structure_window.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: structure_window.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 18:29:33  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.33
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: structure_window.cpp,v 1000.3 2004/06/01 18:29:33 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Authors:  Paul Thiessen
*
* File Description:
*      structure window object for Cn3D
*
* ===========================================================================
*/

#ifdef _MSC_VER
#pragma warning(disable:4018)   // disable signed/unsigned mismatch warning in MSVC
#endif

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbitime.hpp> // avoids some 'CurrentTime' conflict later on...

#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/cdd/Cdd.hpp>
#include <objects/mmdb2/Model_type.hpp>

#include <algorithm>
#include <memory>

#ifdef __WXMSW__
#include <windows.h>
#include <wx/msw/winundef.h>
#endif
#include <wx/wx.h>
#include <wx/html/helpfrm.h>
#include <wx/html/helpctrl.h>
#include <wx/fontdlg.h>
#include <wx/confbase.h>
#include <wx/fileconf.h>
#include <wx/filename.h>
#include <wx/choicdlg.h>

#include "asn_reader.hpp"
#include "cn3d_glcanvas.hpp"
#include "structure_window.hpp"
#include "structure_set.hpp"
#include "opengl_renderer.hpp"
#include "style_manager.hpp"
#include "messenger.hpp"
#include "chemical_graph.hpp"
#include "alignment_manager.hpp"
#include "show_hide_manager.hpp"
#include "show_hide_dialog.hpp"
#include "cn3d_tools.hpp"
#include "cdd_annot_dialog.hpp"
#include "preferences_dialog.hpp"
#include "cdd_ref_dialog.hpp"
#include "cdd_book_ref_dialog.hpp"
#include "cn3d_png.hpp"
#include "wx_tools.hpp"
#include "block_multiple_alignment.hpp"
#include "sequence_set.hpp"
#include "molecule_identifier.hpp"
#include "cdd_splash_dialog.hpp"
#include "command_processor.hpp"
#include "animation_controls.hpp"
#include "cn3d_cache.hpp"

// the application icon (under Windows it is in resources)
#if defined(__WXGTK__) || defined(__WXMAC__)
    #include "cn3d.xpm"
#endif

#include <ncbienv.h>

USING_NCBI_SCOPE;
USING_SCOPE(objects);


BEGIN_SCOPE(Cn3D)

// global strings
static string
    userDir,        // directory of latest user-selected file
    currentFile;    // name of current working file
const string& GetUserDir(void) { return userDir; }
const string& GetWorkingFilename(void) { return currentFile; }

// global working title
static string workingTitle;
const string& GetWorkingTitle(void) { return workingTitle; }
static void SetWorkingTitle(StructureSet *sSet)
{
    if (sSet->IsCDDInMime() && sSet->GetCDDName().size() > 0)
        workingTitle = sSet->GetCDDName();      // for CDD's sent by server
    else if (sSet->IsCDD())
        workingTitle = GetWorkingFilename();    // for CDD's edited by curators
    else if (sSet->objects.size() > 0) {
        workingTitle = sSet->objects.front()->pdbID;
        if (sSet->objects.size() > 1)
            workingTitle += " neighbors";
    } else
        workingTitle = GetWorkingFilename();
}

// favorites stuff
static bool favoriteStylesChanged = false;
static CCn3d_style_settings_set favoriteStyles;
static bool LoadFavorites(void);
static void SaveFavorites(void);


