cn3d_app.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: cn3d_app.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 18:28:05  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.21
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: cn3d_app.cpp,v 1000.3 2004/06/01 18:28:05 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:
*       log and application 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 <ctools/ctools.h>
#include <serial/objostr.hpp>

#include <objects/mmdb1/Biostruc.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/ncbimime/Biostruc_seq.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/mmdb2/Biostruc_model.hpp>
#include <objects/mmdb2/Model_type.hpp>
#include <objects/mmdb1/Biostruc_graph.hpp>
#include <objects/mmdb1/Molecule_graph.hpp>
#include <objects/seqloc/Seq_id.hpp>

#include <algorithm>
#include <vector>

#ifdef __WXMSW__
#include <windows.h>
#include <wx/msw/winundef.h>
#endif
#include <wx/wx.h>
#include <wx/filesys.h>
#include <wx/fs_zip.h>

#include "asn_reader.hpp"
#include "cn3d_app.hpp"
#include "structure_window.hpp"
#include "cn3d_tools.hpp"
#include "structure_set.hpp"
#include "chemical_graph.hpp"
#include "cn3d_glcanvas.hpp"
#include "opengl_renderer.hpp"
#include "messenger.hpp"
#include "alignment_manager.hpp"
#include "cn3d_cache.hpp"

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

#include <ncbi.h>
#include <ncbienv.h>

USING_NCBI_SCOPE;
USING_SCOPE(objects);


// `Main program' equivalent
IMPLEMENT_APP(Cn3D::Cn3DApp)


BEGIN_SCOPE(Cn3D)

// global strings for various directories - will include trailing path separator character
static string
    workingDir,     // current working directory
    programDir,     // directory where Cn3D executable lives
    dataDir,        // 'data' directory with external data files
    prefsDir;       // application preferences directory
const string& GetWorkingDir(void) { return workingDir; }
const string& GetProgramDir(void) { return programDir; }
const string& GetDataDir(void) { return dataDir; }
const string& GetPrefsDir(void) { return prefsDir; }

// top-level window (the main structure window)
static wxFrame *topWindow = NULL;
wxFrame * GlobalTopWindow(void) { return topWindow; }


// Set the NCBI diagnostic streams to go to this method, which then pastes them
// into a wxWindow. This log window can be closed anytime, but will be hidden,
// not destroyed. More serious errors will bring up a dialog, so that the user
// will get a chance to see the error before the program halts upon a fatal error.

class MsgFrame;

static MsgFrame *logFrame = NULL;
static list < string > backLog;

class MsgFrame : public wxFrame
{
public:
    wxTextCtrl *logText;
    int totalChars;
    MsgFrame(const wxString& title,
        const wxPoint& pos = wxDefaultPosition, const wxSize& size = wxDefaultSize) :
        wxFrame(GlobalTopWindow(), wxID_HIGHEST + 5, title, pos, size,
            wxDEFAULT_FRAME_STYLE
#if defined(__WXMSW__)
                | wxFRAME_TOOL_WINDOW | wxFRAME_NO_TASKBAR | wxFRAME_FLOAT_ON_PARENT
#endif
            )
    {
        totalChars = 0;
        SetIcon(wxICON(cn3d));
    }
    ~MsgFrame(void) { logFrame = NULL; logText = NULL; }
private:
    // need to define a custom close window handler, so that window isn't actually destroyed,
    // just hidden when user closes it with system close button
    void OnCloseWindow(wxCloseEvent& event);
    DECLARE_EVENT_TABLE()
};

BEGIN_EVENT_TABLE(MsgFrame, wxFrame)
    EVT_CLOSE(MsgFrame::OnCloseWindow)
END_EVENT_TABLE()

void MsgFrame::OnCloseWindow(wxCloseEvent& event)
{
    if (event.CanVeto()) {
        Show(false);
        event.Veto();
    } else {
        Destroy();
        logFrame = NULL;
    }
}

static bool dialogSevereErrors = true;
void SetDialogSevereErrors(bool status)
{
    dialogSevereErrors = status;
}

void DisplayDiagnostic(const SDiagMessage& diagMsg)
{
    string errMsg;
    diagMsg.Write(errMsg);

