test_obj_convert.cpp

来自「ncbi源码」· C++ 代码 · 共 348 行

/*
 * ===========================================================================
 * PRODUCTION $Log: test_obj_convert.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 20:45:05  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: test_obj_convert.cpp,v 1000.1 2004/06/01 20:45:05 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:  Mike DiCuccio
 *
 * File Description:
 *    Test application for plugins
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbireg.hpp>

#include <gui/core/idocument.hpp>
#include <gui/core/obj_convert.hpp>
#include <gui/core/plugin_arg_dialog.hpp>
#include <gui/core/plugin_exception.hpp>
#include <gui/core/selection_buffer.hpp>
#include <gui/plugin/PluginArgSet.hpp>
#include <gui/objutils/utils.hpp>

#include <objects/seq/Bioseq.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>

USING_NCBI_SCOPE;
USING_SCOPE(objects);


//
// a test exception class
//
class CObjConvertTestException : EXCEPTION_VIRTUAL_BASE public CException
{
public:
    // Enumerated list of document management errors
    enum EErrCode {
        eTestFailed
    };

    // Translate the specific error code into a string representations of
    // that error code.
    virtual const char* GetErrCodeString(void) const
    {
        switch (GetErrCode()) {
        case eTestFailed:   return "eTestFailed";
        default:            return CException::GetErrCodeString();
        }
    }

    NCBI_EXCEPTION_DEFAULT(CObjConvertTestException, CException);
};


class CObjConvertTestApp : public CNcbiApplication
{
public:
    CObjConvertTestApp();

private:
    virtual void Init(void);
    virtual int  Run(void);
    virtual void Exit(void);

    //
    // internal testing routines
    //

    void x_TestObjConvert();
    void x_TestTime();
};


CObjConvertTestApp::CObjConvertTestApp()
{
}


/////////////////////////////////////////////////////////////////////////////
//  Init test for all different types of arguments


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

    // Specify USAGE context
    arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
                              "Object conversion test application");

    arg_desc->AddKey("acc", "Accession", "Accession to test",
                     CArgDescriptions::eString);

    arg_desc->AddDefaultKey("iters", "Iterations", "Iterations to test",
                     CArgDescriptions::eInteger,
#ifdef _DEBUG
                     "1"
#else
                     "10"
#endif
                     );

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

}


int CObjConvertTestApp::Run(void)
{
    CArgs args = GetArgs();

    const size_t MAX_ITERS = args["iters"].AsInteger();
    string acc = args["acc"].AsString();

    CRef<CSeq_id> id(new CSeq_id(acc));
    if (id->Which() == CSeq_id::e_not_set) {
        LOG_POST(Fatal << "don't understand accession " << acc);
    }

    CRef<CObjectManager> obj_mgr(new CObjectManager());
    obj_mgr->RegisterDataLoader(*new CGBDataLoader(),
                                CObjectManager::eDefault);
    CRef<CScope> scope(new CScope(*obj_mgr));
    scope->AddDefaults();

    CRef<CSeq_loc> loc(new CSeq_loc());
    loc->SetWhole(*id);

    // pass 1: load all features into memory and index
    cout << "priming...";
    cout.flush();

    SAnnotSelector sel = CSeqUtils::GetAnnotSelector();
    {{
         CFeat_CI feat_iter(*scope, *loc, sel);
         cout << "done." << endl;
         cout << "found " << feat_iter.GetSize() << " features" << endl;
     }}

    //
    // time raw use of CFeat_CI
    //
    cout << "timing CFeat_CI...";
    cout.flush();

    CStopWatch sw;
    sw.Start();

    {{
         size_t count = 0;
         for (size_t iters = 0;  iters < MAX_ITERS;  ++iters) {
             CFeat_CI feat_iter(*scope, *loc, sel);
             for ( ;  feat_iter;  ++feat_iter) {
                 ++count;
             }
         }
     }}
    double e = sw.Elapsed();

    cout << "done" << endl;
    cout << MAX_ITERS << " iterations in " << e << " seconds = "
        << e / MAX_ITERS << " secs/iter" << endl;