BEGIN_EVENT_TABLE(StructureWindow, wxFrame)
    EVT_CLOSE     (                                         StructureWindow::OnCloseWindow)
    EVT_MENU      (MID_EXIT,                                StructureWindow::OnExit)
    EVT_MENU_RANGE(MID_OPEN, MID_NETWORK_OPEN,              StructureWindow::OnOpen)
    EVT_MENU_RANGE(MID_SAVE_SAME, MID_SAVE_AS,              StructureWindow::OnSave)
    EVT_MENU      (MID_PNG,                                 StructureWindow::OnPNG)
    EVT_MENU_RANGE(MID_ZOOM_IN,  MID_STEREO,                StructureWindow::OnAdjustView)
    EVT_MENU_RANGE(MID_SHOW_HIDE,  MID_SELECT_MOLECULE,     StructureWindow::OnShowHide)
    EVT_MENU_RANGE(MID_DIST_SELECT_RESIDUES, MID_DIST_SELECT_OTHER_ALL, StructureWindow::OnDistanceSelect)
    EVT_MENU      (MID_REFIT_ALL,                           StructureWindow::OnAlignStructures)
    EVT_MENU_RANGE(MID_EDIT_STYLE, MID_ANNOTATE,            StructureWindow::OnSetStyle)
    EVT_MENU_RANGE(MID_ADD_FAVORITE, MID_FAVORITES_FILE,    StructureWindow::OnEditFavorite)
    EVT_MENU_RANGE(MID_FAVORITES_BEGIN, MID_FAVORITES_END,  StructureWindow::OnSelectFavorite)
    EVT_MENU_RANGE(MID_SHOW_LOG,   MID_SHOW_SEQ_V,          StructureWindow::OnShowWindow)
    EVT_MENU_RANGE(MID_CDD_OVERVIEW, MID_CDD_SHOW_REJECTS,  StructureWindow::OnCDD)
    EVT_MENU      (MID_PREFERENCES,                         StructureWindow::OnPreferences)
    EVT_MENU_RANGE(MID_OPENGL_FONT, MID_SEQUENCE_FONT,      StructureWindow::OnSetFont)
    EVT_MENU_RANGE(MID_PLAY, MID_ANIM_CONTROLS,             StructureWindow::OnAnimate)
    EVT_MENU_RANGE(MID_HELP_COMMANDS, MID_ONLINE_HELP,      StructureWindow::OnHelp)
    EVT_MENU      (MID_ABOUT,                               StructureWindow::OnHelp)
    EVT_TIMER     (MID_ANIMATE,                             StructureWindow::OnAnimationTimer)
    EVT_TIMER     (MID_MESSAGING,                           StructureWindow::OnFileMessagingTimer)
    EVT_MENU      (MID_SEND_SELECTION,                      StructureWindow::OnSendSelection)
END_EVENT_TABLE()

StructureWindow::StructureWindow(const wxString& title, const wxPoint& pos, const wxSize& size) :
    wxFrame(NULL, wxID_HIGHEST + 1, title, pos, size, wxDEFAULT_FRAME_STYLE | wxTHICK_FRAME),
    glCanvas(NULL), cddAnnotateDialog(NULL), cddDescriptionDialog(NULL), cddNotesDialog(NULL),
    cddRefDialog(NULL), cddBookRefDialog(NULL), helpController(NULL), helpConfig(NULL),
    cddOverview(NULL), fileMessagingManager("Cn3D"), fileMessenger(NULL), spinIncrement(3.0)
{
    GlobalMessenger()->AddStructureWindow(this);
    animationTimer.SetOwner(this, MID_ANIMATE);
    SetSizeHints(150, 150); // min size
    SetIcon(wxICON(cn3d));

    commandProcessor = new CommandProcessor(this);

    // File menu
    menuBar = new wxMenuBar;
    fileMenu = new wxMenu;
    fileMenu->Append(MID_OPEN, "&Open\tCtrl+O");
    fileMenu->Append(MID_NETWORK_OPEN, "&Network Load\tCtrl+N");
    fileMenu->Append(MID_SAVE_SAME, "&Save\tCtrl+S");
    fileMenu->Append(MID_SAVE_AS, "Save &As...");
    fileMenu->Append(MID_PNG, "&Export PNG");
    fileMenu->AppendSeparator();
    fileMenu->Append(MID_REFIT_ALL, "&Realign Structures");
    fileMenu->AppendSeparator();
    fileMenu->Append(MID_PREFERENCES, "&Preferences...");
    wxMenu *subMenu = new wxMenu;
    subMenu->Append(MID_OPENGL_FONT, "S&tructure Window");
    subMenu->Append(MID_SEQUENCE_FONT, "Se&quence Windows");
    fileMenu->Append(MID_FONTS, "Set &Fonts...", subMenu);
    fileMenu->AppendSeparator();
    fileMenu->Append(MID_EXIT, "E&xit");
    menuBar->Append(fileMenu, "&File");

