test_obj_convert.cpp
上传用户:yhdzpy8989
上传日期:2007-06-13
资源大小:13604k
文件大小:10k
- /*
- * ===========================================================================
- * 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
- *
- * ===========================================================================
- */