    // severe errors get a special error dialog
    if (diagMsg.m_Severity >= eDiag_Error && diagMsg.m_Severity != eDiag_Trace && dialogSevereErrors) {
        wxMessageDialog dlg(NULL, errMsg.c_str(), "Severe Error!", wxOK | wxCENTRE | wxICON_EXCLAMATION);
        dlg.ShowModal();
    }

    // info messages and less severe errors get added to the log
    else {
        if (logFrame) {
            // delete top of log if too big
            if (logFrame->totalChars + errMsg.size() > 100000) {
                logFrame->logText->Clear();
                logFrame->totalChars = 0;
            }
            logFrame->logText->SetInsertionPoint(logFrame->logText->GetLastPosition());
            *(logFrame->logText) << errMsg.c_str();
            logFrame->totalChars += errMsg.size();
        } else {
            // if message window doesn't exist yet, store messages until later
            backLog.push_back(errMsg.c_str());
        }
    }
}

void RaiseLogWindow(void)
{
    if (!logFrame) {
        logFrame = new MsgFrame("Cn3D Message Log", wxPoint(500, 0), wxSize(500, 500));
#ifdef __WXMAC__
        // make empty menu for this window
        wxMenuBar *menuBar = new wxMenuBar;
        logFrame->SetMenuBar(menuBar);
#endif
        logFrame->SetSizeHints(150, 100);
        logFrame->logText = new wxTextCtrl(logFrame, -1, "",
            wxPoint(0,0), logFrame->GetClientSize(), wxTE_RICH | wxTE_MULTILINE | wxTE_READONLY | wxHSCROLL);
        // display any messages received before window created
        while (backLog.size() > 0) {
            *(logFrame->logText) << backLog.front().c_str();
            logFrame->totalChars += backLog.front().size();
            backLog.erase(backLog.begin());
        }
    }
    logFrame->logText->ShowPosition(logFrame->logText->GetLastPosition());
    logFrame->Show(true);
#if defined(__WXMSW__)
    if (logFrame->IsIconized()) logFrame->Maximize(false);
#endif
    logFrame->Raise();
}


BEGIN_EVENT_TABLE(Cn3DApp, wxGLApp)
    EVT_IDLE(Cn3DApp::OnIdle)
END_EVENT_TABLE()

Cn3DApp::Cn3DApp() : wxGLApp()
{
    // setup the diagnostic stream
    SetDiagHandler(DisplayDiagnostic, NULL, NULL);
    SetDiagPostLevel(eDiag_Info);   // report all messages
    SetDiagTrace(eDT_Default);      // trace messages only when DIAG_TRACE env. var. is set
#ifdef _DEBUG
    SetDiagPostFlag(eDPF_File);
    SetDiagPostFlag(eDPF_Line);
#else
    UnsetDiagTraceFlag(eDPF_File);
    UnsetDiagTraceFlag(eDPF_Line);
#endif
    SetupCToolkitErrPost(); // reroute C-toolkit err messages to C++ err streams

    // C++ object verification
    CSerialObject::SetVerifyDataGlobal(eSerialVerifyData_Always);
    CObjectIStream::SetVerifyDataGlobal(eSerialVerifyData_Always);
    CObjectOStream::SetVerifyDataGlobal(eSerialVerifyData_Always);

    if (!InitGLVisual(NULL))
        FATALMSG("InitGLVisual failed");
}

void Cn3DApp::InitRegistry(void)
{
    // first set up defaults, then override any/all with stuff from registry file

    // default log window startup
    RegistrySetBoolean(REG_CONFIG_SECTION, REG_SHOW_LOG_ON_START, false);
    RegistrySetString(REG_CONFIG_SECTION, REG_FAVORITES_NAME, NO_FAVORITES_FILE);

    // default animation controls
    RegistrySetInteger(REG_ANIMATION_SECTION, REG_SPIN_DELAY, 50);
    RegistrySetDouble(REG_ANIMATION_SECTION, REG_SPIN_INCREMENT, 2.0),
    RegistrySetInteger(REG_ANIMATION_SECTION, REG_FRAME_DELAY, 500);

    // default quality settings
    RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_ATOM_SLICES, 10);
    RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_ATOM_STACKS, 8);
    RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_BOND_SIDES, 6);
    RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_WORM_SIDES, 6);
    RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_WORM_SEGMENTS, 6);
    RegistrySetInteger(REG_QUALITY_SECTION, REG_QUALITY_HELIX_SIDES, 12);
    RegistrySetBoolean(REG_QUALITY_SECTION, REG_HIGHLIGHTS_ON, true);
    RegistrySetString(REG_QUALITY_SECTION, REG_PROJECTION_TYPE, "Perspective");

    // default font for OpenGL (structure window)
    wxFont *font = wxFont::New(
#if defined(__WXMSW__)
        12,
#elif defined(__WXGTK__)
        14,
#elif defined(__WXMAC__)
        14,
#endif
        wxSWISS, wxNORMAL, wxBOLD, false);
    if (font && font->Ok())
        RegistrySetString(REG_OPENGL_FONT_SECTION, REG_FONT_NATIVE_FONT_INFO,
			font->GetNativeFontInfoDesc().c_str());
    else
        ERRORMSG("Can't create default structure window font");
    if (font) delete font;

    // default font for sequence viewers
    font = wxFont::New(
#if defined(__WXMSW__)
        10,
#elif defined(__WXGTK__)
        14,
#elif defined(__WXMAC__)
        12,
#endif
        wxROMAN, wxNORMAL, wxNORMAL, false);
    if (font && font->Ok())
        RegistrySetString(REG_SEQUENCE_FONT_SECTION, REG_FONT_NATIVE_FONT_INFO,
			font->GetNativeFontInfoDesc().c_str());
    else
        ERRORMSG("Can't create default sequence window font");
    if (font) delete font;

    // default cache settings
    RegistrySetBoolean(REG_CACHE_SECTION, REG_CACHE_ENABLED, true);
    if (GetPrefsDir().size() > 0)
        RegistrySetString(REG_CACHE_SECTION, REG_CACHE_FOLDER, GetPrefsDir() + "cache");
    else
        RegistrySetString(REG_CACHE_SECTION, REG_CACHE_FOLDER, GetProgramDir() + "cache");
    RegistrySetInteger(REG_CACHE_SECTION, REG_CACHE_MAX_SIZE, 25);

    // default advanced options
    RegistrySetBoolean(REG_ADVANCED_SECTION, REG_CDD_ANNOT_READONLY, true);
#ifdef __WXGTK__
    RegistrySetString(REG_ADVANCED_SECTION, REG_BROWSER_LAUNCH,
        // for launching netscape in a separate window
        "( netscape -noraise -remote 'openURL(<URL>,new-window)' || netscape '<URL>' ) >/dev/null 2>&1 &"
        // for launching netscape in an existing window
//        "( netscape -raise -remote 'openURL(<URL>)' || netscape '<URL>' ) >/dev/null 2>&1 &"
    );
#endif
    RegistrySetInteger(REG_ADVANCED_SECTION, REG_MAX_N_STRUCTS, 10);
    RegistrySetInteger(REG_ADVANCED_SECTION, REG_FOOTPRINT_RES, 15);

    // default stereo options
    RegistrySetDouble(REG_ADVANCED_SECTION, REG_STEREO_SEPARATION, 5.0);
    RegistrySetBoolean(REG_ADVANCED_SECTION, REG_PROXIMAL_STEREO, true);

    // load program registry - overriding defaults if present
    LoadRegistry();
}

static CNcbi_mime_asn1 * CreateMimeFromBiostruc(const wxString& filename, EModel_type model)
{
    // read Biostruc
    CRef < CBiostruc > biostruc(new CBiostruc());
    string err;
    SetDiagPostLevel(eDiag_Fatal); // ignore all but Fatal errors while reading data
    bool okay = (ReadASNFromFile(filename.c_str(), biostruc.GetPointer(), true, &err) ||
                 ReadASNFromFile(filename.c_str(), biostruc.GetPointer(), false, &err));