    // View menu
    wxMenu *menu = new wxMenu;
    menu->Append(MID_ZOOM_IN, "Zoom &In\tz");
    menu->Append(MID_ZOOM_OUT, "Zoom &Out\tx");
    menu->Append(MID_RESTORE, "&Restore");
    menu->Append(MID_RESET, "Rese&t");
    menu->AppendSeparator();
#ifdef __WXMSW__
    menu->Append(MID_NEXT_FRAME, "&Next Frame\tRight");
    menu->Append(MID_PREV_FRAME, "Pre&vious Frame\tLeft");
    menu->Append(MID_FIRST_FRAME, "&First Frame\tDown");
    menu->Append(MID_LAST_FRAME, "&Last Frame\tUp");
#else
    // other platforms don't like to display these long accelerator names
    menu->Append(MID_NEXT_FRAME, "&Next Frame");
    menu->Append(MID_PREV_FRAME, "Pre&vious Frame");
    menu->Append(MID_FIRST_FRAME, "&First Frame");
    menu->Append(MID_LAST_FRAME, "&Last Frame");
#endif
    menu->Append(MID_ALL_FRAMES, "&All Frames\ta");
    menu->AppendSeparator();
    subMenu = new wxMenu;
    subMenu->Append(MID_PLAY, "&Play Frames\tp", "", true);
    subMenu->Check(MID_PLAY, false);
    subMenu->Append(MID_SPIN, "Spi&n\tn", "", true);
    subMenu->Check(MID_SPIN, false);
    subMenu->Append(MID_STOP, "&Stop\ts", "", true);
    subMenu->Check(MID_STOP, true);
    subMenu->AppendSeparator();
    subMenu->Append(MID_ANIM_CONTROLS, "Set Spee&d");
    menu->Append(MID_ANIMATE, "Ani&mation", subMenu);
    menu->AppendSeparator();
    menu->Append(MID_STEREO, "St&ereo", "", true);
    menuBar->Append(menu, "&View");

    // Show-Hide menu
    menu = new wxMenu;
    menu->Append(MID_SHOW_HIDE, "&Pick Structures...");
    menu->AppendSeparator();
    menu->Append(MID_SHOW_ALL, "Show &Everything\te");
    menu->Append(MID_SHOW_DOMAINS, "Show Aligned &Domains\td");
    menu->Append(MID_SHOW_ALIGNED, "Show &Aligned Residues");
    menu->Append(MID_SHOW_SELECTED_RESIDUES, "Show &Selected Residues");
    menu->Append(MID_SHOW_SELECTED_DOMAINS, "Show Selected Do&mains");
    subMenu = new wxMenu;
    subMenu->Append(MID_SHOW_UNALIGNED_ALL, "Show &All");
    subMenu->Append(MID_SHOW_UNALIGNED_ALN_DOMAIN, "Show in Aligned &Domains");
    menu->Append(MID_SHOW_UNALIGNED, "&Unaligned Residues", subMenu);
    menu->AppendSeparator();
    subMenu = new wxMenu;
    subMenu->Append(MID_DIST_SELECT_RESIDUES, "&Residues Only");
    subMenu->Append(MID_DIST_SELECT_ALL, "&All Molecules");
    subMenu->Append(MID_DIST_SELECT_OTHER_RESIDUES, "&Other Residues");
    subMenu->Append(MID_DIST_SELECT_OTHER_ALL, "Other &Molecules");
    menu->Append(MID_DIST_SELECT, "Select by Dis&tance...", subMenu);
    menu->Append(MID_SELECT_MOLECULE, "Select Molecule...\tm");
    menuBar->Append(menu, "Show/&Hide");

