cn3d_app.cpp

ncbi源码

    SetDiagPostLevel(eDiag_Info);
    if (!okay) {
        ERRORMSG("This file is not a valid Biostruc");
        return NULL;
    }

    // remove all but desired model coordinates
    CRef < CBiostruc_model > desiredModel;
    CBiostruc::TModel::const_iterator m, me = biostruc->GetModel().end();
    for (m=biostruc->GetModel().begin(); m!=me; ++m) {
        if ((*m)->GetType() == model) {
            desiredModel = *m;
            break;
        }
    }
    if (desiredModel.Empty()) {
        ERRORMSG("Ack! There's no appropriate model in this Biostruc");
        return NULL;
    }
    biostruc->ResetModel();
    biostruc->SetModel().push_back(desiredModel);

    // package Biostruc inside a mime object
    CRef < CNcbi_mime_asn1 > mime(new CNcbi_mime_asn1());
    CRef < CBiostruc_seq > strucseq(new CBiostruc_seq());
    mime->SetStrucseq(*strucseq);
    strucseq->SetStructure(*biostruc);

    // get list of gi's to import
    vector < int > gis;
    CBiostruc_graph::TMolecule_graphs::const_iterator g,
        ge = biostruc->GetChemical_graph().GetMolecule_graphs().end();
    for (g=biostruc->GetChemical_graph().GetMolecule_graphs().begin(); g!=ge; ++g) {
        if ((*g)->IsSetSeq_id() && (*g)->GetSeq_id().IsGi())
            gis.push_back((*g)->GetSeq_id().GetGi());
    }
    if (gis.size() == 0) {
        ERRORMSG("Can't find any sequence gi identifiers in this Biostruc");
        return NULL;
    }

    // fetch sequences and store in mime
    CRef < CSeq_entry > seqs(new CSeq_entry());
    strucseq->SetSequences().push_back(seqs);
    CRef < CBioseq_set > seqset(new CBioseq_set());
    seqs->SetSet(*seqset);
    for (int i=0; i<gis.size(); ++i) {
        wxString id;
        id.Printf("%i", gis[i]);
        CRef < CBioseq > bioseq = FetchSequenceViaHTTP(id.c_str());
        if (bioseq.NotEmpty()) {
            CRef < CSeq_entry > seqentry(new CSeq_entry());
            seqentry->SetSeq(*bioseq);
            seqset->SetSeq_set().push_back(seqentry);
        } else {
            ERRORMSG("Failed to retrieve all Bioseqs");
            return NULL;
        }
    }

    return mime.Release();
}

bool Cn3DApp::OnInit(void)
{
    INFOMSG("Welcome to Cn3D " << CN3D_VERSION_STRING << "!");
    INFOMSG("built " << __DATE__ << " with wxWidgets " << wxVERSION_NUM_DOT_STRING);

    // set up command line parser
    static const wxCmdLineEntryDesc cmdLineDesc[] = {
        { wxCMD_LINE_SWITCH, "h", "help", "show this help message",
            wxCMD_LINE_VAL_NONE, wxCMD_LINE_OPTION_HELP },
        { wxCMD_LINE_SWITCH, "r", "readonly", "message file is read-only",
            wxCMD_LINE_VAL_NONE, wxCMD_LINE_PARAM_OPTIONAL },
        { wxCMD_LINE_SWITCH, "i", "imports", "show imports window on startup",
            wxCMD_LINE_VAL_NONE, wxCMD_LINE_PARAM_OPTIONAL },
        { wxCMD_LINE_SWITCH, "n", "noalign", "do not show alignment window on startup",
            wxCMD_LINE_VAL_NONE, wxCMD_LINE_PARAM_OPTIONAL },
        { wxCMD_LINE_SWITCH, "f", "force", "force saves to same file",
            wxCMD_LINE_VAL_NONE, wxCMD_LINE_PARAM_OPTIONAL },
        { wxCMD_LINE_OPTION, "m", "message", "message file",
            wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL | wxCMD_LINE_NEEDS_SEPARATOR },
        { wxCMD_LINE_OPTION, "a", "targetapp", "messaging target application name",
            wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL | wxCMD_LINE_NEEDS_SEPARATOR },
        { wxCMD_LINE_OPTION, "o", "model", "model choice: alpha, single, or PDB",
            wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL | wxCMD_LINE_NEEDS_SEPARATOR },
        { wxCMD_LINE_OPTION, "d", "id", "MMDB/PDB ID to load via network",
            wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL | wxCMD_LINE_NEEDS_SEPARATOR },
        { wxCMD_LINE_PARAM, NULL, NULL, "input file",
            wxCMD_LINE_VAL_STRING, wxCMD_LINE_PARAM_OPTIONAL},
        { wxCMD_LINE_NONE }
    };
    commandLine.SetSwitchChars("-");
    commandLine.SetDesc(cmdLineDesc);
    commandLine.SetCmdLine(argc, argv);
    switch (commandLine.Parse()) {
        case 0: TRACEMSG("command line parsed successfully"); break;
        default: return false;  // exit upon either help or syntax error
    }

    // help system loads from zip file
    wxFileSystem::AddHandler(new wxZipFSHandler);

    // set up working directories
    workingDir = wxGetCwd().c_str();
#ifdef __WXGTK__
    if (getenv("CN3D_HOME") != NULL)
        programDir = getenv("CN3D_HOME");
    else
#endif
    if (wxIsAbsolutePath(argv[0]))
        programDir = wxPathOnly(argv[0]).c_str();
    else if (wxPathOnly(argv[0]) == "")
        programDir = workingDir;
    else
        programDir = workingDir + wxFILE_SEP_PATH + wxPathOnly(argv[0]).c_str();
    workingDir = workingDir + wxFILE_SEP_PATH;
    programDir = programDir + wxFILE_SEP_PATH;

    // find or create preferences folder
    wxString localDir;
    wxSplitPath((wxFileConfig::GetLocalFileName("unused")).c_str(), &localDir, NULL, NULL);
    wxString prefsDirLocal = localDir + wxFILE_SEP_PATH + "Cn3D_User";
    wxString prefsDirProg = wxString(programDir.c_str()) + wxFILE_SEP_PATH + "Cn3D_User";
    if (wxDirExists(prefsDirLocal))
        prefsDir = prefsDirLocal.c_str();
    else if (wxDirExists(prefsDirProg))
        prefsDir = prefsDirProg.c_str();
    else {
        // try to create the folder
        if (wxMkdir(prefsDirLocal) && wxDirExists(prefsDirLocal))
            prefsDir = prefsDirLocal.c_str();
        else if (wxMkdir(prefsDirProg) && wxDirExists(prefsDirProg))
            prefsDir = prefsDirProg.c_str();
    }
    if (prefsDir.size() == 0)
        WARNINGMSG("Can't create Cn3D_User folder at either:"
            << "\n    " << prefsDirLocal
            << "\nor  " << prefsDirProg);
    else
        prefsDir += wxFILE_SEP_PATH;

    // set data dir, and register the path in C toolkit registry (mainly for BLAST code)
#ifdef __WXMAC__
    dataDir = programDir + "../Resources/data/";
#else
    dataDir = programDir + "data" + wxFILE_SEP_PATH;
#endif
    Nlm_TransientSetAppParam("ncbi", "ncbi", "data", dataDir.c_str());

    INFOMSG("working dir: " << workingDir.c_str());
    INFOMSG("program dir: " << programDir.c_str());
    INFOMSG("data dir: " << dataDir.c_str());
    INFOMSG("prefs dir: " << prefsDir.c_str());

    // read dictionary
    wxString dictFile = wxString(dataDir.c_str()) + "bstdt.val";
    LoadStandardDictionary(dictFile.c_str());

    // set up registry and favorite styles (must be done before structure window creation)
    InitRegistry();

    // create the main frame window - must be first window created by the app
    structureWindow = new StructureWindow(
        wxString("Cn3D ") + CN3D_VERSION_STRING, wxPoint(0,0), wxSize(500,500));
    SetTopWindow(structureWindow);
    SetExitOnFrameDelete(true); // exit app when structure window is closed
    topWindow = structureWindow;

    // show log if set to do so
    bool showLog = false;
    RegistryGetBoolean(REG_CONFIG_SECTION, REG_SHOW_LOG_ON_START, &showLog);
    if (showLog) RaiseLogWindow();

    // get model type from -o
    EModel_type model = eModel_type_other;
    wxString modelStr;
    if (commandLine.Found("o", &modelStr)) {
        if (modelStr == "alpha")
            model = eModel_type_ncbi_backbone;
        else if (modelStr == "single")
            model = eModel_type_ncbi_all_atom;
        else if (modelStr == "PDB")
            model = eModel_type_pdb_model;
        else
            ERRORMSG("Model type (-o) must be one of alpha|single|PDB");
    }

    // load file given on command line
    if (commandLine.GetParamCount() == 1) {
        wxString filename = commandLine.GetParam(0).c_str();
        INFOMSG("command line file: " << filename.c_str());
        // if -o is present, assume param is a Biostruc file
        if (model != eModel_type_other) {   // -o present
            CNcbi_mime_asn1 *mime = CreateMimeFromBiostruc(filename, model);
            if (mime)
                structureWindow->LoadData(NULL, commandLine.Found("f"), mime);
        } else {
            structureWindow->LoadData(filename.c_str(), commandLine.Found("f"));
        }
    }

    // if no file passed but there is -o, see if there's a -d parameter (MMDB/PDB ID to fetch)
    else if (model != eModel_type_other) {  // -o present
        wxString id;
        if (commandLine.Found("d", &id)) {
            CNcbi_mime_asn1 *mime = LoadStructureViaCache(id.c_str(), model);
            if (mime)
                structureWindow->LoadData(NULL, commandLine.Found("f"), mime);
        } else {
            ERRORMSG("-o requires either -d or Biostruc file name");
        }
    }

    // if no structure loaded, show the logo
    if (!structureWindow->glCanvas->structureSet) {
        structureWindow->glCanvas->renderer->AttachStructureSet(NULL);
        structureWindow->glCanvas->Refresh(false);
    }

    // set up messaging file communication
    wxString messageFilename;
    if (commandLine.Found("m", &messageFilename)) {
        wxString messageApp;
        if (!commandLine.Found("a", &messageApp))
            messageApp = "Listener";
        structureWindow->SetupFileMessenger(
            messageFilename.c_str(), messageApp.c_str(), commandLine.Found("r"));
    }

    // optionally show alignment window
    if (!commandLine.Found("n") && structureWindow->glCanvas->structureSet)
        structureWindow->glCanvas->structureSet->alignmentManager->ShowSequenceViewer();

    // optionally open imports window, but only if any imports present
    if (commandLine.Found("i") && structureWindow->glCanvas->structureSet &&
            structureWindow->glCanvas->structureSet->alignmentManager->NUpdates() > 0)
        structureWindow->glCanvas->structureSet->alignmentManager->ShowUpdateWindow();

    // give structure window initial focus
    structureWindow->Raise();
    structureWindow->SetFocus();

    return true;
}

int Cn3DApp::OnExit(void)
{
    SetDiagHandler(NULL, NULL, NULL);
    SetDiagStream(&cout);

    // save registry
    SaveRegistry();

    // remove dictionary
    DeleteStandardDictionary();

    // destroy log
    if (logFrame) logFrame->Destroy();

    return 0;
}

void Cn3DApp::OnIdle(wxIdleEvent& event)
{
    // process pending redraws
    GlobalMessenger()->ProcessRedraws();

    // call base class OnIdle to continue processing any other system idle-time stuff
    wxApp::OnIdle(event);
}

#ifdef __WXMAC__
// special handler for open file apple event
void Cn3DApp::MacOpenFile(const wxString& filename)
{
    if (filename.size() > 0) {
        INFOMSG("apple open event file: " << filename);
        structureWindow->LoadData(filename, false);
    }
}
#endif

END_SCOPE(Cn3D)

/*
* ---------------------------------------------------------------------------
* $Log: cn3d_app.cpp,v $
* Revision 1000.3  2004/06/01 18:28:05  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.21
*
* Revision 1.21  2004/05/22 15:33:41  thiessen
* fix scrolling bug in log frame
*
* Revision 1.20  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.19  2004/04/19 19:36:07  thiessen
* fix frame switch bug when no structures present
*
* Revision 1.18  2004/03/15 18:19:23  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.17  2004/03/10 23:15:51  thiessen
* add ability to turn off/on error dialogs; group block aligner errors in message log
*
* Revision 1.16  2004/02/19 17:04:47  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.15  2004/01/28 19:27:54  thiessen
* add input asn stream verification
*
* Revision 1.14  2004/01/17 02:11:27  thiessen
* mac fix
*
* Revision 1.13  2004/01/17 01:47:26  thiessen
* add network load
*
* Revision 1.12  2004/01/17 00:17:28  thiessen
* add Biostruc and network structure load
*
* Revision 1.11  2004/01/08 15:31:02  thiessen
* remove hard-coded CDTree references in messaging; add Cn3DTerminated message upon exit
*
* Revision 1.10  2003/12/03 15:46:36  thiessen
* adjust so spin increment is accurate
*
* Revision 1.9  2003/12/03 15:07:09  thiessen
* add more sophisticated animation controls
*
* Revision 1.8  2003/11/15 16:08:35  thiessen
* add stereo
*
* Revision 1.7  2003/10/13 14:16:31  thiessen
* add -n option to not show alignment window
*
* Revision 1.6  2003/10/13 13:23:31  thiessen
* add -i option to show import window
*
* Revision 1.5  2003/07/17 18:47:01  thiessen
* add -f option to force save to same file
*
* Revision 1.4  2003/06/21 20:54:03  thiessen
* explicitly show bottom of log when new text appended
*
* Revision 1.3  2003/05/29 14:34:19  thiessen
* force serial object verification
*
* Revision 1.2  2003/03/13 16:57:14  thiessen
* fix favorites load/save problem
*
* Revision 1.1  2003/03/13 14:26:18  thiessen
* add file_messaging module; split cn3d_main_wxwin into cn3d_app, cn3d_glcanvas, structure_window, cn3d_tools
*
*/