () ;
-           	wxEndBusyCursor();
-           	/*if ( filter == 6 ) */return true ;
-		}   	
-       	else
-		{
-        	wxBeginBusyCursor();
-   		    g->Close () ;
-   		    wxEndBusyCursor();
-   		    if ( filter == 6 ) return false ;
-		}    
-	}    
-	
-    // Trying UReadSeq package
-    if ( filter == 2 || filter == 3 || filter == 4 || filter == -1 )
-	{
-        TUReadSeq u ( path ) ;
-		//        if ( u.error == 0 && u.seqs.GetCount() > 0 )
-        if ( u.error == 0 )
-		{
-			TGenBank gb ;
-			u.convert ( gb ) ;
-			newGB ( gb ) ;
-			return true ;
-		}
-	}
-	
-    // Trying CLONE format
-    if ( filter == 0 || filter == -1 )
-	{
-        TClone clone ;
-        clone.LS = LS ;
-        clone.load ( path ) ;
-        if ( clone.success )
-		{
-			newCLONE ( clone ) ;
-			return true ;
-		}
-	}
-	
-    return false ;
-}
-
-/** \brief Creates a new module with a phylogenetic tree
- */
-TPhyloTree *MyFrame::newPhyloTree ( wxString title )
-{
-	TPhyloTree *subframe = new TPhyloTree(getCommonParent(), txt("t_phylogenetic_tree")) ;
-	
-	setChild ( subframe ) ;
-	
-	// Give it an icon
-#ifdef __WXMSW__
-	subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-	subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-	
-	subframe->initme() ;
-	mainTree->addChild(subframe,TYPE_MISC) ;
-	subframe->Maximize() ;
-	return subframe ;
-}
-
-/** \brief Creates a new entry from an XML file (GenBankXML; DNA or amino acids)
- */
-void MyFrame::newXML (  TXMLfile &xml , wxString title )
-{
-	int n ;
-	for ( n = 0 ; n < xml.countVectors() ; n++ )
-	{
-		TVector *nv = xml.getVector ( n ) ;
-		short type = nv->getType() ;
-		if ( !title.IsEmpty() ) nv->setName ( title ) ;
-		nv->addDescription ( _T("\n") + wxGetUserName() ) ;
-		if ( type == TYPE_AMINO_ACIDS )
-			newAminoAcids ( nv , nv->getName() ) ;
-		else
-			newFromVector ( nv , type ) ;
-	}
-}
-
-/** \brief Creates a new entry from a CLONE import
- */
-MyChild *MyFrame::newCLONE ( TClone &clone )
-{
-    MyChild *subframe = new MyChild(getCommonParent(), txt("imported_vector"),
-                                    wxPoint(-1, -1), wxSize(-1, -1),
-                                    wxDEFAULT_FRAME_STYLE);
-    setChild ( subframe ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    
-    subframe->initme() ;
-    int type = TYPE_VECTOR ;
-    clone.remap ( subframe->vec ) ;
-    subframe->vec->setDescription ( subframe->vec->getDescription() + _T("\n") + wxGetUserName() ) ;
-    subframe->vec->setWindow ( subframe ) ;
-    subframe->initPanels() ;
-    mainTree->addChild(subframe,type) ;
-    subframe->Maximize() ;
-	return subframe ;
-}
-
-/** \brief Creates a new entry from a PDB import
- */
-void MyFrame::newPDB ( TPDB &pdb , wxString title )
-{
-    pdb.remap () ;
-    for ( int a = 0 ; a < pdb.seqres.size() ; a++ )
-	{
-        newAminoAcids ( pdb.seqres[a].v , pdb.seqres[a].v->getName() ) -> Activate () ;
-        delete pdb.seqres[a].v ;
-	}    
-}
-
-/** \brief Creates a new entry from a GenBank import
- 
- This function can actually open multiple sequences from one and the same
- GenBank structure. This is used, for example, when opening alignments.
- */
-void MyFrame::newGB ( TGenBank &gb , wxString title )
-{
-    int n ;
-    TVector *nv ;
-    wxArrayTVector vv ;
-    wxArrayChildBase vc ;
-    wxArrayString vs ;
-    bool alignment = false ;
-	//    wxStartTimer () ;
-    gb.vs.Clear () ;
-    gb.vi.Clear () ;
-	
-    for ( n = 0 ; n < gb.vs_l.size() ; n++ )
-	{
-        nv = new TVector ;
-        gb.remap ( nv , gb.vs_l[n] , gb.vi_l[n] ) ;
-        gb.vs_l[n].Clear () ;
-        gb.vi_l[n].Clear () ;
-		
-        mylog ( "GenBank import" , "remapped " + nv->getName() ) ;
-        vs.Add ( nv->getSequence() ) ;
-        vv.Add ( nv ) ;
-        nv->setDescription ( nv->getDescription() + _T("\n") + wxGetUserName() ) ;
-        if ( nv->getSequenceLength() != vv[0]->getSequenceLength() ) alignment = false ;
-        else if ( nv->getSequence().find ( '-' ) != -1 ) alignment = true ;
-        mylog ( "GenBank import" , "added " + nv->getName() ) ;
-	}
-    if ( gb.vs_l.size() == 1 ) alignment = false ;
-    
-    // Removing alignment artifacts from sequences
-    for ( n = 0 ; n < vv.GetCount() ; n++ )
-        vv[n]->removeAlignmentArtifacts () ;
-    mylog ( "GenBank import" , "artifacts removed" ) ;
-	
-	/*
-	 // Ask if GenBank alignment should be opened as such (not using this right now)
-	 if ( alignment )
-	 {
-	 if ( wxYES != wxMessageBox ( txt("t_possible_alignment") ,
-	 title , wxYES_NO|wxICON_QUESTION ) )
-	 {
-	 alignment = false ;
-	 }        
-	 }*/
-	
-    wxBeginBusyCursor() ;
-    for ( n = 0 ; n < gb.vs_l.size() ; n++ )
-	{
-        nv = vv[n] ;
-        if ( gb.vs_l.size() == 1 && !title.IsEmpty() && nv->getName().IsEmpty() )
-			nv->setName ( title ) ;
-        short type = TUReadSeq::getSeqType ( nv->getSequence() ) ;
-        if ( type == TYPE_AMINO_ACIDS )
-			vc.Add ( newAminoAcids ( nv , nv->getName() ) ) ;
-        else
-			vc.Add ( newFromVector ( nv , type ) ) ;
-        mylog ( "GenBank import" , "child added" ) ;
-	}
-    vv.Clear () ;
-	
-    if ( alignment )
-	{
-        runAlignment ( vs , vc ) ;
-	}
-	//    wxMessageBox ( wxString::Format ( "%dms" , wxGetElapsedTime() ) ) ;
-    wxEndBusyCursor() ;
-}
-
-
-/** \brief Creates a new DNA entry from a TVector structure
- 
- This is a very important function. Virtually all import/open/enter
- functions call this one to create the actual window containing
- that data.
- */
-MyChild* MyFrame::newFromVector ( TVector *nv , int type )
-{
-    if ( !nv ) return NULL ;
-	myapp()->sw.Start () ;
-    MyChild *subframe = new MyChild(getCommonParent(), _T(""),
-                                    wxPoint(-1, -1), wxSize(-1, -1),
-                                    wxDEFAULT_FRAME_STYLE);
-    myass ( subframe , "MyFrame::newFromVector" ) ;
-    setChild ( subframe ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme() ;
-    delete subframe->vec ;
-    subframe->vec = nv ;
-    subframe->vec->setWindow ( subframe ) ;
-	
-    subframe->initPanels() ;
-    mainTree->addChild(subframe,type) ;
-    children.Last()->Activate () ;
-	
-    return subframe ;
-}
-
-
-/** \brief Handles OnSize events
- */
-void MyFrame::OnSize(wxSizeEvent& event)
-{
-    wxLayoutAlgorithm layout;
-    layout.LayoutFrame(this);
-	/*#ifdef __WXMSW__
-	 if ( lastChild )
-	 {
-	 setActiveChild ( lastChild ) ;
-	 lastChild->Refresh() ;
-	 }    
-	 #endif*/
-}
-
-
-/** \brief Sets the icon size for the toolbar
- */
-void MyFrame::InitToolBar(wxToolBar* toolBar)
-{
-	wxSize ns ;
-	if ( useTwoToolbars )
-	{
-#ifdef __WXMSW__
-		ns = wxSize ( 22 , 22 ) ;
-#else
-		if ( toolBar == mainToolBar ) ns = wxSize ( 48 , 48 ) ;
-		else ns = wxSize ( 36 , 36 ) ;
-#endif
-	}
-	else
-	{
-#ifdef __WXMSW__
-		ns = wxSize ( 22 , 22 ) ;
-#else
-		ns = wxSize ( 32 , 32 ) ;
-#endif
-	}
-	
-	toolBar->SetToolBitmapSize ( ns ) ;
-}
-
-wxChoice *MyFrame::AddFontsizeTool ( wxToolBar* toolBar , int id )
-{
-	toolBar->AddControl ( new wxStaticText ( toolBar , -1 , txt("t_fontsize") ) ) ;
-#ifdef __WXMSW__
-	int width = 40 ;
-#else
-	int width = 60 ;
-#endif
-    wxChoice *fontsize = new wxChoice ( toolBar , id , wxDefaultPosition , wxSize ( width , -1 ) ) ;
-    toolBar->AddControl ( fontsize ) ;	
-    fontsize->Append ( _T(" 6") ) ;
-    fontsize->Append ( _T(" 8") ) ;
-    fontsize->Append ( _T("10") ) ;
-    fontsize->Append ( _T("12") ) ;
-    fontsize->Append ( _T("14") ) ;
-    fontsize->Append ( _T("16") ) ;
-    fontsize->Append ( _T("18") ) ;
-    fontsize->Append ( _T("20") ) ;
-    fontsize->Append ( _T("22") ) ;
-    fontsize->Append ( _T("24") ) ;
-    fontsize->Append ( _T("26") ) ;
-    fontsize->Append ( _T("28") ) ;
-    fontsize->Append ( _T("36") ) ;
-    fontsize->Append ( _T("48") ) ;
-    fontsize->SetStringSelection ( _T("12") ) ;
-    return fontsize ;
-}
-
-/** \brief Adds a tool to a given toolbar
- */
-void MyFrame::addTool ( wxToolBar* toolBar , int id )
-{
-	if ( mainToolBar && toolBar != mainToolBar ) return ;
-	
-	if ( id == MDI_TEXT_IMPORT )
-		toolBar->AddTool( MDI_TEXT_IMPORT ,
-						 bitmaps[0],
-						 txt("m_new_sequence") ) ;  
-	else if ( id == MDI_FILE_IMPORT )
-		toolBar->AddTool( MDI_FILE_IMPORT, 
-						 bitmaps[14],
-						 txt("m_importtxt") );
-	else if ( id == MDI_FILE_OPEN )
-		toolBar->AddTool( MDI_FILE_OPEN, 
-						 bitmaps[1],
-						 txt("m_opentxt") );
-	else if ( id == MDI_FILE_SAVE )
-        toolBar->AddTool( MDI_FILE_SAVE, 
-						 txt("m_txt_store_in_db"),
-						 myapp()->frame->bitmaps[2] ,
-						 myapp()->frame->bitmaps[27] ,
-						 wxITEM_NORMAL , txt("m_txt_store_in_db") ) ;
-	else if ( id == SEQ_PRINT )
-        toolBar->AddTool( SEQ_PRINT, 
-						 txt("m_print_sequence"),
-						 myapp()->frame->bitmaps[16] ,
-						 myapp()->frame->bitmaps[29] ,
-						 wxITEM_NORMAL , txt("m_print_sequence") ) ;
-	else if ( id == MDI_UNDO )
-	{
-        toolBar->AddSeparator() ;
-        toolBar->AddTool( MDI_UNDO, txt("m_undo_text"),
-						 myapp()->frame->bitmaps[3] ,
-						 myapp()->frame->bitmaps[28] ,
-						 wxITEM_NORMAL , txt("m_undo_text") ) ;
-	}
-	else if ( id == MDI_COPY )
-        toolBar->AddTool( MDI_COPY, txt("m_copy_text") , 
-						 myapp()->frame->bitmaps[5] , 
-						 myapp()->frame->bitmaps[24] ,
-						 wxITEM_NORMAL , txt("m_copy_text") ) ;
-}
-
-/** \brief Adds default tools to a given toolbar
- */
-void MyFrame::addDefaultTools(wxToolBar* toolBar)
-{
-	if ( mainToolBar && toolBar != mainToolBar ) return ;
- 	toolBar->AddSeparator() ;
- 	toolBar->AddTool( MDI_ALIGNMENT, myapp()->frame->bitmaps[17] , txt("m_alignment_text") ) ;
- 	toolBar->AddTool( MDI_IMAGE_VIEWER, myapp()->frame->bitmaps[18] , txt("m_imageviewer_text") ) ;
- 	toolBar->AddTool( MDI_CALCULATOR, myapp()->frame->bitmaps[20] , txt("m_calculator_text") ) ;
- 	toolBar->AddTool( PROGRAM_OPTIONS, myapp()->frame->bitmaps[21] , txt("m_options_text") ) ;
- 	toolBar->AddTool( MDI_EXTERNAL_INTERFACE, myapp()->frame->bitmaps[19] , txt("m_external_text") ) ;
-}
-
-/** \brief Adds cut,copy,paste (and find) tools to a given toolbar
- */
-void MyFrame::addCCPFTools(wxToolBar* toolBar, bool findbutton )
-{
-	if ( mainToolBar && toolBar != mainToolBar ) return ;
-    toolBar->AddSeparator() ;
-    toolBar->AddTool( MDI_CUT, txt("m_cut_text") , 
-					 myapp()->frame->bitmaps[4] , myapp()->frame->bitmaps[23] ,
-					 wxITEM_NORMAL , txt("m_cut_text") ) ;
-    toolBar->AddTool( MDI_COPY, txt("m_copy_text") , 
-					 myapp()->frame->bitmaps[5] , myapp()->frame->bitmaps[24] ,
-					 wxITEM_NORMAL , txt("m_copy_text") ) ;
-    toolBar->AddTool( MDI_PASTE, txt("m_paste_text") , 
-					 myapp()->frame->bitmaps[6] , myapp()->frame->bitmaps[25] ,
-					 wxITEM_NORMAL , txt("m_paste_text") ) ;
-    if ( findbutton )
-		toolBar->AddTool( MDI_FIND, txt("m_find_text") , 
-                         myapp()->frame->bitmaps[22] , myapp()->frame->bitmaps[26] ,
-                         wxITEM_NORMAL , txt("m_find_text") ) ;
-    if ( !mainToolBar ) toolBar->AddSeparator () ;
-}
-
-#define UGLY_MENU_UPDATE(x,y) if(GetMenuBar()&&GetMenuBar()->FindItem(x))GetMenuBar()->FindItem(x)->Enable(y);
-
-/**	\brief Updates cut, copy, paste, find icons
- */
-void MyFrame::updateCCP ( ChildBase *c )
-{
-    if ( !mainToolBar && !c ) return ;
-    wxToolBar *tb = mainToolBar ? mainToolBar : c->toolbar ;
-	tb->EnableTool ( MDI_FILE_SAVE , c ? c->allow_save : false ) ;
-	tb->EnableTool ( MDI_UNDO , c ? c->allow_undo : false ) ;
-	tb->EnableTool ( SEQ_PRINT , c ? c->allow_print : false ) ;
-	tb->EnableTool ( MDI_CUT , c ? c->allow_cut : false ) ;
-	tb->EnableTool ( MDI_COPY , c ? c->allow_copy : false ) ;
-	tb->EnableTool ( MDI_PASTE , c ? c->allow_paste : false ) ;
-	tb->EnableTool ( MDI_FIND , c ? c->allow_find : false ) ;
-	
-	UGLY_MENU_UPDATE ( MDI_FILE_SAVE , c ? c->allow_save : false ) ;
-	UGLY_MENU_UPDATE ( SEQ_PRINT , c ? c->allow_print : false ) ;
-	UGLY_MENU_UPDATE ( MDI_CUT , c ? c->allow_cut : false ) ;
-	UGLY_MENU_UPDATE ( MDI_COPY , c ? c->allow_copy : false ) ;
-	UGLY_MENU_UPDATE ( MDI_PASTE , c ? c->allow_paste : false ) ;
-	UGLY_MENU_UPDATE ( MDI_MARK_ALL , c ? !c->allow_paste : false ) ;
-	UGLY_MENU_UPDATE ( MDI_COPY_TO_NEW , c ? !c->allow_paste : false ) ;
-	UGLY_MENU_UPDATE ( MDI_AS_NEW_FEATURE , c ? !c->allow_paste : false ) ;
-	UGLY_MENU_UPDATE ( MDI_FIND , c ? c->allow_find : false ) ;
-}
-
-/** \brief Generates a basic tooblar
- */
-void MyFrame::setDummyToolbar ( ChildBase *c )
-{
-    wxToolBar *toolBar = c->CreateToolBar(wxNO_BORDER | wxTB_FLAT | wxTB_HORIZONTAL |wxTB_DOCKABLE);
-    toolBar->Reparent ( c ) ;
-    c->toolbar = toolBar ;
-    myapp()->frame->InitToolBar(toolBar);
-	addTool ( toolBar , MDI_TEXT_IMPORT ) ;
-	addTool ( toolBar , MDI_FILE_OPEN ) ;
-    c->toolbar = toolBar ;
-}
-
-/** \brief Creates a new alignment window
- */
-TAlignment *MyFrame::runAlignment ( wxArrayString &vs , wxArrayChildBase &vc , TVector *nv )
-{
-	//    Thaw () ;
-    TAlignment *subframe = new TAlignment ( getCommonParent() , _T("Alignment") ) ;
-    setChild ( subframe ) ;
-    
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-    if ( locked == 0 ) subframe->Activate () ;
-	
-    if ( nv )
-	{
-        subframe->fromVector ( nv ) ;
-	}
-    else if ( vs.GetCount() == 0 )
-	{
-        wxCommandEvent ev ;
-        subframe->OnSettings ( ev ) ;
-	}
-    else
-	{
-        subframe->prealigned ( vs , vc ) ;
-	}
-	
-    if ( locked == 0 ) subframe->Show() ;
-    
-    mainTree->addChild ( subframe , TYPE_ALIGNMENT ) ;
-    mainTree->Refresh () ;
-    activateChild ( children.GetCount()-1 ) ;
-    return subframe ;
-}
-
-/** \brief Handles the Alignment menu event, calls MyFrame::runAlignment
- */
-void MyFrame::OnAlignment(wxCommandEvent& event)
-{
-    wxArrayString vs ; // Dummy
-    wxArrayChildBase vc ; // Dummy
-    runAlignment ( vs , vc ) ;
-}
-
-/** \brief Handles the Manage Database menu event
- */
-void MyFrame::OnManageDatabase(wxCommandEvent& event)
-{
-    TManageDatabaseDialog mdd ( this , txt("m_manage_dbtxt") ) ;
-	mdd.ShowModal () ;
-}
-
-/** \brief Handles the Program Options menu event, and stores the options in the local database
- */
-void MyFrame::OnProgramOptions(wxCommandEvent& event)
-{
-    ProgramOptionsDialog pod ( this , txt("t_program_options" ) ) ;
-    global_enzyme_rules->setup_options ( pod.globalEnzymesPanel ) ;
-    int r = pod.ShowModal() ;
-    if ( r != wxID_OK ) return ;
-	
-   	wxBeginBusyCursor() ;
-	
-	bool useTwoToolbarsBefore = useTwoToolbars ;
-	
-    // retrieving options
-	//    TEnzymeRules oo == *global_enzyme_rules ;
-    global_enzyme_rules->lookup_options ( pod.globalEnzymesPanel ) ;
-    enhancedRefresh = pod.enhancedDisplay->GetValue() ;
-    showVectorTitle = pod.vectorTitle->GetValue() ;
-    showVectorLength = pod.vectorLength->GetValue() ;
-    loadLastProject = pod.loadLastProject->GetValue() ;
-    useMetafile = pod.useMetafile->GetValue() ;
-    showSplashScreen = pod.showSplashScreen->GetValue() ;
-    checkUpdate = pod.checkUpdate->GetValue() ;
-    useInternalHelp = pod.useInternalHelp->GetValue() ;
-    useOnlineHelp = pod.useOnlineHelp->GetValue() ;
-    doRegisterStuff = pod.doRegisterStuff->GetValue() ;
-    editFeatureMode = pod.editFeatureMode->GetSelection() ;
-    showStopCodon = pod.showStopCodon->GetSelection() ;    
-    showEnzymePos = pod.showEnzymePos->GetValue() ;
-	useTwoToolbars = pod.useTwoToolbars->GetValue() ;
-	showToolTips =  pod.showToolTips->GetValue() ;
-	showLowercaseDNA = pod.showLowercaseDNA->GetValue() ;
-	
-	long l ;
-	pod.orfLength->GetValue().ToLong ( &l ) ;
-	if ( l < 10 ) l = 10 ;
-	orfLength = l ;
-	
-	proxy = pod.proxyName->GetValue() + _T(":") + pod.proxyPort->GetValue() ;
-	if ( proxy == _T(":") ) proxy = _T("") ;
-	wxURL::SetDefaultProxy ( proxy ) ;
-	
-	wxToolTip::Enable ( showToolTips ) ;
-    if ( pod.use_nonstandard_translation_table->GetValue() )
-    	nonstandard_translation_table = pod.translation_tables[pod.nonstandard_translation_table->GetSelection()] ;
-    else nonstandard_translation_table = -1 ;
-    aa_color = pod.aacol ;
-    stopcodon = showStopCodon == 0 ? '|' : '*' ;
-    wxString lang = pod.language->GetStringSelection() ;
-    if ( lang != lang_string || useTwoToolbars != useTwoToolbarsBefore )
-	{
-        wxMessageDialog md ( this , txt("t_effect_after_restart" ) ) ;
-        md.ShowModal () ;
-	}
-    
-    // Storing options
-    LS->startRecord() ;
-    LS->setOption ( _T("USEMETAFILE") , useMetafile ) ;
-    LS->setOption ( _T("ENHANCEDREFRESH") , enhancedRefresh ) ;
-    LS->setOption ( _T("LANGUAGE") , lang ) ;
-    LS->setOption ( _T("SHOWVECTORTITLE") , showVectorTitle ) ;
-    LS->setOption ( _T("SHOWVECTORLENGTH") , showVectorLength ) ;
-    LS->setOption ( _T("LOADLASTPROJECT") , loadLastProject ) ;
-    LS->setOption ( _T("SHOWSPLASHSCREEN") , showSplashScreen ) ;
-    LS->setOption ( _T("CHECKUPDATE") , checkUpdate ) ;
-    LS->setOption ( _T("USEINTERNALHELP") , useInternalHelp ) ;
-    LS->setOption ( _T("USEONLINEHELP") , useOnlineHelp ) ;
-    LS->setOption ( _T("REGISTERSTUFF") , doRegisterStuff ) ;
-    LS->setOption ( _T("EDITFEATUREMODE") , editFeatureMode ) ;
-    LS->setOption ( _T("SHOWSTOPCODON") , showStopCodon ) ;
-    LS->setOption ( _T("SHOWENZYMEPOS") , showEnzymePos ) ;
-    LS->setOption ( _T("AA_RED") , aa_color.Red() ) ;
-    LS->setOption ( _T("AA_GREEN") , aa_color.Green() ) ;
-    LS->setOption ( _T("AA_BLUE") , aa_color.Blue() ) ;
-    LS->setOption ( _T("nonstandard_translation_table") , nonstandard_translation_table ) ;
-	LS->setOption ( _T("use_two_toolbars") , useTwoToolbars ) ;
-    LS->setOption ( _T("SHOWTIP") , pod.showTips->GetValue() ) ;
-    LS->setOption ( _T("SHOWTOOLTIPS") , pod.showToolTips->GetValue() ) ;
-    LS->setOption ( _T("SHOWLOWERCASEDNA") , showLowercaseDNA ) ;
-	LS->setOption ( _T("ORFLENGTH") , orfLength ) ;
-    LS->setOption ( _T("PROXY") , proxy ) ;
-    global_enzyme_rules->save_global_settings() ; //!!!!!!! fix this!
-    LS->endRecord() ;
-    for ( int a = 0 ; a < children.GetCount() ; a++ )
-	{
-	    if ( !children[a]->vec ) continue ;
-	    children[a]->vec->recalculateCuts() ;
-		//	    children[a]->vec->updateDisplay() ;
-		children[a]->EnforceRefesh () ;
-	}    
-	//   	if ( GetActiveChild() ) GetActiveChild()->EnforceRefesh () ;
-   	wxEndBusyCursor() ;
-}
-
-/** \brief Handles the Load Project menu event
- */
-void MyFrame::OnProjectLoad(wxCommandEvent& event)
-{
-    // Are all objects stored in a database?
-    int a ;
-    wxString notindb ;
-    for ( a = 0 ; a < children.GetCount() ; a++ )
-	{
-        if ( children[a]->def == _T("dna") )
-		{
-			MyChild *c = (MyChild*) children[a] ;
-			if ( c->vec->getDatabase().IsEmpty() )
-				notindb += _T("\n") + c->getName() ;
-		}
-	}
-    if ( !notindb.IsEmpty() )
-	{
-        notindb = txt("t_following_not_in_db_open") + 
-		notindb + txt("t_following_end_open") ;
-        wxMessageDialog md ( this , notindb ,
-							txt("msg_box") , wxICON_EXCLAMATION|wxYES|wxNO ) ;
-        if ( md.ShowModal() != wxID_YES ) return ;
-	}
-	
-    // All are stored, or loading anyway
-    TManageDatabaseDialog mdd ( this , txt("m_project_opentxt") ,
-							   ACTION_MODE_LOAD|ACTION_MODE_PROJECT ) ;
-    mdd.ShowModal () ;
-}
-
-/** \brief Handles the Save Project menu event
- */
-void MyFrame::OnProjectSave(wxCommandEvent& event)
-{
-    // Are all objects stored in a database?
-    int a ;
-    wxString notindb ;
-    for ( a = 0 ; a < children.GetCount() ; a++ )
-	{
-        if ( children[a]->def == _T("dna") )
-		{
-			MyChild *c = (MyChild*) children[a] ;
-			if ( c->vec->getDatabase().IsEmpty() )
-				notindb += _T("\n") + c->getName() ;
-		}
-	}
-    if ( !notindb.IsEmpty() )
-	{
-        notindb = txt("t_following_not_in_db") + notindb + txt("t_following_end") ;
-        wxMessageDialog md ( this , notindb ,
-							txt("msg_box") , wxICON_EXCLAMATION|wxYES|wxNO ) ;
-        if ( md.ShowModal() != wxID_YES ) return ;
-	}
-	
-    // All are stored, or saving anyway
-    TManageDatabaseDialog mdd ( this , txt("m_project_savetxt") ,
-							   ACTION_MODE_SAVE|ACTION_MODE_PROJECT ) ;
-    mdd.ShowModal () ;
-}
-
-/** \brief Handles the Close Project menu event
- */
-void MyFrame::OnProjectClose(wxCommandEvent& event)
-{
-    int a ;
-    if ( tb_mychild )
-	{
-    	tb_mychild->Close ( TRUE ) ;
-    	delete tb_mychild ;
-    	tb_mychild = NULL ;
-	}   	
-    lastChild = NULL ;
-    for ( a = 0 ; a < children.GetCount() ; a++ )
-	{
-		//        children[a]->Close() ;
-        delete children[a] ;
-	}
-    children.Clear() ;
-    project.name = txt("project") ;
-    project.desc = _T("") ;
-    project.db = _T("") ;
-    mainTree->initme() ;
-    Refresh () ;
-}
-
-/** \brief Stores the last open project for reopening on program start
- */
-void MyFrame::rememberLastProject ()
-{
-    wxString sql ;
-	
-    sql = _T("DELETE FROM stuff WHERE s_type='LASTPROJECT'") ;
-    LS->getObject ( sql ) ;
-	LS->getObject ( wxString::Format ( _T("INSERT INTO stuff (s_type,s_name,s_value) VALUES ('LASTPROJECT','NAME','%s')") , project.name.c_str() ) ) ;
-	LS->getObject ( wxString::Format ( _T("INSERT INTO stuff (s_type,s_name,s_value) VALUES ('LASTPROJECT','DATABASE','%s')") , project.db.c_str() ) ) ;
-}
-
-/** \brief Creates a new amino acid entry from a string
- */
-TAminoAcids *MyFrame::newAminoAcids ( wxString aa , wxString title )
-{
-    TVector nv ;
-    nv.setSequence ( aa ) ;
-    return newAminoAcids ( &nv , title ) ;
-}
-
-/** \brief Creates a new amino acid entry from a TVector structure
- 
- This function basically does the same as MyFrame::newFromVector,
- but for amino acid sequences instead of DNA
- */
-TAminoAcids *MyFrame::newAminoAcids ( TVector *nv , wxString title )
-{
-    int a ;
-    if ( title.IsEmpty() ) title = _T("Surprise!") ;
-	
-    mylog ( "MyFrame::newAminoAcids" , "1" ) ;    
-    TAminoAcids *subframe = new TAminoAcids ( (wxWindow*) getCommonParent() , title ) ;
-    setChild ( subframe ) ;
-	
-    mylog ( "MyFrame::newAminoAcids" , "2" ) ;    
-    subframe->vec->setFromVector ( *nv ) ;
-    
-    mylog ( "MyFrame::newAminoAcids" , "3" ) ;    
-    wxString seq = subframe->vec->getSequence() ;
-    seq.Replace ( _T("|") , _T("") , true ) ;
-    subframe->vec->setSequence ( seq ) ;
-    
-    mylog ( "MyFrame::newAminoAcids" , "4" ) ;    
-    subframe->vec->setWindow ( subframe ) ;
-    subframe->vec->setType ( TYPE_AMINO_ACIDS ) ;
-    subframe->vec->setName ( title ) ;
-    subframe->vec->undo.clear() ;
-	
-    mylog ( "MyFrame::newAminoAcids" , "5" ) ;    
-    for ( a = 0 ; a < nv->items.size() ; a++ )
-	{
-        nv->items[a].setType ( VIT_MISC ) ;
-        nv->items[a].setDirection ( 1 ) ;
-	}
-    
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    mylog ( "MyFrame::newAminoAcids" , "6" ) ;    
-    mainTree->addChild ( subframe , TYPE_AMINO_ACIDS ) ; 
-    mylog ( "MyFrame::newAminoAcids" , "6a" ) ;    
-    subframe->initme () ;
-    mylog ( "MyFrame::newAminoAcids" , "7" ) ;    
-    if ( locked != 0 ) return subframe ;
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-    subframe->Activate () ;
-    children.Last()->Activate () ;
-    mylog ( "MyFrame::newAminoAcids" , "8" ) ;    
-    return subframe ;
-}
-
-/** \brief Creates a new sequencing entry from an ABI file
- */
-TABIviewer *MyFrame::newABI ( wxString filename , wxString title )
-{
-    if ( title.IsEmpty() ) title = _T("Surprise!") ;
-    TABIviewer *subframe = new TABIviewer ( getCommonParent() , title ) ;
-    subframe->filename = filename ;
-    subframe->vec->setType ( TYPE_SEQUENCE ) ;
-    subframe->vec->addDescription ( _T("\n") + wxGetUserName() ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-	
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-    
-    setChild ( subframe ) ;
-    mainTree->addChild ( subframe , TYPE_SEQUENCE ) ;
-	
-    if ( LS->getOption ( _T("SHOWABIHORIZONTAL") , false ) )
-	{
-        subframe->sc->SilentRefresh () ;
-        wxCheckBox *horiz = (wxCheckBox*) subframe->FindWindowById ( ALIGN_HORIZ ) ;
-        myass ( horiz , _T("NULL") ) ;
-        if ( horiz ) horiz->SetValue ( true ) ;
-        wxCommandEvent event ;
-        subframe->OnHorizontal(event) ;
-	}    
-	
-    if ( myapp()->clp[_T("view-sequencing-reverse-complement")] == _T("1") )
-	{
-		subframe->toggle_inv_compl () ;
-		myapp()->clp.erase(_T("view-sequencing-reverse-complement")) ;
-	}
-	
-    subframe->Activate () ;
-    children.Last()->Activate () ;
-	
-    return subframe ;
-}
-
-/** \brief Runs a blast search by invoking MyFrame::OnExternalInterface
- */
-void MyFrame::blast ( wxString seq , wxString prg )
-{
-	int a ;
-	for ( a = 0 ; a < children.GetCount() && children[a]->getName() != _T("External Interface") ; a++ ) ;
-	if ( a == children.GetCount() ) // Create new external interface
-	{
-	    wxCommandEvent event ;
-	    OnExternalInterface ( event ) ;
-	}
-	activateChild ( a ) ;
-	ExternalInterface *ei = (ExternalInterface*) children[a] ;
-	ei->runBlast ( seq , prg ) ;
-	return ;
-	
-	/*
-	 // Obsolete
-	 #ifdef __WXMSW__
-	 wxString unique = wxNow() ;
-	 unique.Replace ( ":" , "_" ) ;
-	 unique.Replace ( "/" , "_" ) ;
-	 unique.Replace ( " " , "_" ) ;
-	 
-	 wxString hd = myapp()->homedir ;
-	 wxString exe = hd + "\\blastcl3.exe" ; // WINDOWS-SPECIFIC!
-	 wxString ifile = hd + "\\blasts\\temp_" + unique + ".tmp" ;
-	 wxString ofile = hd + "\\blasts\\blast_results_" + unique + ".html" ;
-	 wxString bfile = hd + "\\blasts\\batch_" + unique + ".bat" ;
-	 
-	 wxString blast_dir = hd + "\\blasts" ;
-	 if ( !wxDir::Exists ( blast_dir ) )
-	 wxMkdir ( blast_dir ) ;
-	 
-	 // Writing temporary blast file
-	 wxFile out ( ifile , wxFile::write ) ;
-	 out.Write ( seq ) ;
-	 out.Close () ;
-	 
-	 wxFile batch ( bfile , wxFile::write ) ;
-	 batch.Write ( "@echo off\n" ) ;
-	 
-	 // Creating blast command line
-	 exe += " -p \"" + prg + "\"" ;
-	 exe += " -i \"" + ifile + "\"" ;
-	 exe += " -o \"" + ofile + "\"" ;
-	 exe += " -Tt" ; // Create HTML
-	 batch.Write ( exe + "\n" ) ;
-	 
-	 // Starting browser
-	 exe = "start " ;
-	 exe += myapp()->getHTMLCommand ( ofile ) ;
-	 batch.Write ( exe + "\n" ) ;
-	 
-	 // Delete temporary files
-	 batch.Write ( "del \"" + ifile + "\"\n" ) ;
-	 batch.Write ( "del \"" + bfile + "\"\n" ) ;
-	 
-	 // Run it
-	 batch.Close() ;
-	 wxExecute ( bfile ) ;
-	 #endif
-	 */
-}
-
-/** \brief Creates a new external interface for NCBI/BLAST searching
- */
-void MyFrame::OnExternalInterface(wxCommandEvent& event)
-{
-    ExternalInterface *subframe = new ExternalInterface ( getCommonParent() , txt("t_external_interface") ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-	
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-    
-    mainTree->addChild ( subframe , TYPE_MISC ) ;
-    setChild ( subframe ) ;
-    activateChild ( children.GetCount()-1 ) ;
-}
-
-/** \brief Invokes the image viewer module
- */
-void MyFrame::OnImageViewer(wxCommandEvent& event)
-{
-    TImageDisplay *subframe = new TImageDisplay ( getCommonParent() , txt("t_image_viewer") ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-	
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-    
-    mainTree->addChild ( subframe , TYPE_MISC ) ;
-    setChild ( subframe ) ;
-    activateChild ( children.GetCount()-1 ) ;
-}
-
-/** \brief Handles the Calculator menu event by calling MyFrame::RunCalculator
- */
-void MyFrame::OnCalculator(wxCommandEvent& event)
-{
-    RunCalculator () ;
-}    
-
-/** \brief Handles the Dot plot menu event
- */
-void MyFrame::OnDotPlot(wxCommandEvent& event)
-{
-    TDotPlot *subframe = new TDotPlot ( getCommonParent() , txt("t_dotplot") ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-	
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-	
-    mainTree->addChild ( subframe , TYPE_MISC ) ;
-    setChild ( subframe ) ;
-    activateChild ( children.GetCount()-1 ) ;
-	
-	//    return subframe ;
-}
-
-
-
-/** \brief Handles the Graph menu event by calling MyFrame::RunGraph
- */
-void MyFrame::OnGraph(wxCommandEvent& event)
-{
-	wxString seq = _T("MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLIEGRGIPGNSS") ; // GST
-	//	char *s2 = new char[seq.length()+5] ;
-	//	strcpy ( s2 , seq.mb_str() ) ;
-	
-	wxString ret ;
-	wxArrayFloat af[3] ;
-	for ( int a = 0 ; a < 3 ; a++ )
-	{
- 		int b = a==0?14:(a==1?21:28) ;
-		string s = ncoils_function ( seq.mb_str() , b ) ;
-		wxString t ( s.c_str() , wxConvUTF8 ) ;
-		wxArrayString ta ;
-		explode ( _T("\n") , t , ta ) ;
-		for ( b = 0 ; b < seq.length() ; b++ )
-		{
-  			if ( b >= ta.GetCount() ) break ;
-  			t = ta[b].Mid ( 18 ) ;
-  			double prob ;
-  			t.ToDouble ( &prob ) ;
-  			af[a].Add ( (float) prob ) ;
-  			ret += wxString::Format ( _T("%1.4f, ") , (float) prob ) ;
-		}
-        ret += _T("\n") ;
-	}	
-	wxMessageBox ( ret ) ;
-	
-	/*    TGraph *g = RunGraph() ;
-	 g->gd->SetupDummy() ;
-	 g->gd->AutoScale () ;
-	 g->gd->UpdateDisplay () ;*/
-}    
-
-/** \brief Invokes the calculator module
- */
-TCalculator *MyFrame::RunCalculator ()
-{
-    TCalculator *subframe = new TCalculator ( getCommonParent() , txt("t_calculator") ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-	
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-    
-    mainTree->addChild ( subframe , TYPE_MISC ) ;
-    setChild ( subframe ) ;
-    activateChild ( children.GetCount()-1 ) ;
-    return subframe ;
-}
-
-/** \brief Invokes the graph module
- */
-TGraph *MyFrame::RunGraph ()
-{
-    TGraph *subframe = new TGraph ( getCommonParent() , txt("t_graph") ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme () ;
-	
-    subframe->Show() ;
-    subframe->Maximize() ;
-    subframe->showName() ;
-    
-    mainTree->addChild ( subframe , TYPE_MISC ) ;
-    setChild ( subframe ) ;
-    activateChild ( children.GetCount()-1 ) ;
-    return subframe ;
-}
-
-/** \brief Returns the standard File menu, with variations
- \param _save Include "Save" menu option
- \param _exp Include "Export" menu option
- \param _print Include "Print" menu option
- */
-wxMenu *MyFrame::getFileMenu ( int options )
-{
-    wxMenu *file_menu = new wxMenu;
-    file_menu->Append(MDI_FILE_OPEN, txt("m_open") , txt("m_opentxt") );
-    if ( 0 < ( options & FILE_MENU_SAVE )  ) file_menu->Append(MDI_FILE_SAVE, txt("m_store_in_db") , txt("m_txt_store_in_db") ) ;
-    file_menu->Append(MDI_FILE_SAVE_ALL, txt("m_store_in_db_all") ) ;
-    file_menu->Append(MDI_FILE_IMPORT, txt("m_import") , txt("m_importtxt") );
-    file_menu->Append(MDI_TEXT_IMPORT, txt("m_text_import") , txt("m_text_importtxt") );
-    if ( 0 < ( options & FILE_MENU_EXPORT ) ) file_menu->Append(MDI_EXPORT, txt("m_export") , txt("m_export_txt") );
-    file_menu->AppendSeparator();
-    file_menu->Append(MDI_PROJECT_LOAD, txt("m_project_open") , txt("m_project_opentxt") );    
-    file_menu->Append(MDI_PROJECT_SAVE, txt("m_project_save") , txt("m_project_savetxt") );    
-    file_menu->Append(MDI_PROJECT_CLOSE, txt("m_project_close") , txt("m_project_closetxt") );    
-    file_menu->AppendSeparator();
-    if ( 0 < ( options & FILE_MENU_PRINT ) ) file_menu->Append(MDI_PRINT_IMAGE, txt("m_print_image") , txt("m_print_image_txt") );
-    if ( 0 < ( options & FILE_MENU_PRINT_RESTRICTIONS ) ) file_menu->Append(MDI_PRINT_RESTRICTION_LIST, txt("m_print_restrictions") , txt("m_print_restrictions_txt") );
-    file_menu->Append(SEQ_PRINT, txt("m_print_sequence") ) ;
-    file_menu->Append(MDI_PRINT_REPORT, txt("m_print_report") , txt("m_print_report_txt") );
-    file_menu->AppendSeparator();
-    file_menu->Append(MDI_QUIT, txt("m_exit") , txt("m_exittxt") ) ;
-    return file_menu ;    
-}
-
-/** \brief Returns the standard Tools menu, with variations
- \param _pcr Include PCR menu option
- */
-wxMenu *MyFrame::getToolMenu ( bool _pcr )
-{
-    wxMenu *tool_menu = new wxMenu;
-    tool_menu->Append(MDI_ENZYME_EDITOR, txt("m_enzyme") ) ;
-    tool_menu->Append(MDI_ALIGNMENT, txt("m_alignment") , txt("m_alignmenttxt") ) ;
-    tool_menu->Append(MDI_RESTRICTION, txt("m_enzymeeditor") , txt("m_enzymeeditortxt") ) ;
-    tool_menu->Append(MDI_LIGATION, txt("m_ligation") );
-    if ( _pcr ) tool_menu->Append(MDI_RUN_PCR, txt("m_pcr") );
-    tool_menu->Append(MDI_MANAGE_DATABASE, txt("m_manage_db") , txt("m_manage_dbtxt") ) ;
-    tool_menu->Append(MDI_IMAGE_VIEWER, txt("m_image_viewer") , txt("m_image_viewer_txt") ) ;
-    tool_menu->Append(MDI_EXTERNAL_INTERFACE, txt("m_external_interface") ) ;
-    tool_menu->Append(MDI_CALCULATOR, txt("m_calculator") , txt("m_calculator_txt") ) ;
-    tool_menu->Append(MDI_SEQUENCING_ASSISTANT, txt("m_sequencing_assistant") ) ;
-    tool_menu->Append(MDI_DOTPLOT, txt("m_dotplot") ) ;
-    tool_menu->Append(MDI_RESTRICTION_IDENTIFIER, txt("m_restriction_identifier") ) ;
-	//    tool_menu->Append(MDI_GRAPH, txt("m_graph") , txt("m_graph_txt") ) ; // TESTING, Deactivated in release
-	//	tool_menu->Append(MDI_CLONING_ASSISTANT, txt("m_cloning_assistant") ) ; // Deactivated in release
-    tool_menu->Append(PROGRAM_OPTIONS, txt("m_options") , txt("m_options_txt") ) ;
-    return tool_menu ;
-}
-
-/** \brief Returns the standard Help menu
- */
-wxMenu *MyFrame::getHelpMenu ()
-{
-    wxMenu *help_menu = new wxMenu;
-    help_menu->Append(MDI_HELP, txt("m_help_content") ) ;
-    help_menu->Append(MDI_ABOUT, txt("m_about") );
-    help_menu->Append(MDI_HOMEPAGE, txt("m_homepage") );
-    return help_menu ;
-}
-
-/** \brief Adds a child, if it is not already in the children list
- \param ch Pointer to child
- */
-void MyFrame::setChild ( ChildBase *ch )
-{
-    int a ;
-    for ( a = 0 ; a < children.GetCount() && children[a] != ch ; a++ ) ;
-    if ( a == children.GetCount() )
-	{
-        children.Add ( ch ) ;
-        update_child_list = true ;
-	}
-}
-
-/** \brief Safely removes a child from the children list
- \param ch Pointer to child
- */
-void MyFrame::removeChild ( ChildBase *ch )
-{
-    unsigned int a ;
-    for ( a = 0 ; a < children.GetCount() && children[a] != ch ; a++ ) ;
-    if ( a == children.GetCount() ) return ;
-    children[a]->Disable () ;
-    children[a]->Hide() ;
-	//    children[a] = children[children.GetCount()-1] ;
-	//    children.pop_back () ;
-    children.RemoveAt ( a ) ;
-    lastChild = NULL ;
-    activateChild ( 0 ) ;
-    
-    if ( children.size() == 0 )
-	{
-		while ( count_help () > 1 ) pop_help() ;
-		ChildBase c ;
-		updateCCP ( &c ) ;
-	}
-    notifyChildrenChanged() ;
-}
-
-/** \brief Activates a child (brings to front, makes visible, etc.)
- \param a Number of child in children list
- */
-void MyFrame::activateChild ( int a )
-{
-    if ( a >= children.GetCount() ) a = 0 ;
-    if ( children.GetCount() )
-	{
-		children[a]->Activate () ;
-		mainTree->EnsureVisible ( children[a]->inMainTree ) ;
-		mainTree->SelectItem ( children[a]->inMainTree ) ;
-	}
-    else setActiveChild ( NULL ) ;
-    wxSafeYield () ;
-}
-
-/** \brief Locks/unlocks display, counts (un)lock requests
- \param lock Lock if true, unlock if not
- */
-void MyFrame::lockDisplay ( bool lock )
-{
-    if ( lock )
-	{
-        if ( locked == 0 ) { mainTree->Freeze() ; Freeze() ; }
-        locked++ ;
-	}
-    else
-	{
-        locked-- ;
-        if ( locked == 0 )
-		{
-			mainTree->Thaw() ;
-			Thaw() ;
-			if ( !children.IsEmpty() )
-			{
-				if ( GetActiveChild() ) GetActiveChild()->Activate() ;
-				else children.Last()->Activate () ;
-			}
-		}    
-	}        
-}    
-
-/** \brief Is display locked?
- */
-bool MyFrame::isLocked ()
-{
-    return ( locked != 0 ) ;
-}    
-
-/** \brief Is a child activation sequence running?
- */
-bool MyFrame::isActivating ()
-{
-    return activating ;
-}    
-
-/** \brief Is a new version available online?
- 
- This function is currently a mess, due to bugs in wxWidgets,
- but it basically works...
- */
-wxString MyFrame::check4update ()
-{
-    wxString text , file ;
-	myExternal ex ;
-	
-#ifdef __WXMSW__
-	file = _T("currentversion.txt") ;
-#endif
-	
-#ifdef __WXMAC__
-	file = _T("mac_currentversion.txt") ;
-#endif
-	
-	text = check4update_sub ( ex.getText ( _T("http://gentle.magnusmanske.de/") + file ) ) ;
-//	if ( text.IsEmpty() ) // Fallback
-//		text = check4update_sub ( ex.getText ( _T("http://www.uni-koeln.de/math-nat-fak/biochemie/klein/gentle/") + file ) ) ;
-	
-	if ( text == _T("-") ) text = _T("") ;
-    return text ;
-}
-
-wxString MyFrame::check4update_sub ( wxString text )
-{
-    bool error = true ;    
-	if ( !text.IsEmpty() ) error = false ;
-	
-    if ( !error )
-	{
-	    wxString it = text ;
-	    wxString td = text ;
-        td = td.BeforeFirst ( '\n' ) ;
-        td = td.BeforeFirst ( '\r' ) ;
-        
-        wxString lu = LS->getOption ( _T("LAST_UPDATE") , _T("") ) ;
-        if ( lu.IsEmpty() ) // Assuming new installation of the latest version, so no update
-		{
-			lu = td ;
-			LS->setOption ( _T("LAST_UPDATE") , lu ) ;
-		}
-		
-        if ( td > lu )
-		{
-			wxString msg = it.AfterFirst ( '\n' ) ;
-			msg += _T("\n(") + wxString ( txt("t_you_use_version") ) + myapp()->get_GENtle_version() + _T(")") ;
-			wxMessageDialog md ( this , msg , txt("t_new_version" ) ,
-								wxOK | wxCANCEL | wxCENTRE | wxICON_INFORMATION ) ;
-			if ( wxID_OK != md.ShowModal() )
-				return _T("-") ;
-			
-			return td ;
-		}
-	}
-    else
-	{
-        // Cannot connect to check for update
-        // SetStatusText ( txt("t_update_warning") , 1 ) ;
-        // wxMessageBox ( _T("Error") , text ) ;
-	}    
-    return _T("") ;
-}
-
-/** \brief Download the new version of GENtle
- \param ver New version
- */
-void MyFrame::update2version ( wxString ver )
-{
-    wxString do_run ;
-    wxProgressDialog pd ( _T("Updating...") , _T("Downloading installer...") , 2 , NULL , 0 ) ;
-    myExternal ex ;
-    ex.pd = &pd ;
-	
-	wxString sourcefile , sourcefile2 , localfile ;
-	
-#ifdef __WXMSW__
-    localfile = myapp()->homedir + _T("\\GENtleSetup.exe") ;
-	sourcefile = _T("http://gentle.magnusmanske.de/GENtleSetup.exe") ;
-	sourcefile2 = _T("http://www.uni-koeln.de/math-nat-fak/biochemie/klein/gentle/GENtleSetup.exe") ; // Fallback
-#endif
-	
-#ifdef __WXMAC__
-	localfile = wxString(wxGetUserHome()) + _T("/Desktop/GENtle.pkg.zip") ;
-	sourcefile = _T("http://gentle.magnusmanske.de/GENtle.pkg.zip") ;
-	sourcefile2 = _T("http://www.uni-koeln.de/math-nat-fak/biochemie/klein/gentle/GENtle.pkg.zip") ; // Fallback
-#endif
-	
-    if ( ex.copyFile ( sourcefile , localfile ) > 0 )
-	{
-        if ( ex.copyFile ( sourcefile2 , localfile ) > 0 )
-		{
-            wxMessageBox ( _T("Couldn't read setup file") ) ;
-            wxExit() ; // Hard exit
-		}
-	}    
-	
-#ifdef __WXMSW__
-    do_run = _T("\"") + localfile + _T("\" /D=\"") ;
-    do_run += myapp()->homedir ;
-    do_run += _T("\"") ;
-    LS->setOption ( _T("LAST_UPDATE") , ver ) ;
-	dying = true ;
-    if ( 0 == wxExecute ( do_run , wxEXEC_ASYNC ) ) return ; // 0 means the process couldn't start :-(
-    wxExit() ; // Hard exit
-#endif
-	
-#ifdef __WXMAC__
-	do_run = _T("unzip -o ") + localfile + _T(" -d ") + wxGetUserHome() + _T("/Desktop") ;
-	wxExecute ( do_run , wxEXEC_SYNC ) ;
-	wxRemoveFile ( localfile ) ;
-	localfile = wxString(wxGetUserHome()) + _T("/Desktop/GENtle_package.pkg") ;
-	do_run = _T("open ") + localfile ;
-    LS->setOption ( _T("LAST_UPDATE") , ver ) ;
-	dying = true ;
-	wxExecute ( do_run , wxEXEC_ASYNC ) ;
-    Destroy() ;
-#endif
-}
-
-/** \brief Handles SashDrag events (sash between the main tree and the current child
- */
-void MyFrame::OnSashDrag(wxSashEvent& event)
-{
-    if (event.GetDragStatus() == wxSASH_STATUS_OUT_OF_RANGE)
-        return;
-	
-    switch (event.GetId())
-    {
-        case FRAME_SASH_TOP:
-        {
-            m_topWindow->SetDefaultSize(wxSize(1000, event.GetDragRect().height));
-            break;
-        }
-        case FRAME_SASH_1:
-        {
-            m_leftWindow1->SetDefaultSize(wxSize(event.GetDragRect().width, 1000));
-            break;
-        }
-        case FRAME_SASH_2:
-        {
-            m_leftWindow2->SetDefaultSize(wxSize(event.GetDragRect().width, 1000));
-            break;
-        }
-        case FRAME_SASH_BOTTOM:
-        {
-            m_bottomWindow->SetDefaultSize(wxSize(1000, event.GetDragRect().height));
-            break;
-        }
-    }
-    wxLayoutAlgorithm layout;
-    layout.LayoutFrame(this);
-	Refresh () ;
-	
-    // Leaves bits of itself behind sometimes
-	//    GetClientWindow()->Refresh();    
-}
-
-/** \brief Creates a temporary database, or uses one from the cache
- \param name Name of the database to use
- */
-TStorage *MyFrame::getTempDB ( wxString name )
-{
-    unsigned int a ;
-    for ( a = 0 ; a < dbcache.GetCount() && dbcache[a]->getDBname() != name ; a++ ) ;
-    if ( a == dbcache.GetCount() ) 
-        dbcache.Add ( new TStorage ( TEMP_STORAGE , name ) ) ;
-    return dbcache[a] ;
-}
-
-/** \brief Sets the active child
- \param c Pointer to the child
- */
-void MyFrame::setActiveChild ( ChildBase *c )
-{
-    lastChild = c ;
-    if ( !IsShown() ) return ;
-    if ( locked != 0 ) return ;
-    if ( activating ) return ;
-    unsigned int a ;
-    for ( a = 0 ; a < children.GetCount() ; a++ )
-	{
-		ChildBase *d = children[a] ;
-		if ( d != c )
-		{
-			if ( d->IsShown() ) d->Hide () ;
-			if ( d->IsEnabled() ) d->Disable () ;
-		}
-	}
-    if ( children.GetCount() == 0 && GetMenuBar() != menu_bar ) SetMenuBar ( menu_bar ) ;
-    if ( !c ) return ;
-    activating = true ;
-	//    wxSafeYield() ;
-    if ( !c->IsEnabled() ) c->Enable() ;
-	if ( c->menubar && GetMenuBar() != c->menubar )
-		c->SetMyMenuBar () ;
-	//SetMenuBar ( c->menubar ) ;
-    wxSize s = c->GetParent()->GetClientSize() ;
-    if ( c->GetSize() != s )
-	{
-		if ( c->vec ) c->vec->updateDisplay() ;
-		c->SetSize ( s ) ;
-	}
-    if ( mainTree && c->inMainTree.IsOk() && mainTree->GetSelection() != c->inMainTree )
-        mainTree->SelectItem ( c->inMainTree ) ;
-    if ( !c->IsShown() ) c->Show() ;
-	//    c->Refresh () ;
-    wxSafeYield () ;
-    activating = false ;
-}
-
-/** \brief Returns the base window for all children
- */
-wxWindow *MyFrame::getCommonParent()
-{
-    return m_leftWindow2 ;
-}
-
-/** \brief Bug-patch function to catch illegal events
- */
-void MyFrame::BollocksMenu(wxCommandEvent& event)
-{
-    if ( !lastChild ) return ;
-    if ( event.GetId() == MDI_NEXT_WINDOW ||
-		event.GetId() == MDI_PREV_WINDOW )
-	{
-		int a = getChildIndex ( lastChild ) ;
-		if ( event.GetId() == MDI_NEXT_WINDOW ) a++ ;
-		else a-- ;
-		if ( a < 0 ) a = children.GetCount()-1 ;
-		if ( a >= children.GetCount() ) a = 0 ;
-		if ( a >= 0 && a <= children.GetCount() )
-		{
-			mainTree->EnsureVisible ( children[a]->inMainTree ) ;
-			mainTree->SelectItem ( children[a]->inMainTree ) ;
-			children[a]->EnforceRefesh () ;
-		}
-		return ;
-	}
-    if ( lastChild->def != _T("dna") ) return ;
-    lastChild->ProcessEvent ( event ) ;
-}
-
-/** \brief Reroutes context menu events to online tools
- */
-void MyFrame::OnlineTools(wxCommandEvent& event)
-{
-    online_tools->take_event ( event ) ;
-}
-
-/** \brief Reroutes menu events from the frame to the active child
- */
-void MyFrame::RerouteMenu(wxCommandEvent& event) 
-{
-    bool b = false ;
-    if ( lastChild ) b = lastChild->ProcessEvent ( event ) ;
-	//    if ( !b ) ProcessEvent ( event ) ;
-}
-
-/** \brief Gets the number of a child in the children list
- \param c Pointer to child
- */
-int MyFrame::getChildIndex ( ChildBase *c )
-{
-    int a ;
-    for ( a = 0 ; a < children.GetCount() && children[a] != c ; a++ ) ;
-    return a ;
-}
-
-
-/** \brief Closes MDI child via (Crtl-F4)
- */
-void MyFrame::OnMDIClose(wxCommandEvent& event)
-{
-    if ( lastChild ) lastChild->Close ( TRUE ) ;
-}
-
-/** \brief Creates/reuses a virtual gel
- */
-TVirtualGel *MyFrame::useGel ( wxString type )
-{
-	int a ;
-	TVirtualGel *gel ;
-	for ( a = 0 ; a < children.GetCount() ; a++ )
-	{
- 		if ( children[a]->def != _T("GEL") ) continue ;
- 		gel = (TVirtualGel*) children[a] ;
- 		if ( gel->type == type ) return gel ;
-	}    
-	
-	gel = new TVirtualGel ( getCommonParent() , _T("GEL ") + type ) ;
-	gel->type = type ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    gel->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    gel->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    gel->initme () ;
-	
-    gel->Show() ;
-    gel->Maximize() ;
-    gel->showName() ;
-    
-    mainTree->addChild ( gel , TYPE_MISC ) ;
-    setChild ( gel ) ;
-    activateChild ( children.GetCount()-1 ) ;
-	return gel ;
-}    
-
-/** \brief Handles the menu request for running the test suite
- */
-void MyFrame::TestMenu(wxCommandEvent& event)
-{
-#ifdef MYTEST
-    if ( test_suite == NULL ) test_suite = new TTestSuite ;
-    test_suite->Step () ;
-    wxCommandEvent ev ( wxEVT_COMMAND_MENU_SELECTED , Y___ ) ;
-    wxPostEvent ( this , ev ) ;
-#endif
-}
-
-
-void MyFrame::push_help ( wxString name )
-{
-	help_name.push_back ( name ) ;
-}
-
-void MyFrame::pop_help ()
-{
-	if ( help_name.size() == 0 ) return ;
-	help_name.pop_back() ;
-}
-
-wxString MyFrame::get_help ()
-{
-	if ( help_name.size() == 0 ) return _T("") ;
-	return help_name[help_name.size()-1] ;
-}
-
-void MyFrame::OnSequencingAssistant(wxCommandEvent& event)
-{
-    TSequencingAssistantDialog sa ( getCommonParent(), txt("t_sequencing_assistant") );
-    if ( wxID_OK != sa.ShowModal() ) return ; // Cancel
-    
-    int sel_seq = sa.sequence->GetSelection() ;
-    int sel_abi1 = sa.abi1->GetSelection() ;
-    int sel_abi2 = sa.abi2->GetSelection() ;
-	
-    if ( sel_seq == wxNOT_FOUND || sel_seq == 0 ) return ; // No sequence selected
-    if ( sel_abi1 <= 0 && sel_abi2 <= 0 ) return ; // No ABI selected
-    sa.fix_rev_compl () ;
-    
-    // Alignment call
-    wxArrayString vs ;
-    wxArrayChildBase vc ;
-    ChildBase *seq = sa.dna[sel_seq] ;
-    ChildBase *abi1 = sel_abi1 <= 0 ? NULL : sa.abi[sa.abi1->GetSelection()] ;
-    ChildBase *abi2 = sel_abi2 <= 0 ? NULL : sa.abi[sa.abi2->GetSelection()] ;
-    
-    // Put 5'->3' first
-    if ( abi1 && abi2 && ((TABIviewer*)abi1)->get_inv_compl() && !((TABIviewer*)abi2)->get_inv_compl() )
-	{
-		ChildBase *abi3 = abi1 ;
-		abi1 = abi2 ;
-		abi2 = abi3 ;
-	}
-    
-    vs.Add ( seq->getName() ) ;
-    vc.Add ( seq ) ;
-    if ( abi1 )
-	{
-	    vs.Add ( abi1->getName() ) ;
-	    vc.Add ( abi1 ) ;
-	}
-    if ( abi2 )
-	{
-	    vs.Add ( abi2->getName() ) ;
-	    vc.Add ( abi2 ) ;
-	}
-    
-    TAlignment *ali = runAlignment ( vs , vc , NULL ) ;
-    ali->algorithm = 1 ;
-    ali->redoAlignments () ;
-}
-
-void MyFrame::OnCloningAssistant(wxCommandEvent& event)
-{
-    TCloningAssistant *subframe = new TCloningAssistant(getCommonParent(), txt("t_cloning_assistant") );
-    myass ( subframe , "MyFrame::OnCloningAssistant" ) ;
-    setChild ( subframe ) ;
-	
-    // Give it an icon
-#ifdef __WXMSW__
-    subframe->SetIcon(wxIcon(_T("chrt_icn")));
-#elif __WXMAC__
-#else
-    subframe->SetIcon(wxIcon( mondrian_xpm ));
-#endif
-	
-    subframe->initme() ;
-    mainTree->addChild(subframe,TYPE_MISC) ;
-    children.Last()->Activate () ;
-	//    subframe->Show ( TRUE ) ;
-	//    subframe->EnforceRefesh () ;
-	//    subframe->Activate () ;
-}
-
-void MyFrame::OnLigation(wxCommandEvent& event)
-{
-    TLigationDialog ld ( this , txt("t_ligation") ) ;
-    long l ;
-    for ( l = 0 ; l < myapp()->frame->children.GetCount() ; l++ )
-	{
-        MyChild *p = (MyChild*) myapp()->frame->children[l] ;
-        if ( p->def == _T("dna") && !p->vec->isCircular() )
-		{
-			ld.vv.Add ( p->vec ) ;
-		}
-	}
-    
-    ld.init () ;
-    ld.ShowModal() ;
-    if ( !ld.doLigate ) return ;
-    for ( l = 0 ; l < ld.ligates.size() ; l++ )
-	{
-        if ( !ld.ligates[l].getSequence().IsEmpty() )
-		{
-			TVector *v = new TVector ;
-			v->setFromVector ( ld.ligates[l] ) ;
-			for ( int a = 0 ; a < v->items.size() ; a++ )
-				v->items[a].r1 = -1 ; // Resetting item radius to "recalc"
-			myapp()->frame->newFromVector ( v ) ;
-		}
-	}
-    myapp()->frame->lastCocktail.Clear () ;
-}
-
-void MyFrame::OnStoreAll(wxCommandEvent& event)
-{
-	TStoreAllDialog dlg ( this , txt("t_store_all_dialog") ) ;
-	dlg.ShowModal() ;
-}
-
-void MyFrame::notifyChildrenChanged()
-{
-    int a ;
-    for ( a = 0 ; a < children.GetCount() ; a++ )
-	{
-        children[a]->otherChildrenChanged() ;
-	}
-}
-
-//******************************************************************* TTestSuite
-
-#ifdef MYTEST
-
-TTestSuite::TTestSuite ()
-{
-    srand ( time(NULL) );
-    cnt = 0 ;
-}    
-
-void TTestSuite::pressKey ( ChildBase *ac )
-{
-	if ( ac->def == _T("dna") ) vectorPressKey ( ac ) ;
-	if ( ac->def == _T("AminoAcids") ) vectorPressKey ( ac ) ;
-	if ( ac->def == _T("PrimerDesign") ) vectorPressKey ( ac ) ;
-}    
-
-void TTestSuite::action ( ChildBase *ac )
-{
-	if ( ac->def == _T("dna") ) vectorAction ( ac ) ;
-	if ( ac->def == _T("AminoAcids") ) aaAction ( ac ) ;
-}
-
-void TTestSuite::editMode ( ChildBase *ac )
-{
-	wxCommandEvent event ;
-    mylog ( "Testsuite:Edit mode" , "" ) ;
-    if ( ac->def == _T("dna") ) ((MyChild*)ac)->OnEditMode(event) ;
-    if ( ac->def == _T("PrimerDesign") ) ((TPrimerDesign*)ac)->OnEditMode(event) ;
-    if ( ac->def == _T("AminoAcids") )
-	{
-        ((TAminoAcids*)ac)->OnEditMode(event) ;
-	}    
-}
-
-void TTestSuite::vectorPressKey ( ChildBase *ac )
-{
-	//    if ( !ac->cSequence ) { mylog ("D'oh!",""); return ;}
-    wxKeyEvent ev ( wxEVT_CHAR_HOOK ) ;
-    ev.m_altDown = false ;
-    ev.m_controlDown = rand() % 2 ;
-    ev.m_metaDown = false ;
-    ev.m_shiftDown = rand() % 2 ;
-    int r = rand () % 40 ;
-    if ( r > 14 ) r = 9 + r % 6 ;
-    wxString msg ;
-    ev.m_keyCode = 'A' ; // Default
-    if ( r == 0 ) { ev.m_keyCode = 'A' ; msg = _T("A") ; }
-    if ( r == 1 ) { ev.m_keyCode = 'C' ; msg = _T("C") ; }
-    if ( r == 2 ) { ev.m_keyCode = 'T' ; msg = _T("G") ; }
-    if ( r == 3 ) { ev.m_keyCode = 'G' ; msg = _T("T") ; }
-    if ( r == 4 ) { ev.m_keyCode = WXK_BACK ; msg = _T("BACK") ; }
-    if ( r == 5 ) { ev.m_keyCode = WXK_DELETE ; msg = _T("DEL") ; }
-    if ( r == 6 ) { ev.m_keyCode = WXK_HOME ; msg = _T("HOME") ; }
-    if ( r == 7 ) { ev.m_keyCode = WXK_END ; msg = _T("END") ; }
-    if ( r == 8 ) { ev.m_keyCode = WXK_INSERT ; msg = _T("INSERT") ; }
-    if ( r == 9 ) { ev.m_keyCode = WXK_RIGHT ; msg = _T("RIGHT") ; }
-    if ( r == 10 ) { ev.m_keyCode = WXK_LEFT ; msg = _T("LEFT") ; }
-    if ( r == 11 ) { ev.m_keyCode = WXK_UP ; msg = _T("UP") ; }
-    if ( r == 12 ) { ev.m_keyCode = WXK_DOWN ; msg = _T("DOWN") ; }
-    if ( r == 13 ) { ev.m_keyCode = WXK_PRIOR ; msg = _T("PRIOR") ; }
-    if ( r == 14 ) { ev.m_keyCode = WXK_NEXT ; msg = _T("NEXT") ; }
-    mylog ( "Testsuite:Key" , wxString::Format ( "%s" , msg.c_str() ) ) ;
-    if ( ac->def == _T("PrimerDesign") ) ((TPrimerDesign*)ac)->sc->OnCharHook(ev) ;
-    else ac->cSequence->OnCharHook(ev) ;
-}
-
-void TTestSuite::vectorAction ( ChildBase *ac )
-{
-    MyChild *c = (MyChild*) ac ;
-    wxCommandEvent ev ;
-    int r = rand() % 24 ;
-    mylog ( "Testsuite:Message" , wxString::Format ( "%d" , r ) ) ;
-    switch ( r )
-	{
-	    case  0 : c->OnAA_none ( ev ) ; break ;
-	    case  1 : c->OnAA_known ( ev ) ; break ;
-	    case  2 : c->OnAA_all ( ev ) ; break ;
-	    case  3 : c->OnAA_three ( ev ) ; break ;
-	    case  4 : c->OnAA_one ( ev ) ; break ;
-	    case  5 : c->OnAA_three_1 ( ev ) ; break ;
-	    case  6 : c->OnAA_three_2 ( ev ) ; break ;
-	    case  7 : c->OnAA_three_3 ( ev ) ; break ;
-	    case  8 : c->OnAA_three_M1 ( ev ) ; break ;
-	    case  9 : c->OnAA_three_M2 ( ev ) ; break ;
-	    case 10 : c->OnAA_three_M3 ( ev ) ; break ;
-	    case 11 : c->OnCircularLinear ( ev ) ; break ;
-	    case 12 : c->OnMarkAll ( ev ) ; break ;
-	    case 13 : c->OnCut ( ev ) ; break ;
-	    case 14 : c->OnCopy ( ev ) ; break ;
-			//     	    case 15 : c->OnPaste ( ev ) ; break ; // Might paste *real* clipboard;-)
-	    case 16 : c->OnCopyToNew ( ev ) ; break ;
-	    case 17 : c->OnViewMode ( ev ) ; break ;
-	    case 18 : c->OnORFs ( ev ) ; break ;
-	    case 19 : c->OnToggleFeatures ( ev ) ; break ;
-	    case 20 : c->OnToggleRestriction ( ev ) ; break ;
-	    case 21 : c->OnToggleIDNA ( ev ) ; break ;
-	    case 22 : c->Undo ( ev ) ; break ;
-	    case 23 : if ( c->cSequence ) c->OnRunPCR ( ev ) ; break ;
-	}    
-}	
-
-void TTestSuite::aaAction ( ChildBase *ac )
-{
-    wxCommandEvent ev ;
-	TAminoAcids *aa = (TAminoAcids*) ac ;
-	
-	int r = rand() % 15 ;
-	if ( r == 0 )
-	{
-		int num = aa->inlinePlot->GetCount() ;
-		num = rand() % num ;
-		mylog ( "TTestSuite::aaAction" , wxString::Format ( "Inline plot to %d" , num ) ) ;
-		aa->inlinePlot->SetSelection ( num ) ;
-		aa->OnIP ( ev ) ;
-	}
-	else if ( r == 1 ) { mylog ( "TTestSuite::aaAction" , "OnHorizontal" ) ; aa->OnHorizontal ( ev ) ; }
-	else if ( r == 2 ) { mylog ( "TTestSuite::aaAction" , "MarkAll" ) ; aa->OnMarkAll ( ev ) ; }
-	else if ( r == 3 ) { mylog ( "TTestSuite::aaAction" , "Cut" ) ; aa->OnCut ( ev ) ; }
-	//	else if ( r == 4 ) aa->OnPhotometer ( ev ) ; // Works, too many boring calculators ;-)
-	else
-	{    
- 		int num = aa->lb->GetCount() ;
- 		num = rand() % num ;
- 		mylog ( "TTestSuite::aaAction" , wxString::Format ( "ListBox to %d" , num ) ) ; 
- 		aa->lb->SetSelection ( num , true ) ;
-    	aa->OnListBox ( ev ) ;
-	}   	
-}	
-
-void TTestSuite::mouseEvent ( ChildBase *ac )
-{
-	SequenceCanvas *can = ac->cSequence ;
-	if ( !can && ac->def == _T("PrimerDesign") ) can = ((TPrimerDesign*)ac)->sc ;
-	if ( !can ) return ;
-	
-	wxArrayInt vi ;
-	vi.Add ( wxEVT_ENTER_WINDOW ) ;
-	vi.Add ( wxEVT_LEAVE_WINDOW ) ;
-	vi.Add ( wxEVT_LEFT_DOWN ) ;
-	vi.Add ( wxEVT_LEFT_UP ) ;
-	//	vi.Add ( wxEVT_LEFT_DCLICK ) ;
-	vi.Add ( wxEVT_MIDDLE_DOWN ) ;
-	vi.Add ( wxEVT_MIDDLE_UP ) ;
-	vi.Add ( wxEVT_MIDDLE_DCLICK ) ;
-	//	vi.Add ( wxEVT_RIGHT_DOWN ) ;
-	vi.Add ( wxEVT_RIGHT_UP ) ;
-	vi.Add ( wxEVT_RIGHT_DCLICK ) ;
-	vi.Add ( wxEVT_MOTION ) ;
-	vi.Add ( wxEVT_MOUSEWHEEL ) ;
-	
-	int et = vi[rand()%vi.GetCount()] ;
-	
-	wxMouseEvent event ( et ) ;
-	int w , h ;
-	can->GetClientSize ( &w , &h ) ;
-	event.m_x = rand() % w ;
-	event.m_y = rand() % h ;
-	can->OnEvent ( event ) ;
-}	
-
-void TTestSuite::Step()
-{
-    if ( cnt == 0 ) start = wxGetLocalTime() ;
-    MyFrame *f = myapp()->frame ;
-	
-    ChildBase *ac = f->GetActiveChild () ;
-    if ( !ac ) return ; // No child open
-    
-    cnt++ ;
-    if ( cnt > 1000000 )
-	{
-	    wxMessageBox ( _T("1000K") ) ;
-	    wxExit() ;
-	}    
-    int r = rand() ;
-    r %= 10 ;
-    
-    wxString x ;
-    x = ac->getName() ;
-    x += _T(" [") + ac->def + _T("] ") ;
-    x += wxString::Format ( _T(" [%ds, #%d]") , wxGetLocalTime()-start , cnt ) ;
-    if ( ac->vec ) x += wxString::Format ( _T(", seq : %d") , ac->vec->getSequenceLength() ) ;
-    if ( ac->cSequence ) x += wxString::Format ( _T(", EditMode : %d") , ac->cSequence->getEditMode() ) ;
-    if ( ac->cSequence ) x += wxString::Format ( _T(", Overwrite : %d") , ac->cSequence->doOverwrite() ) ;
-    if ( ac->cSequence ) x += wxString::Format ( _T(", Mark %d-%d") , ac->cSequence->markedFrom() , ac->cSequence->markedTo() ) ;
-    x += wxString::Format ( _T(", r=%d") , r ) ;
-    mylog ( "Testsuite:Status" , x ) ;
-    
-    if ( r < 6 ) pressKey ( ac ) ;
-	//   	else if ( r == 6 ) mouseEvent ( ac ) ;
-   	else if ( r == 7 ) editMode ( ac ) ;
-   	else if ( r == 8 )
-	{
-	    r = rand() % f->children.GetCount() ;
-	    mylog ( "Testsuite:Activate" , wxString::Format ( "%d" , r ) ) ;
-	    f->activateChild ( r ) ;
-	}    
-   	else if ( r == 9 ) action ( ac ) ;
-}            
-
-#endif
-
-// DROP TARGET
-
-/** \brief Handles dropped file name(s)
- */
-bool MyFrameDropTarget::OnDropFiles(wxCoord x, wxCoord y, const wxArrayString& filenames)
-{
-    int a , b ;
-    for ( a = 0 ; a < filenames.GetCount() ; a++ )
-	{
-		wxString path = filenames[a] ;
-		for ( b = path.length() - 1 ; path.GetChar(b) != '\\' && path.GetChar(b) != '/' ; b-- ) ;
-		wxString file = path.substr ( b+1 ) ;
-		myapp()->frame->importFile ( file , path , -1 ) ;
-	}
-    return true ;
-}
-
-// Project
-
-/** \brief Constructor
- */
-TProject::TProject ()
-{
-	enzyme_rules = NULL ;
-}
-
-TEnzymeRules *TProject::getEnzymeRules () { return enzyme_rules ; }
-void TProject::setEnzymeRules ( TEnzymeRules *er ) { enzyme_rules = er ; }
-
 
=== removed directory '.pc/remove_clustalw.patch'
=== removed file '.pc/remove_clustalw.patch/Makefile.am'
--- .pc/remove_clustalw.patch/Makefile.am	2010-06-15 16:38:33 +0000
+++ .pc/remove_clustalw.patch/Makefile.am	1970-01-01 00:00:00 +0000
@@ -1,244 +0,0 @@
-SUFFIXES=.cpp .rc
-
-bin_PROGRAMS = GENtle
-
-EXTRA_DIST = mondrian.xpm \
-variables.csv \
-blank.db \
-default.tab \
-marker.txt \
-bitmaps/align.bmp \
-bitmaps/cocktail.bmp \
-bitmaps/display_features.bmp \
-bitmaps/helpcs.bmp \
-bitmaps/new.xpm \
-bitmaps/plasmid_linear.bmp \
-bitmaps/print.xpm \
-bitmaps/settings_tool.bmp \
-bitmaps/alignment.bmp \
-bitmaps/copy.bmp \
-bitmaps/display_restriction.bmp \
-bitmaps/help.xpm \
-bitmaps/open.bmp \
-bitmaps/preview.bmp \
-bitmaps/project.bmp \
-bitmaps/splash.bmp \
-bitmaps/align_tool.bmp \
-bitmaps/copy.xpm \
-bitmaps/draft.xbm \
-bitmaps/image.bmp \
-bitmaps/open.xpm \
-bitmaps/preview.xpm \
-bitmaps/protein.bmp \
-bitmaps/tick.bmp \
-bitmaps/bitmap1.bmp \
-bitmaps/cut.bmp \
-bitmaps/drawing.xbm\
-bitmaps/mode_both.bmp \
-bitmaps/orfs.bmp \
-bitmaps/primer.bmp \
-bitmaps/redo.bmp \
-bitmaps/undo.bmp \
-bitmaps/bitmap2.bmp \
-bitmaps/cut.xpm       \
-bitmaps/flowchar.xbm \
-bitmaps/mode_edit.bmp \
-bitmaps/paste.bmp \
-bitmaps/primer_export.bmp \
-bitmaps/save.bmp \
-bitmaps/web.bmp \
-bitmaps/calc.bmp \
-bitmaps/Helix.bmp \
-bitmaps/mode_view.bmp \
-bitmaps/paste.xpm \
-bitmaps/primer_import.bmp \
-bitmaps/save.xpm \
-bitmaps/write.xbm\
-bitmaps/calc_tool.bmp \
-bitmaps/dirplain.xbm \
-bitmaps/help.bmp \
-bitmaps/new.bmp \
-bitmaps/plasmid_circular.bmp \
-bitmaps/print.bmp \
-bitmaps/scissors.bmp
-
-
-GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite -lsqlite3 -lmysqlclient -ltinyxml
-GENtle_LDFLAGS = -s
-GENtle_SOURCES = TXMLfile.cpp\
-TVectorTree.cpp\
-TVirtualGel.cpp\
-TVectorEditorItems.cpp\
-TVectorEditorEnzymes.cpp\
-TVectorEditor.cpp\
-TVector.cpp\
-SCFtype.cpp\
-TStoreAllDialog.cpp\
-TDotPlot.cpp\
-TUndo.cpp\
-TUReadSeq.cpp\
-TStorage.cpp\
-TSilmutDialog.cpp\
-TRestrictionEditor.cpp\
-TPrimer.cpp\
-TPrimerDialog.cpp\
-TPDB.cpp\
-TLigationDialog.cpp\
-TMainTree.cpp\
-todo.cpp\
-TItemEditDialog.cpp\
-TImageDisplay.cpp\
-TIMGreader.cpp\
-TextImportDialog.cpp\
-TClone.cpp\
-SequenceTypes.cpp\
-TCalculator.cpp\
-SequenceTypeRestriction.cpp\
-SequenceTypePlot.cpp\
-SequenceTypeFeature.cpp\
-SequenceTypeDNA.cpp\
-SequenceTypeAlign.cpp\
-SequenceTypeABI.cpp\
-SequenceTypeAA.cpp\
-SequenceCanvas.cpp\
-SendHTTP.cpp\
-RestrictionEnzymes.cpp\
-ProgramOptionsDialog.cpp\
-PlasmidCanvasLinear.cpp\
-PrimerDesign.cpp\
-PlasmidCanvasHandlers.cpp\
-PlasmidCanvasCircular.cpp\
-PlasmidCanvas.cpp\
-MyFrame.cpp\
-MyChild.cpp\
-MiscDialogs.cpp\
-ManageDatabase.cpp\
-main.cpp\
-GenBank.cpp\
-FindSequenceDialog.cpp\
-ExternalNCBI.cpp\
-ExternalInterface.cpp\
-ExternalBLAST.cpp\
-ChildBase.cpp\
-CoolCanvas.cpp\
-AminoAcids.cpp\
-Alignment.cpp\
-ABIviewer.cpp\
-ABItype.cpp\
-TAlignmentDialog.cpp\
-AutoAnnotate.cpp\
-TGraph.cpp\
-TGraphDisplay.cpp\
-TGraphScale.cpp\
-CGview.cpp\
-ureadseq.c\
-ncoils.cpp\
-TPhylip.cpp\
-TPhyloTree.cpp\
-PCR_Troubleshoot.cpp\
-TProteolysis.cpp\
-clustalw/alnscore.cpp\
-clustalw/amenu.cpp\
-clustalw/calcgap.cpp\
-clustalw/calcprf1.cpp\
-clustalw/calcprf2.cpp\
-clustalw/calctree.cpp\
-clustalw/clustalw.cpp\
-clustalw/gcgcheck.cpp\
-clustalw/interfac.cpp\
-clustalw/malign.cpp\
-clustalw/palign.cpp\
-clustalw/prfalign.cpp\
-clustalw/random.cpp\
-clustalw/readmat.cpp\
-clustalw/sequence.cpp\
-clustalw/showpair.cpp\
-clustalw/trees.cpp\
-clustalw/util.cpp\
-ipc/element.cpp\
-ipc/gp_out.cpp\
-ipc/ipc.cpp\
-ipc/pars.cpp\
-CloneManager.cpp\
-CloningAssistant.cpp\
-TSequencingAssistantDialog.cpp\
-AlignmentAppearanceDialog.cpp\
-SequenceTypeAAstructure.cpp\
-OnlineTools.cpp\
-TEliteLaChromLogDialog.cpp\
-TRestrictionIdentifier.cpp\
-TRestrictionIdentifier.h\
-CloningAssistant.h\
-AlignmentAppearanceDialog.h\
-TSequencingAssistantDialog.h\
-OnlineTools.h\
-CloneManager.h\
-enums.h \
-lin_sqlite.h \
-lin_sqlite3.h \
-TXMLfile.h\
-SCFtype.h\
-TStoreAllDialog.h\
-TDotPlot.h\
-AutoAnnotate.h\
-CGview.h\
-TAlignmentDialog.h\
-TGraph.h\
-TVectorTree.h\
-TVirtualGel.h\
-TVectorEditor.h\
-TVector.h\
-TUndo.h\
-TUReadSeq.h\
-TStorage.h\
-TSilmutDialog.h\
-TRestrictionEditor.h\
-TPrimer.h\
-TPrimerDialog.h\
-TPDB.h\
-TLigationDialog.h\
-TMainTree.h\
-TItemEditDialog.h\
-TImageDisplay.h\
-TIMGreader.h\
-TextImportDialog.h\
-TClone.h\
-TCalculator.h\
-SequenceCanvas.h\
-SendHTTP.h\
-RestrictionEnzymes.h\
-ProgramOptionsDialog.h\
-PrimerDesign.h\
-PlasmidCanvas.h\
-MyFrame.h\
-MyChild.h\
-MiscDialogs.h\
-ManageDatabase.h\
-main.h\
-GenBank.h\
-FindSequenceDialog.h\
-ExternalInterface.h\
-TProteolysis.h\
-PCR_Troubleshoot.h\
-ChildBase.h\
-CoolCanvas.h\
-AminoAcids.h\
-Alignment.h\
-ABIviewer.h\
-ABItype.h\
-ureadseq.h\
-TPhylip.h\
-TPhyloTree.h\
-TEliteLaChromLogDialog.h\
-ncoils.h\
-clustalw/clustalw.h\
-clustalw/dayhoff.h \
-clustalw/general.h \
-clustalw/matrices.h \
-clustalw/param.h \
-clustalw/xmenu.h\
-ipc/element.h\
-ipc/global.h\
-ipc/gp_out.h\
-ipc/ipc.h\
-ipc/parse.h
 
=== removed directory '.pc/remove_tinyxml.patch'
=== removed file '.pc/remove_tinyxml.patch/Makefile.am'
--- .pc/remove_tinyxml.patch/Makefile.am	2010-06-15 16:38:33 +0000
+++ .pc/remove_tinyxml.patch/Makefile.am	1970-01-01 00:00:00 +0000
@@ -1,250 +0,0 @@
-SUFFIXES=.cpp .rc
-
-bin_PROGRAMS = GENtle
-
-EXTRA_DIST = mondrian.xpm \
-variables.csv \
-blank.db \
-default.tab \
-marker.txt \
-bitmaps/align.bmp \
-bitmaps/cocktail.bmp \
-bitmaps/display_features.bmp \
-bitmaps/helpcs.bmp \
-bitmaps/new.xpm \
-bitmaps/plasmid_linear.bmp \
-bitmaps/print.xpm \
-bitmaps/settings_tool.bmp \
-bitmaps/alignment.bmp \
-bitmaps/copy.bmp \
-bitmaps/display_restriction.bmp \
-bitmaps/help.xpm \
-bitmaps/open.bmp \
-bitmaps/preview.bmp \
-bitmaps/project.bmp \
-bitmaps/splash.bmp \
-bitmaps/align_tool.bmp \
-bitmaps/copy.xpm \
-bitmaps/draft.xbm \
-bitmaps/image.bmp \
-bitmaps/open.xpm \
-bitmaps/preview.xpm \
-bitmaps/protein.bmp \
-bitmaps/tick.bmp \
-bitmaps/bitmap1.bmp \
-bitmaps/cut.bmp \
-bitmaps/drawing.xbm\
-bitmaps/mode_both.bmp \
-bitmaps/orfs.bmp \
-bitmaps/primer.bmp \
-bitmaps/redo.bmp \
-bitmaps/undo.bmp \
-bitmaps/bitmap2.bmp \
-bitmaps/cut.xpm       \
-bitmaps/flowchar.xbm \
-bitmaps/mode_edit.bmp \
-bitmaps/paste.bmp \
-bitmaps/primer_export.bmp \
-bitmaps/save.bmp \
-bitmaps/web.bmp \
-bitmaps/calc.bmp \
-bitmaps/Helix.bmp \
-bitmaps/mode_view.bmp \
-bitmaps/paste.xpm \
-bitmaps/primer_import.bmp \
-bitmaps/save.xpm \
-bitmaps/write.xbm\
-bitmaps/calc_tool.bmp \
-bitmaps/dirplain.xbm \
-bitmaps/help.bmp \
-bitmaps/new.bmp \
-bitmaps/plasmid_circular.bmp \
-bitmaps/print.bmp \
-bitmaps/scissors.bmp
-
-
-GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite -lsqlite3 -lmysqlclient
-GENtle_LDFLAGS = -s
-GENtle_SOURCES = TXMLfile.cpp\
-TVectorTree.cpp\
-TVirtualGel.cpp\
-TVectorEditorItems.cpp\
-TVectorEditorEnzymes.cpp\
-TVectorEditor.cpp\
-TVector.cpp\
-SCFtype.cpp\
-TStoreAllDialog.cpp\
-TDotPlot.cpp\
-TUndo.cpp\
-TUReadSeq.cpp\
-TStorage.cpp\
-TSilmutDialog.cpp\
-TRestrictionEditor.cpp\
-TPrimer.cpp\
-TPrimerDialog.cpp\
-TPDB.cpp\
-TLigationDialog.cpp\
-TMainTree.cpp\
-todo.cpp\
-TItemEditDialog.cpp\
-TImageDisplay.cpp\
-TIMGreader.cpp\
-TextImportDialog.cpp\
-TClone.cpp\
-SequenceTypes.cpp\
-TCalculator.cpp\
-SequenceTypeRestriction.cpp\
-SequenceTypePlot.cpp\
-SequenceTypeFeature.cpp\
-SequenceTypeDNA.cpp\
-SequenceTypeAlign.cpp\
-SequenceTypeABI.cpp\
-SequenceTypeAA.cpp\
-SequenceCanvas.cpp\
-SendHTTP.cpp\
-RestrictionEnzymes.cpp\
-ProgramOptionsDialog.cpp\
-PlasmidCanvasLinear.cpp\
-PrimerDesign.cpp\
-PlasmidCanvasHandlers.cpp\
-PlasmidCanvasCircular.cpp\
-PlasmidCanvas.cpp\
-MyFrame.cpp\
-MyChild.cpp\
-MiscDialogs.cpp\
-ManageDatabase.cpp\
-main.cpp\
-GenBank.cpp\
-FindSequenceDialog.cpp\
-ExternalNCBI.cpp\
-ExternalInterface.cpp\
-ExternalBLAST.cpp\
-ChildBase.cpp\
-CoolCanvas.cpp\
-AminoAcids.cpp\
-Alignment.cpp\
-ABIviewer.cpp\
-ABItype.cpp\
-TAlignmentDialog.cpp\
-AutoAnnotate.cpp\
-TGraph.cpp\
-TGraphDisplay.cpp\
-TGraphScale.cpp\
-CGview.cpp\
-ureadseq.c\
-ncoils.cpp\
-TPhylip.cpp\
-TPhyloTree.cpp\
-PCR_Troubleshoot.cpp\
-TProteolysis.cpp\
-tinyxml/tinyxmlparser.cpp\
-tinyxml/tinyxmlerror.cpp\
-tinyxml/tinyxml.cpp\
-tinyxml/tinystr.cpp\
-clustalw/alnscore.cpp\
-clustalw/amenu.cpp\
-clustalw/calcgap.cpp\
-clustalw/calcprf1.cpp\
-clustalw/calcprf2.cpp\
-clustalw/calctree.cpp\
-clustalw/clustalw.cpp\
-clustalw/gcgcheck.cpp\
-clustalw/interfac.cpp\
-clustalw/malign.cpp\
-clustalw/palign.cpp\
-clustalw/prfalign.cpp\
-clustalw/random.cpp\
-clustalw/readmat.cpp\
-clustalw/sequence.cpp\
-clustalw/showpair.cpp\
-clustalw/trees.cpp\
-clustalw/util.cpp\
-ipc/element.cpp\
-ipc/gp_out.cpp\
-ipc/ipc.cpp\
-ipc/pars.cpp\
-CloneManager.cpp\
-CloningAssistant.cpp\
-TSequencingAssistantDialog.cpp\
-AlignmentAppearanceDialog.cpp\
-SequenceTypeAAstructure.cpp\
-OnlineTools.cpp\
-TEliteLaChromLogDialog.cpp\
-TRestrictionIdentifier.cpp\
-TRestrictionIdentifier.h\
-CloningAssistant.h\
-AlignmentAppearanceDialog.h\
-TSequencingAssistantDialog.h\
-OnlineTools.h\
-CloneManager.h\
-enums.h \
-lin_sqlite.h \
-lin_sqlite3.h \
-TXMLfile.h\
-SCFtype.h\
-TStoreAllDialog.h\
-TDotPlot.h\
-AutoAnnotate.h\
-CGview.h\
-TAlignmentDialog.h\
-TGraph.h\
-TVectorTree.h\
-TVirtualGel.h\
-TVectorEditor.h\
-TVector.h\
-TUndo.h\
-TUReadSeq.h\
-TStorage.h\
-TSilmutDialog.h\
-TRestrictionEditor.h\
-TPrimer.h\
-TPrimerDialog.h\
-TPDB.h\
-TLigationDialog.h\
-TMainTree.h\
-TItemEditDialog.h\
-TImageDisplay.h\
-TIMGreader.h\
-TextImportDialog.h\
-TClone.h\
-TCalculator.h\
-SequenceCanvas.h\
-SendHTTP.h\
-RestrictionEnzymes.h\
-ProgramOptionsDialog.h\
-PrimerDesign.h\
-PlasmidCanvas.h\
-MyFrame.h\
-MyChild.h\
-MiscDialogs.h\
-ManageDatabase.h\
-main.h\
-GenBank.h\
-FindSequenceDialog.h\
-ExternalInterface.h\
-TProteolysis.h\
-PCR_Troubleshoot.h\
-ChildBase.h\
-CoolCanvas.h\
-AminoAcids.h\
-Alignment.h\
-ABIviewer.h\
-ABItype.h\
-ureadseq.h\
-TPhylip.h\
-TPhyloTree.h\
-TEliteLaChromLogDialog.h\
-ncoils.h\
-tinyxml/tinyxml.h\
-tinyxml/tinystr.h\
-clustalw/clustalw.h\
-clustalw/dayhoff.h \
-clustalw/general.h \
-clustalw/matrices.h \
-clustalw/param.h \
-clustalw/xmenu.h\
-ipc/element.h\
-ipc/global.h\
-ipc/gp_out.h\
-ipc/ipc.h\
-ipc/parse.h
 
=== removed file '.pc/remove_tinyxml.patch/TXMLfile.cpp'
--- .pc/remove_tinyxml.patch/TXMLfile.cpp	2010-06-15 16:38:33 +0000
+++ .pc/remove_tinyxml.patch/TXMLfile.cpp	1970-01-01 00:00:00 +0000
@@ -1,256 +0,0 @@
-/** \file
-	\brief The TXMLfile class
-*/
-#include "TXMLfile.h"
-
-TXMLfile::TXMLfile ()
-    {
-    TiXmlBase::SetCondenseWhiteSpace ( true ) ;
-    _success = false ;
-    }
-    
-void TXMLfile::parse ( wxString text )
-    {
-    TiXmlDocument doc ;
-    doc.Parse ( text.mb_str() ) ;
-    if ( doc.Error() )
-        {
-        _success = false ;
-        return ;
-        }
-    analyze ( doc ) ;   
-    }
-
-void TXMLfile::load ( wxString file ) 
-    {
-//	 wxStartTimer() ;
-    TiXmlDocument doc ( file.mb_str() );
-    bool ok = doc.LoadFile();
-/*
-	 // Alternative (faster?) opening method
-	 char *x ;
-	 wxFile f ( file ) ;
-	 if ( !f.IsOpened() ) { _success = false ; return ; }
-	 x = new char [ f.Length() + 5 ] ;
-	 f.Read ( x , f.Length() ) ;
-	 x[f.Length()] = 0 ;
-	 if ( *x != '<' ) { delete x ; _success = false ; return ; }
-	 TiXmlDocument doc ( "" );
-	 doc.Parse ( (const char*) x ) ;
-	 bool ok = !doc.Error() ;
-	 delete x ;
-*/
-//	 cout << "Done in " << wxGetElapsedTime() << " ms\n" ;
-    if ( !ok || doc.Error() )
-        {
-        _success = false ;
-        return ;
-        }
-
-    analyze ( doc ) ;
-    }
-
-void TXMLfile::analyze ( const TiXmlDocument &doc )
-    {
-    if ( doc.FirstChild ( "GBSeq" ) )
-        {
-        readGBSeq ( doc.FirstChild ( "GBSeq" ) ) ;
-        }
-    else if ( doc.FirstChild ( "GBSet" ) )
-        {
-        TiXmlNode *x = doc.RootElement() ;// ( _T("GBSet") ) ;
-        for ( x = x->FirstChild ( "GBSeq" ) ; x ; x = x->NextSibling ( "GBSeq" ) )
-           readGBSeq ( x ) ;
-        }
-    _success = _v.GetCount() > 0 ;
-    }
-    
-int TXMLfile::countVectors ()
-    {
-    return _v.GetCount() ;
-    }
-    
-TVector *TXMLfile::getVector ( int a )
-    {
-    return _v[a] ;
-    }
-    
-
-// private
-
-wxString TXMLfile::t ( const char *txt )
-    {
-    return txt ? wxString ( txt , wxConvUTF8 ) : _T("") ;
-    }
-
-wxString TXMLfile::t ( TiXmlText *txt )
-    {
-    return txt && txt->Value() ? wxString ( txt->Value() , wxConvUTF8 ) : wxString() ;
-    }
-
-void TXMLfile::readGBSeq ( TiXmlNode *base )
-    {
-    myass ( base , _T("TXMLfile::readGBSeq") ) ;
-    TVector *v = new TVector ;
-    v->setType ( TYPE_VECTOR ) ; // Dummy
-    
-    int a ;
-    TiXmlNode *n ;
-    TiXmlElement *e ;
-    wxString s ;
-    TiXmlHandle h ( base ) ;
-    
-    wxString n1 = t ( h.FirstChild("GBSeq_definition").FirstChild().Text() ) ;
-    wxString n2 = t ( h.FirstChild("GBSeq_locus").FirstChild().Text() ) ;
-    if ( !n1.IsEmpty() && n1.Freq ( '\n' ) == 0 && n2.Freq ( ' ' ) == 0 )
-	    n2 = n1 + _T("(") + n2 + _T("))") ;
-    
-    v->setName ( n2 ) ;
-    v->setSequence ( t ( h.FirstChild("GBSeq_sequence").FirstChild().Text() ) . MakeUpper() ) ;
-    
-    e = h.FirstChild("GBSeq_topology").Element() ;
-    if ( e ) // topology
-        {
-        s = t ( e->Attribute ( "value" ) ) . MakeUpper() ;
-        if ( s == _T("CIRCULAR") ) v->setCircular ( true ) ;
-        }
-//	 cout << "Up to features took " << wxGetElapsedTime() << " ms\n" ;
-
-    // Features
-    for ( n = h.FirstChild("GBSeq_feature-table").FirstChild("GBFeature").Node() ; n ;
-            n = n->NextSibling("GBFeature") )
-        {
-        TVectorItem i ;
-        TiXmlHandle h2 ( n ) ;
-        s = t ( h2.FirstChild("GBFeature_key").FirstChild().Text() ) . MakeUpper() ;
-        
-        // Dummy values
-        i.name = _T("") ;
-        i.from = 1 ;
-        i.to = 1 ;
-        i.setType ( 0 ) ;
-        i.setDirection ( 1 ) ;
-        i.setType ( s ) ;
-        readGBqualifiers ( i , n ) ;
-        
-        vector <TVectorItem> vi ;
-        readGBintervals ( vi , i , n ) ;
-        for ( a = 0 ; a < vi.size() ; a++ )
-           v->items.push_back ( vi[a] ) ;
-        }
-//	 cout << "Features took " << wxGetElapsedTime() << " ms\n" ;
-
-	// The rest
-	for ( n = h.Node()->FirstChild() ; n ; n = n->NextSibling() )
-		{
-		wxString x = t ( n->Value() ) ;
-		if ( x == _T("GBSeq_definition") ) continue ;
-		if ( x == _T("GBSeq_locus") ) continue ;
-		if ( x == _T("GBSeq_sequence") ) continue ;
-		if ( x == _T("GBSeq_feature-table") ) continue ;
-		x = get_sub_desc ( n ) ;
-		v->addDescription ( x ) ;
-		}
-        
-    // Sorting by size, just for fun
-    // Only for less than 100 items
-    for ( a = 1 ; v->items.size() < 100 && a < v->items.size() ; a++ )
-        {
-        if ( v->getItemLength(a-1) < v->getItemLength(a) )
-           {
-           TVectorItem i = v->items[a] ;
-           v->items[a] = v->items[a-1] ;
-           v->items[a-1] = i ;
-           a = 0 ;
-           }
-        }
-        
-    v->updateDisplay() ;
-    v->recalculateCuts () ;
-    _v.Add ( v ) ;
-//	 cout << "The rest took " << wxGetElapsedTime() << " ms\n" ;
-    }
-
-wxString TXMLfile::get_sub_desc ( TiXmlNode *base , int depth )
-	{
-	if ( !base ) return _T("") ; // Just fore safety...
-	wxString name = t ( base->Value() ) ;
-	if ( name.Left ( 6 ) == _T("GBSeq_") ) name = name.Mid(6,1).Upper() + name.Mid ( 7 ) ;
-	wxString ret ;
-	ret = wxString ( (wxChar)' ' , depth * 2 ) ;
-	ret += name ;
-	ret += _T("\n") ;
-	TiXmlNode *n ;
-	for ( n = base->FirstChild() ; n ; n = n->NextSibling() )
-		ret += get_sub_desc ( n , depth + 1 ) ;
-	return ret ;
-	}
-    
-void TXMLfile::readGBqualifiers ( TVectorItem &i , TiXmlNode *n )
-    {
-    TiXmlNode *n2 = n->FirstChild("GBFeature_quals") ;
-    if ( !n2 ) return ;    
-    for ( n2 = n2->FirstChild("GBQualifier") ; n2 ; n2 = n2->NextSibling("GBQualifier") )
-        {
-        TiXmlHandle h ( n2 ) ;
-        wxString name = t ( h.FirstChild("GBQualifier_name").FirstChild().Text() ) . MakeUpper() ;
-        wxString value = t ( h.FirstChild("GBQualifier_value").FirstChild().Text() ) ;
-        if ( name.IsEmpty() ) continue ;
-        i.setParam ( _T("/") + name , value ) ;
-        if ( name == _T("CODON_START") ) i.setRF ( atoi ( value.mb_str() ) ) ;
-        if ( name == _T("GENE") || name == _T("LABEL") ) i.name = value ;
-        if ( name == _T("PRODUCT") || name == _T("NOTE") || name == _T("REGION_NAME") )
-           {
-           if ( !i.desc.IsEmpty() ) i.desc += _T("\n") ;
-           i.desc += value ;
-           }
-        }
-    if ( i.name.IsEmpty() && i.desc.length() < 10 )
-        {
-        i.name = i.desc ;
-        i.desc = _T("") ;
-        }
-    if ( i.name.IsEmpty() )
-    	{
-	    wxString try2 = i.desc ; 
-	    while ( try2.Right ( 1 ) == _T("\n") ) try2 = try2.Left ( try2.length() - 1 ) ;
-     	try2 = try2.AfterLast('\n').AfterLast('\r') ;
-	if ( !try2.IsEmpty() && try2.length() < 20 ) i.name = try2 ;
-    	}    
-    if ( i.name.IsEmpty() )
-        {
-        char u[100] ;
-        sprintf ( u , "short_itemtype%d" , i.getType() ) ;
-        i.name = wxString ( txt(u) , wxConvUTF8 ) ;
-        wxString d2 = i.desc ;
-        int k = d2.find ( _T("\n") ) ;
-        if ( k > -1 ) d2.erase ( k ) ;
-        if ( i.name.length() * 2 >= d2.length() )
-           i.name = d2 ;
-        }
-    }
-    
-void TXMLfile::readGBintervals ( vector <TVectorItem> &vi , const TVectorItem &i , TiXmlNode *n )
-    {
-    TiXmlNode *n2 = n->FirstChild("GBFeature_intervals") ;
-    if ( !n2 ) return ;
-    for ( n2 = n2->FirstChild("GBInterval") ; n2 ; n2 = n2->NextSibling("GBInterval") )
-        {
-        TiXmlHandle h ( n2 ) ;
-        wxString from = t ( h.FirstChild("GBInterval_from").FirstChild().Text() ) ;
-        wxString to = t ( h.FirstChild("GBInterval_to").FirstChild().Text() ) ;
-        if ( from.IsEmpty() || to.IsEmpty() ) continue ;
-        TVectorItem j = i ;
-        j.from = atoi ( from.mb_str() ) ;
-        j.to = atoi ( to.mb_str() ) ;
-        if ( j.from > j.to )
-           {
-           int o = j.from ;
-           j.from = j.to ;
-           j.to = o ;
-           j.setDirection ( -1 ) ;
-           }
-        vi.push_back ( j ) ;
-        }
-    }
-    
 
=== removed file '.pc/remove_tinyxml.patch/TXMLfile.h'
--- .pc/remove_tinyxml.patch/TXMLfile.h	2010-06-15 16:38:33 +0000
+++ .pc/remove_tinyxml.patch/TXMLfile.h	1970-01-01 00:00:00 +0000
@@ -1,40 +0,0 @@
-/** \file
-	\brief The TXMLfile class
-*/
-#ifndef _TXMLFILE_H_
-#define _TXMLFILE_H_
-
-#include "main.h"
-
-class TVector ;
-class TiXmlNode ;
-class TVectorItem ;
-class TiXmlDocument ;
-
-/// This class is a wrapper around the tinyxml software, specialized for GenBankXML format
-class TXMLfile
-    {
-    public :
-    TXMLfile () ; ///< Constructor
-    ~TXMLfile () {} ; ///< Dummy destructor
-	
-    void load ( wxString file ) ; ///< Load XML from file
-    void parse ( wxString text ) ; ///< Pass XML as string
-    bool success () { return _success ; } ///< Errors during parsing?
-    int countVectors () ; ///< How many vectors were made from the XML?
-    TVector *getVector ( int a ) ; ///< Returns pointer to one of the vectors
-    
-    private :
-    void analyze ( const TiXmlDocument &doc ) ; ///< Parse single/multiple sequences
-    void readGBSeq ( TiXmlNode *base ) ; ///< The actual parser
-    wxString t ( TiXmlText *txt ) ; ///< Safe text conversion
-    wxString t ( const char *txt ) ; ///< Safe text conversion
-    void readGBqualifiers ( TVectorItem &i , TiXmlNode *n ) ; ///< Part of the parser
-    void readGBintervals ( vector <TVectorItem> &vi , const TVectorItem &i , TiXmlNode *n ) ; ///< Part of the parser
-    wxString get_sub_desc ( TiXmlNode *base , int depth = 0 ) ;
-    bool _success ; ///< Internal success marker
-    wxArrayTVector _v ; ///< The generated vectors
-    } ;
-
-#endif
-
 
=== removed file '.pc/remove_tinyxml.patch/main.h'
--- .pc/remove_tinyxml.patch/main.h	2010-06-15 16:38:33 +0000
+++ .pc/remove_tinyxml.patch/main.h	1970-01-01 00:00:00 +0000
@@ -1,354 +0,0 @@
-/** \file
-	\brief Contains defines, global functions, includes, and the MyApp class
-*/
-#ifndef _MAIN_H_
-#define _MAIN_H_
-
-//#define __DEBIAN__
-
-#define GENTLE_VERSION_MAJOR 1
-#define GENTLE_VERSION_MINOR 9
-#define GENTLE_VERSION_SUB 4
-
-typedef unsigned int uint ;
-
-/**	\fn myass ( bool b , wxString msg )
-	\brief "My assertion" - little inside joke...
-	\param b The condition given in the call. No assertion when b is FALSE.
-	\param msg The message string to write into errout.
-*/
-
-/**	\def MYDEBUG
-	\brief Turns on output of the myass function; should not be used for releases
-*/
-
-/**	\def MYLOG
-	\brief Turns on output of logging; should not be used for releases
-*/
-
-/**	\def MYTEST
-	\brief Turns on both MYDEBUG and MYLOG; should not be used for releases
-*/
-
-//#define MYDEBUG
-//#define MYLOG
-//#define MYTEST
-
-#ifdef MYTEST
-	#ifndef MYLOG
-		#define MYLOG
-	#endif // MYLOG
-	#ifndef MYDEBUG
-		#define MYDEBUG
-	#endif // MYDEBUG
-#endif // MYTEST
-
-/**	\def MYSPINBOXSIZE
-	\brief Width of spin box, for windows only
-*/
-#ifdef __WXMSW__
-	#define MYSPINBOXSIZE 80
-#else
-	#define MYSPINBOXSIZE -1
-#endif
-
-#include "wx/wxprec.h"
-
-/**	\def MYFONTSIZE
-	\brief Main tree font size
-*/
-#ifdef __WXMAC__
-	#define MYFONTSIZE 10
-#else
-	#define MYFONTSIZE 8
-#endif
-
-/**	\def MYSPINBOXSIZE
-	\brief List box style, for GTK only
-*/
-#ifdef __WXGTK__
-	#define MYLISTBORDER wxSIMPLE_BORDER
-#else
-	#define MYLISTBORDER 0
-#endif
-
-#ifdef __BORLANDC__
-    #pragma hdrstop
-#endif
-
-#ifndef WX_PRECOMP
-    #include "wx/wx.h"
-    #include "wx/notebook.h"
-#endif
-
-#include <wx/toolbar.h>
-#include <wx/filesys.h>
-#include <wx/fs_inet.h>
-#include <wx/file.h>
-#include <wx/dialup.h>
-#include <wx/utils.h>
-#include <wx/numdlg.h>
-#include <wx/timer.h>
-
-#ifdef _UNICODE
-	#define wxUSE_UNICODE 1
-#endif
-
-#if defined(__WXGTK__) || defined(__WXMOTIF__)
-    #include "mondrian.xpm"
-    #include "bitmaps/new.xpm"
-    #include "bitmaps/open.xpm"
-    #include "bitmaps/save.xpm"
-    #include "bitmaps/copy.xpm"
-    #include "bitmaps/cut.xpm"
-    #include "bitmaps/paste.xpm"
-    #include "bitmaps/print.xpm"
-    #include "bitmaps/help.xpm"
-#endif
-
-#include <math.h>
-#include <vector>
-
-using namespace std ;
-
-/** \def MYPEN(_a)
-	\brief Creates or reuses a solid pen with size 1. _a is of type wxColour
-*/
-
-/** \def MYBRUSH(_a)
-	\brief Creates or reuses a solid brush. _a is of type wxColour
-*/
-
-/** \def MYFONT(_a,_b,_c,_d)
-	\brief Creates or reuses a font. Parameters are the same as wxCreateFont
-*/
-
-#define MYPEN(_a) (wxThePenList->FindOrCreatePen ( _a , 1 , wxSOLID ) )
-#define MYBRUSH(_a) (wxTheBrushList->FindOrCreateBrush ( _a , wxSOLID ) )
-#define MYFONT(_a,_b,_c,_d) (wxTheFontList->FindOrCreateFont(_a,_b,_c,_d) )
-
-// Don't you *EVER* turn this on again!!!!
-//#define TIXML_USE_STL
-#include "tinyxml/tinyxml.h"
-
-#include <wx/wx.h>
-#include <wx/toolbar.h>
-#include <wx/treectrl.h>
-#include <wx/listctrl.h>
-#include <wx/snglinst.h>
-#include <wx/laywin.h>
-#include <wx/progdlg.h>
-#include <wx/mimetype.h>
-#include <wx/textfile.h>
-#include <wx/dir.h>
-#include <wx/html/helpctrl.h>
-#include <wx/url.h>
-#include <wx/protocol/http.h>
-WX_DECLARE_STRING_HASH_MAP( wxString, wxHashString );
-
-/** \brief Style for Process Dialog */
-#define wxPD_ALL (wxPD_AUTO_HIDE|wxPD_APP_MODAL|wxPD_CAN_ABORT|wxPD_ELAPSED_TIME|wxPD_ESTIMATED_TIME|wxPD_REMAINING_TIME)
-
-#define TYPE_VECTOR 0 /**< \brief Vector type */
-#define TYPE_FRAGMENT 1 /**< \brief Fragment type */
-#define TYPE_SEQUENCE 2 /**< \brief Sequence type */
-#define TYPE_PRIMER 3 /**< \brief Primer type */
-#define TYPE_ALIGNMENT 4 /**< \brief Alignment type */
-#define TYPE_AMINO_ACIDS 5 /**< \brief Amino acid type */
-#define TYPE_MISC 6 /**< \brief Misc type */
-
-#define FEAT_NONE 0  /**< \brief Do not draw feature  */
-#define FEAT_ALPHA 1  /**< \brief Draw feature as alpha helix */
-#define FEAT_BETA 2  /**< \brief Draw feature as beta sheet */
-#define FEAT_MUT 3  /**< \brief Draw feature as mutation */
-#define FEAT_NOLINE 4  /**< \brief Draw feature without line  */
-#define FEAT_VLINE 5  /**< \brief Draw feature as vertical line */
-
-#define DAM_METHYLATION 1 /**< \brief Show DAM methylation */
-#define DCM_METHYLATION 2 /**< \brief Show DCM methylation */
-#define ALL_METHYLATION_ENZYMES ( DAM_METHYLATION + DCM_METHYLATION ) /**< \brief Show all methylations */
-
-class MyFrame ;
-
-/** \class MyApp
-	\brief Application class
-*/
-class MyApp : public wxApp
-    {
-    public:
-    virtual bool OnInit();
-    virtual int OnExit () ;
-    virtual void init_txt ( wxString lang , wxString csv , wxHashString *target = NULL , int ln = 1 ) ;
-    virtual void do_my_ass ( bool b , wxString msg = _T("") ) ;
-    virtual void do_my_log ( wxString function , wxString msg = _T("") ) ;
-    virtual wxString getHTMLCommand ( wxString command ) ; ///< Returns the command line for running a browser
-    virtual wxString getFileFormatApplication ( wxString type ) ; ///< Returns application associated with a file type
-    virtual wxString getFileFormatCommand ( wxString type , wxString file ) ; ///< Returns the command line for running this file
-    virtual wxString get_GENtle_version () ; ///< Returns the GENtle version string
-	virtual wxString getLocalDBname () ; ///< Returns the filename of the default local database
-	virtual void launchBrowser ( wxString url ) ;
-    
-    MyFrame *frame; ///< The application frame
-    wxMimeTypesManager mtm ; ///< The MIME types manager
-    wxString homedir ; ///< Directory of the application
-    wxString bmpdir ; ///< Directory of the bitmaps
-    wxString slash ; ///< The platform-dependent directory separator slash
-    int programVersion ; ///< The database access program version
-    int dbWarningIssued ; ///< Was a database warning issued?
-    wxHashString _text ; ///< Contains the current GUI translation.
-    wxHashString clp ; ///< Command line parameters
-	 wxCSConv *isoconv ; ///< UTF-8 conversion helper
-		wxStopWatch sw ;
-    
-    private :
-    virtual void registerFileExtension ( wxString extension ) ; ///< Registers a file extension to GENtle (windows only).
-    virtual void registerProtocol ( wxString extension ) ; ///< Registers a protocol to GENtle (windows only).
-    wxFile *errout ; ///< The ERROR.txt file handler for do_my_ass
-    wxFile *logout ; ///< The LOG.txt file handler for do_my_log
-    int total_log_time ; ///< The log timer for do_my_log
-    int total_log_counter ; ///< The log counter for do_my_log
-    wxSingleInstanceChecker *m_checker ; ///< Checks if another instance is running
-    wxString theRealLocalDb ;
-    };
-
-class TUndo ;
-class ChildBase ;
-class TVector ;
-class TRestrictionEnzyme ;
-class TStorage ;
-class TProtease ;
-class TVectorItem ;
-class SeqBasic ;
-class TProteaseCut ;
-
-WX_DEFINE_ARRAY(ChildBase *, wxArrayChildBase);
-WX_DEFINE_ARRAY(TRestrictionEnzyme *, wxArrayTRestrictionEnzyme);
-WX_DEFINE_ARRAY(TStorage *, wxArrayTStorage);
-WX_DEFINE_ARRAY(TProtease *,wxArrayTProtease);
-WX_DEFINE_ARRAY(TVectorItem *,wxArrayTVectorItem);
-WX_DEFINE_ARRAY(SeqBasic *,wxArraySeqBasic);
-WX_DEFINE_ARRAY(TProteaseCut *,wxArrayTProteaseCut);
-WX_DECLARE_OBJARRAY(float, wxArrayFloat);
-
-#ifndef _wxArrayTVector
-	#define _wxArrayTVector
-	WX_DEFINE_ARRAY(TVector *, wxArrayTVector);
-#endif
-
-/** \brief Clear wxArray of pointers and delete the not-NULL-pointer objects */
-#define CLEAR_DELETE(__x) { while ( !__x.IsEmpty() ) { if ( __x[0] ) { delete __x[0] ; } __x.RemoveAt ( 0 ) ; } }
-
-/** \brief Create a wxString of __l times the __c char */
-#define FILLSTRING(__x,__c,__l) { __x = wxString ( __c , __l ) ; }
-
-
-#include "enums.h"
-#include "TVector.h"
-#include "TUReadSeq.h"
-#include "TPhylip.h"
-#include "ipc/ipc.h"
-#include "ncoils.h"
-#include "CGview.h"
-#include "AutoAnnotate.h"
-#include "ChildBase.h"
-#include "OnlineTools.h"
-#include "TSequencerData.h"
-#include "ABItype.h"
-#include "SCFtype.h"
-#include "CloningAssistant.h"
-#include "MiscDialogs.h"
-#include "TStorage.h"
-#include "TPrimer.h"
-#include "TIMGreader.h"
-#include "PlasmidCanvas.h"
-#include "SequenceCanvas.h"
-#include "TDotPlot.h"
-#include "TStoreAllDialog.h"
-#include "TSequencingAssistantDialog.h"
-#include "MyFrame.h"
-#include "MyChild.h"
-#include "TRestrictionEditor.h"
-#include "TClone.h"
-#include "GenBank.h"
-#include "TPDB.h"
-#include "CloneManager.h"
-#include "TXMLfile.h"
-#include "TVectorTree.h"
-#include "TMainTree.h"
-#include "RestrictionEnzymes.h"
-#include "TImageDisplay.h"
-#include "TVirtualGel.h"
-//#include "TRestrictionIdentifier.h"
-#include "TCalculator.h"
-#include "TGraph.h"
-#include "TPhyloTree.h"
-#include "Alignment.h"
-#include "AminoAcids.h"
-#include "ABIviewer.h"
-#include "ExternalInterface.h"
-#include "TItemEditDialog.h"
-#include "PrimerDesign.h"
-
-#define PI 3.14 /**< \brief Just PI */
-#define IUPAC_A 1 /**< \brief IUPAC bit for A */
-#define IUPAC_C 2 /**< \brief IUPAC bit for C */
-#define IUPAC_G 4 /**< \brief IUPAC bit for G */
-#define IUPAC_T 8 /**< \brief IUPAC bit for T */
-
-#define MINI_DISPLAY_ORIGINAL 0 /**< \brief Display mini-canvas at original width */
-#define MINI_DISPLAY_REAL 1 /**< \brief Display mini-canvas at real width */
-#define MINI_DISPLAY_CONDENSED 2 /**< \brief Display mini-canvas as condensed width */
-
-#include "ureadseq.h"
-
-
-// ---------------------------------------------------------------------------
-// global functions
-// ---------------------------------------------------------------------------
-
-#ifdef MYDEBUG
-	#define myass(a,b) myapp()->do_my_ass(a,b)
-#else
-	#define myass(a,b)
-#endif
- 
-#ifdef MYLOG
-	#define mylog(a,b) myapp()->do_my_log(a,b)	
-#else
-	#define mylog(a,b)
-#endif
-
-#define CHAR2WX(__c) wxString((char*)l,wxConvUTF8)
-
-/** \brief Insert wxString "t" into wxString "s" at position "from" */
-void wxStringInsert ( wxString &s , int from , wxString t ) ;
-
-/** \brief Chop wxString "s" into parts "r" separated by "sep" */
-void explode ( wxString sep , wxString s , wxArrayString &r ) ;
-
-/** \brief Join wxStrings in "r" while putting "sep"s between them */
-wxString implode ( wxString sep , wxArrayString &r ) ;
-/*
-/** \brief Returns the current language version of the "item" /
-char* txt ( wxString item ) ;
-
-/** \brief Returns the current language version of the "item" /
-char* txt ( char *item ) ;
-*/
-/** \brief Returns the current language version of the "item" */
-wxString txt ( wxString item ) ;
-
-/** \brief Returns the current language version of the "item" */
-wxString txt ( char *item ) ;
-
-/** \brief Returns a pointer to the application */
-MyApp *myapp () ;
-
-/** \brief Compares the values of two int pointers */
-int cmpint(int *first, int *second) ;
-
-/** \brief Compares the values of two TRestrictionEnzyme pointers */
-int cmpre(TRestrictionEnzyme *first, TRestrictionEnzyme *second) ;
-
-#endif
-// _MAIN_H__
 
=== modified file 'Makefile.am'
--- Makefile.am	2013-03-16 14:37:00 +0000
+++ Makefile.am	2014-08-05 04:14:21 +0000
@@ -63,7 +63,11 @@
 bitmaps/scissors.bmp
 
 
+<<<<<<< TREE
 GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite3 -lmysqlclient -ltinyxml
+=======
+GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite -lsqlite3 -lmysqlclient
+>>>>>>> MERGE-SOURCE
 GENtle_LDFLAGS = -s
 GENtle_SOURCES = TXMLfile.cpp\
 TVectorTree.cpp\
@@ -137,6 +141,28 @@
 TPhyloTree.cpp\
 PCR_Troubleshoot.cpp\
 TProteolysis.cpp\
+tinyxml/tinyxmlparser.cpp\
+tinyxml/tinyxmlerror.cpp\
+tinyxml/tinyxml.cpp\
+tinyxml/tinystr.cpp\
+clustalw/alnscore.cpp\
+clustalw/amenu.cpp\
+clustalw/calcgap.cpp\
+clustalw/calcprf1.cpp\
+clustalw/calcprf2.cpp\
+clustalw/calctree.cpp\
+clustalw/clustalw.cpp\
+clustalw/gcgcheck.cpp\
+clustalw/interfac.cpp\
+clustalw/malign.cpp\
+clustalw/palign.cpp\
+clustalw/prfalign.cpp\
+clustalw/random.cpp\
+clustalw/readmat.cpp\
+clustalw/sequence.cpp\
+clustalw/showpair.cpp\
+clustalw/trees.cpp\
+clustalw/util.cpp\
 ipc/element.cpp\
 ipc/gp_out.cpp\
 ipc/ipc.cpp\
@@ -213,6 +239,14 @@
 TPhyloTree.h\
 TEliteLaChromLogDialog.h\
 ncoils.h\
+tinyxml/tinyxml.h\
+tinyxml/tinystr.h\
+clustalw/clustalw.h\
+clustalw/dayhoff.h \
+clustalw/general.h \
+clustalw/matrices.h \
+clustalw/param.h \
+clustalw/xmenu.h\
 ipc/element.h\
 ipc/global.h\
 ipc/gp_out.h\
 
=== modified file 'MyFrame.cpp'
--- MyFrame.cpp	2014-06-25 13:55:53 +0000
+++ MyFrame.cpp	2014-08-05 04:14:21 +0000
@@ -586,7 +586,7 @@
 	{
         wxHtmlHelpController *hc = new wxHtmlHelpController ( wxHF_DEFAULT_STYLE|wxHF_OPEN_FILES ) ;
         helpfile += myapp()->homedir ;
-        helpfile += _T("/help/") ;
+        helpfile += _T("\\help\\") ;
         helpfile += lang_string ;
         helpfile += _T(".hhp") ;
         hc->AddBook ( helpfile ) ;
 
=== modified file 'TXMLfile.cpp'
--- TXMLfile.cpp	2014-06-25 13:55:53 +0000
+++ TXMLfile.cpp	2014-08-05 04:14:21 +0000
@@ -50,7 +50,7 @@
     analyze ( doc ) ;
     }
 
-void TXMLfile::analyze ( TiXmlDocument &doc )
+void TXMLfile::analyze ( const TiXmlDocument &doc )
     {
     if ( doc.FirstChild ( "GBSeq" ) )
         {
 
=== modified file 'TXMLfile.h'
--- TXMLfile.h	2010-06-15 16:38:33 +0000
+++ TXMLfile.h	2014-08-05 04:14:21 +0000
@@ -25,7 +25,7 @@
     TVector *getVector ( int a ) ; ///< Returns pointer to one of the vectors
     
     private :
-    void analyze ( TiXmlDocument &doc ) ; ///< Parse single/multiple sequences
+    void analyze ( const TiXmlDocument &doc ) ; ///< Parse single/multiple sequences
     void readGBSeq ( TiXmlNode *base ) ; ///< The actual parser
     wxString t ( TiXmlText *txt ) ; ///< Safe text conversion
     wxString t ( const char *txt ) ; ///< Safe text conversion
 
=== modified file 'main.h'
--- main.h	2010-06-15 16:38:33 +0000
+++ main.h	2014-08-05 04:14:21 +0000
@@ -129,11 +129,7 @@
 
 // Don't you *EVER* turn this on again!!!!
 //#define TIXML_USE_STL
-#ifndef __DEBIAN__
 #include "tinyxml/tinyxml.h"
-#else
-#include "tinyxml.h"
-#endif
 
 #include <wx/wx.h>
 #include <wx/toolbar.h>