    // Style menu
    menu = new wxMenu;
    menu->Append(MID_EDIT_STYLE, "Edit &Global Style");
    // favorites
    favoritesMenu = new wxMenu;
    favoritesMenu->Append(MID_ADD_FAVORITE, "&Add/Replace");
    favoritesMenu->Append(MID_REMOVE_FAVORITE, "&Remove");
    favoritesMenu->Append(MID_FAVORITES_FILE, "&Change File");
    favoritesMenu->AppendSeparator();
    LoadFavorites();
    SetupFavoritesMenu();
    menu->Append(MID_FAVORITES, "&Favorites", favoritesMenu);
    // rendering shortcuts
    subMenu = new wxMenu;
    subMenu->Append(MID_WORM, "&Worms", "", true);
    subMenu->Append(MID_TUBE, "&Tubes", "", true);
    subMenu->Append(MID_WIRE, "Wir&e", "", true);
    subMenu->Append(MID_BNS, "&Ball and Stick", "", true);
    subMenu->Append(MID_SPACE, "&Space Fill", "", true);
    subMenu->AppendSeparator();
    subMenu->Append(MID_SC_TOGGLE, "&Toggle Sidechains");
    menu->Append(MID_RENDER, "&Rendering Shortcuts", subMenu);
    // coloring shortcuts
    subMenu = new wxMenu;
    subMenu->Append(MID_SECSTRUC, "&Secondary Structure", "", true);
    subMenu->Append(MID_ALIGNED, "&Aligned", "", true);
    wxMenu *subMenu2 = new wxMenu;
    subMenu2->Append(MID_IDENTITY, "I&dentity", "", true);
    subMenu2->Append(MID_VARIETY, "&Variety", "", true);
    subMenu2->Append(MID_WGHT_VAR, "&Weighted Variety", "", true);
    subMenu2->Append(MID_INFO, "&Information Content", "", true);
    subMenu2->Append(MID_FIT, "&Fit", "", true);
    subMenu2->Append(MID_BLOCK_FIT, "&Block Fit", "", true);
    subMenu2->Append(MID_BLOCK_Z_FIT, "&Normalized Block Fit", "", true);
    subMenu2->Append(MID_BLOCK_ROW_FIT, "Block &Row Fit", "", true);
    subMenu->Append(MID_CONS, "Sequence &Conservation", subMenu2);
    subMenu->Append(MID_OBJECT, "&Object", "", true);
    subMenu->Append(MID_DOMAIN, "&Domain", "", true);
    subMenu->Append(MID_MOLECULE, "&Molecule", "", true);
    subMenu->Append(MID_RAINBOW, "&Rainbow", "", true);
    subMenu->Append(MID_HYDROPHOB, "&Hydrophobicity", "", true);
    subMenu->Append(MID_CHARGE, "Char&ge", "", true);
    subMenu->Append(MID_TEMP, "&Temperature", "", true);
    subMenu->Append(MID_ELEMENT, "&Element", "", true);
    menu->Append(MID_COLORS, "&Coloring Shortcuts", subMenu);
    //annotate
    menu->AppendSeparator();
    menu->Append(MID_ANNOTATE, "A&nnotate");
    menuBar->Append(menu, "&Style");

    // Window menu
    windowMenu = new wxMenu;
    windowMenu->Append(MID_SHOW_SEQ_V, "Show &Sequence Viewer");
    windowMenu->Append(MID_SHOW_LOG, "Show Message &Log");
    windowMenu->Append(MID_SHOW_LOG_START, "Show Log on Start&up", "", true);
    bool showLog = false;
    RegistryGetBoolean(REG_CONFIG_SECTION, REG_SHOW_LOG_ON_START, &showLog);
    windowMenu->Check(MID_SHOW_LOG_START, showLog);
    menuBar->Append(windowMenu, "&Window");

    // CDD menu
    bool readOnly;
    RegistryGetBoolean(REG_ADVANCED_SECTION, REG_CDD_ANNOT_READONLY, &readOnly);
    menu = new wxMenu;
    menu->Append(MID_CDD_OVERVIEW, "CDD &Overview");
    menu->AppendSeparator();
    menu->Append(MID_EDIT_CDD_NAME, "Edit &Name");
    menu->Enable(MID_EDIT_CDD_NAME, !readOnly);
    menu->Append(MID_EDIT_CDD_DESCR, "Edit &Description");
    menu->Enable(MID_EDIT_CDD_DESCR, !readOnly);
    menu->Append(MID_EDIT_CDD_NOTES, "Edit No&tes");
    menu->Enable(MID_EDIT_CDD_NOTES, !readOnly);