    //
    // time direct use of CObjectConverter
    //
    cout << "timing CObjectConverter...";
    cout.flush();

    sw.Start();
    {{
         size_t size = 0;
         for (size_t iters = 0;  iters < MAX_ITERS;  ++iters) {
             CObjConverter::TObjList objs;
             CObjectConverter::Convert(*scope, *loc,
                                       CSeq_feat::GetTypeInfo(), objs);
             size += objs.size();
         }
     }}
    e = sw.Elapsed();

    cout << "done" << endl;
    cout << MAX_ITERS << " iterations in " << e << " seconds = "
        << e / MAX_ITERS << " secs/iter" << endl;

    //
    // time use of CObjectCache
    //
    cout << "timing CObjectConverter...";
    cout.flush();

    sw.Start();
    {{
         size_t sum = 0;
         CConvertCache cache;
         for (size_t iters = 0;  iters < MAX_ITERS;  ++iters) {
             const CObjectConverter::TObjList& objs =
                 cache.Convert(*scope, *loc,
                               CSeq_feat::GetTypeInfo());
             sum += objs.size();
         }
     }}
    e = sw.Elapsed();

    cout << "done" << endl;
    cout << MAX_ITERS << " iterations in " << e << " seconds = "
        << e / MAX_ITERS << " secs/iter" << endl;

    return 0;
}


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


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



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


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




/*
 * ===========================================================================
 * $Log: test_obj_convert.cpp,v $
 * Revision 1000.1  2004/06/01 20:45:05  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 *
 * Revision 1.6  2004/06/01 18:04:02  dicuccio
 * Tweak to avoid warning message
 *
 * Revision 1.5  2004/05/21 22:27:41  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.4  2004/05/03 17:53:53  dicuccio
 * Tweaked makefiles to support new gui_objutils library
 *
 * Revision 1.3  2004/01/21 12:38:19  dicuccio
 * redesigned CObjectCOnverter API to eliminate temporary object creation
 *
 * Revision 1.2  2004/01/15 16:28:02  dicuccio
 * FIxed compilation errors - test_obj_convert now works
 *
 * Revision 1.1  2004/01/08 11:35:03  dicuccio
 * Initial revision
 *
 * Revision 1.14  2003/10/24 02:13:15  ucko
 * Fix for new CPluginArgDialog interface
 *
 * Revision 1.13  2003/10/07 17:26:15  dicuccio
 * FIxed for URL -> Value conversion
 *
 * Revision 1.12  2003/09/29 15:42:05  dicuccio
 * Deprecated gui/scope.hpp.  Merged gui/core/types.hpp into gui/types.hpp
 *
 * Revision 1.11  2003/09/04 14:01:52  dicuccio
 * Introduce IDocument and IView as abstract base classes for CDocument and CView
 *
 * Revision 1.10  2003/07/17 11:59:50  friedman
 * Include CSelectionBuffer::TSelList for SertArgs. Test Boolesn/Flag dialog widgets.
 *
 * Revision 1.9  2003/07/16 15:22:36  dicuccio
 * Implemented tool tips for arguments
 *
 * Revision 1.8  2003/06/20 14:47:41  dicuccio
 * Revised handling of plugin registration (moved GetInfo() out of plugin factory
 * and into each handler as a static function)
 *
 * Revision 1.7  2003/05/19 13:36:00  dicuccio
 * Moved gui/core/plugin/ -> gui/plugin/.  Merged gui/core/algo, gui/core/doc/,
 * and gui/core/view/ into one library (gui/core/)
 *
 * Revision 1.6  2003/05/09 16:49:01  dicuccio
 * Added explicit check so that default set-constraint arguments will have their
 * values shown
 *
 * Revision 1.5  2003/04/25 14:15:24  dicuccio
 * Fix compilation errors resulting from changes to plugin API
 *
 * Revision 1.4  2003/04/21 15:13:15  dicuccio
 * Added real-life test arguments
 *
 * Revision 1.3  2003/04/16 11:39:50  dicuccio
 * Added torture-test menu with many entries
 *
 * Revision 1.2  2003/03/28 19:20:19  dicuccio
 * Added default argument for testing
 *
 * Revision 1.1  2003/03/20 19:57:28  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */