test_taxtree.cpp

来自「ncbi源码」· C++ 代码 · 共 308 行

/*
 * ===========================================================================
 * PRODUCTION $Log: test_taxtree.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 21:13:30  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: test_taxtree.cpp,v 1000.2 2004/06/01 21:13:30 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:  Mike DiCuccio
 *
 * File Description:
 *
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <gui/utils/fltk_utils.hpp>
#include <gui/utils/message_box.hpp>
#include <gui/widgets/fl/status_bar_ex.hpp>
#include <gui/widgets/tax_tree/tax_tree.hpp>
#include <gui/widgets/tax_tree/tax_tree_ds.hpp>

#include <objects/entrez2/entrez2_client.hpp>
#include <objects/entrez2/Entrez2_eval_boolean.hpp>
#include <objects/entrez2/Entrez2_boolean_exp.hpp>
#include <objects/entrez2/Entrez2_boolean_element.hpp>
#include <objects/entrez2/Entrez2_boolean_reply.hpp>
#include <objects/entrez2/Entrez2_id_list.hpp>

#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>

#include <gui/utils/dialog.hpp>
#include <FL/Fl.H>
#include <FL/Fl_Double_Window.H>
#include <FL/Fl_Menu_Bar.H>
#include <FL/Fl_Group.H>
#include <FL/Fl_Box.H>
#include <FL/Fl_Input.H>
#include <FL/Fl_Choice.H>

// #include "entrez2_ds.hpp"


BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);

#include "test_taxtree_.cpp"


CTaxTreeTestDlg::CTaxTreeTestDlg()
{
    m_Window.reset(x_CreateWindow());
    m_Tree->SetReporter(m_StatusBar);
}


void CTaxTreeTestDlg::x_OnSubmitQuery()
{
    CFltkCursorGuard WAIT_GUARD;
    CStatusBarGuard LOCK(*m_StatusBar, "Submitting query...");

    string query = m_Query->value();
    if (query.empty()) {
        return;
    }

    //
    // prepare the Entrez query
    //
    CEntrez2_eval_boolean req;
    req.SetReturn_UIDs(true);
    CEntrez2_boolean_exp& exp = req.SetQuery();

    // set the database we're querying
    exp.SetDb().Set("nucleotide");

    // set the query
    CRef<CEntrez2_boolean_element> elem(new CEntrez2_boolean_element());
    elem->SetStr(query);
    exp.SetExp().push_back(elem);

    // set some limits - if num > 0, we assume it's correct
	CRef<CEntrez2_boolean_reply> query_res;
    try {
        // now, submit our query.  this gets us the UIDs we want
        query_res = x_GetClient().AskEval_boolean(req);

        const CEntrez2_id_list& ids = query_res->GetUids();
        vector<int> uids;
        uids.reserve(ids.GetNum());

        _TRACE("query: " << query << " UIDs: " << ids.GetNum());
        CTaxTreeDS_ObjMgr::TUidVec seq_ids;
        seq_ids.reserve(uids.size());

        CEntrez2_id_list::TConstUidIterator iter = ids.GetConstUidIterator();
        for (size_t i = 0;  i < ids.GetNum();  ++i, ++iter) {
            uids.push_back(*iter);

            CRef<CSeq_id> id(new CSeq_id());
            id->SetGi(*iter);
            seq_ids.push_back(id);
        }

        if ( !m_ObjMgr ) {
            m_ObjMgr.Reset(new CObjectManager());
            m_ObjMgr->RegisterDataLoader(*new CGBDataLoader(),
                                         CObjectManager::eDefault);
            m_Scope.Reset(new CScope(*m_ObjMgr));
            m_Scope->AddDefaults();
        }

        m_DataSource.Reset(new CTaxTreeDS_ObjMgr(*m_Scope, seq_ids));

        // m_DataSource.Reset(new CTaxTreeDS_Entrez2(uids));

        m_Tree->SetDataSource(*m_DataSource);
        // m_Tree->SetGis(uids);
    }
    catch (CException& e) {
        LOG_POST(Info << "exception: " << e.what());
        LOG_POST(Info << "query failed; reconnecting...");
    }
}


void CTaxTreeTestDlg::x_OnShowRelatedSeqs()
{
    CTaxTreeDataSource::TUidVec gis;
    m_Tree->GetSelectedUids(gis);
    if (gis.size() != 1) {
        NcbiMessageBox("Please select one and only one sequence");
        return;
    }

    CStatusBarGuard LOCK(*m_StatusBar, "Submitting query...");

    int gi = gis.front();
    vector<int> gis_n;
    x_GetClient().GetNeighbors(gi, "nucleotide", "nucleotide_nucleotide",
                               gis_n);

    m_StatusBar->SetMessage("Found " +
                            NStr::IntToString(gis_n.size()) +
                            " related sequences");

    // m_Tree->SetGis(gis);
}


CEntrez2Client& CTaxTreeTestDlg::x_GetClient()
{
    if ( !m_Client ) {
        m_Client.Reset(new CEntrez2Client());
    }
    return *m_Client;
}





class CTestTreeApp : public CNcbiApplication
{
private:
    virtual void Init(void);
    virtual int  Run(void);
    virtual void Exit(void);
};


void CTestTreeApp::Init(void)
{
    // Create command-line argument descriptions class
    auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);

    // Specify USAGE context
    arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
                              "CTreeBrowser demo program");


    // Setup arg.descriptions for this application
    SetupArgDescriptions(arg_desc.release());
}


int CTestTreeApp::Run(void)
{
    // Get arguments
    CArgs args = GetArgs();

    char *argv[1];
    argv[0] = "app";
    CTaxTreeTestDlg window;
    window.Show(1, argv);

    return 0;
}


/////////////////////////////////////////////////////////////////////////////
//  Cleanup


void CTestTreeApp::Exit(void)
{
    SetDiagStream(0);
}

/////////////////////////////////////////////////////////////////////////////
//  MAIN

END_NCBI_SCOPE
USING_SCOPE(ncbi);

int main(int argc, const char* argv[])
{
    // Execute main application function
    return CTestTreeApp().AppMain(argc, argv, 0, eDS_Default, 0);
}


/*
 * ===========================================================================
 * $Log: test_taxtree.cpp,v $
 * Revision 1000.2  2004/06/01 21:13:30  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 *
 * Revision 1.9  2004/05/28 19:27:51  dicuccio
 * Compilation fixes
 *
 * Revision 1.8  2004/05/21 22:27:55  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.7  2004/05/13 17:31:46  dicuccio
 * Renamed data source file
 *
 * Revision 1.6  2004/04/20 20:18:37  gorelenk
 * Fixed error in implementations of
 * CTaxTreeTestDlg::x_OnShowRelatedSeqs and
 * CTaxTreeTestDlg::x_OnSubmitQuery .
 *
 * Revision 1.5  2004/01/28 01:08:11  ucko
 * Use CTaxTreeDS_ObjMgr rather than CTaxTreeDS_Entrez2, which isn't
 * (yet) in the tree.
 *
 * Revision 1.4  2004/01/27 18:49:26  dicuccio
 * Restored functionality
 *
 * Revision 1.3  2003/12/23 15:39:19  dicuccio
 * Altered the data source - expose an ITreeIterator; the widget no longer
 * directly creates a CTaxon1 class.  Chaned storage notion from 'gi' to 'uid'
 *
 * Revision 1.2  2003/12/22 22:00:19  ucko
 * Don't try to call SetGi, since it doesn't seem to exist yet....
 *
 * Revision 1.1  2003/12/22 19:43:01  dicuccio
 * Initial revision
 *
 * Revision 1.1  2003/12/09 19:08:16  dicuccio
 * Moved test_treebrowser from widgets/FLU/demo to here
 *
 * Revision 1.1  2003/12/09 15:51:31  dicuccio
 * Deprecated Fl_Toggle_Tree - replaced with Flu_Tree_Browser.  Added CTreeBrowser
 * as a standard tree interface
 *
 * Revision 1.2  2003/08/21 12:06:42  dicuccio
 * Many bug fixes - Fl_Toggle_Tree is nearly completed.  Reimplemented correct
 * clipping of the widget to its extent.  Added scroll bar (not yet working).
 * Removed dead code
 *
 * Revision 1.1  2003/07/30 12:25:25  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */