test_density_map.cpp
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上传日期:2007-06-13
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- /*
- * ===========================================================================
- * PRODUCTION $Log: test_density_map.cpp,v $
- * PRODUCTION Revision 1000.0 2004/06/01 21:22:02 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: test_density_map.cpp,v 1000.0 2004/06/01 21:22:02 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/ncbiapp.hpp>
- #include <corelib/ncbienv.hpp>
- #include <corelib/ncbiargs.hpp>
- #include <corelib/ncbitime.hpp>
- #include <objmgr/object_manager.hpp>
- #include <objtools/data_loaders/genbank/gbloader.hpp>
- #include <objmgr/scope.hpp>
- #include <objmgr/bioseq_handle.hpp>
- #include <objmgr/seq_vector.hpp>
- #include <objmgr/feat_ci.hpp>
- #include <gui/objutils/density_map.hpp>
- using namespace ncbi;
- using namespace ncbi::objects;
- class CTestDensityMap : public CNcbiApplication
- {
- public:
- void Init();
- int Run();
- };
- void CTestDensityMap::Init(void)
- {
- // Prepare command line descriptions
- auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);
- // input file containing the SAGE data (default = stdin)
- arg_desc->AddKey("id", "Accession", "Accession to test",
- CArgDescriptions::eString);
- arg_desc->AddDefaultKey("iters", "Iterations", "Iterations to test",
- CArgDescriptions::eInteger, "10");
- arg_desc->AddDefaultKey("window", "WindowSize", "Number of bases per bin",
- CArgDescriptions::eInteger, "10000");
- // Pass argument descriptions to the application
- //
- SetupArgDescriptions(arg_desc.release());
- }
- int CTestDensityMap::Run(void)
- {
- CArgs args = GetArgs();
- string id_str = args["id"].AsString();
- int iters = args["iters"].AsInteger();
- int window = args["window"].AsInteger();
- CSeq_id id(id_str);
- if (id.Which() == CSeq_id::e_not_set) {
- LOG_POST(Fatal << "can't interpret id = " << id_str);
- }
- CRef<CObjectManager> obj_mgr(new CObjectManager());
- obj_mgr->RegisterDataLoader(*new CGBDataLoader(), CObjectManager::eDefault);
- CScope scope(*obj_mgr);
- scope.AddDefaults();
- CBioseq_Handle handle = scope.GetBioseqHandle(id);
- //
- // first pass: retrieves all features. We can ignore this pass
- //
- SAnnotSelector sel;
- sel.SetAnnotType(CSeq_annot::TData::e_Ftable)
- .SetOverlapType(SAnnotSelector::eOverlap_TotalRange)
- .SetResolveMethod(SAnnotSelector::eResolve_All)
- .SetDataSource("")
- .SetFeatType(CSeqFeatData::e_Gene)
- ;
-
- CFeat_CI iter(handle, 0, 0, sel);
- cout << "iterations: " << iters << endl;
- cout << "seq size: " << handle.GetSeqVector().size() << endl;
- cout << "window: " << window << endl;
- cout << id_str << ": " << iter.GetSize() << " features" << endl;
- CStopWatch sw;
- sw.Start();
- TSeqPos sum = 0;
- int i;
- for (i = 0; i < iters; ++i) {
- CFeat_CI iter(handle, 0, 0, sel);
- sum += iter.GetSize();
- }
- double e1 = sw.Elapsed();
- cout << "overhead time: " << e1 << " seconds" << endl;
- cout << "overhead/iter: " << e1 / double(iters) << endl;
- cout << endl;
- sw.Start();
- TSeqPos max = 0;
- vector<TSeqPos> bins;
- for (i = 0; i < iters; ++i) {
- sum += max = CDensityMap<int>::GetDensityMap(handle, 0, 0, window, sel, bins);
- }
- double e2 = sw.Elapsed();
- cout << "density map: " << bins.size() << endl;
- cout << "map max: " << max << endl;
- cout << "map time: " << e2 << " seconds" << endl;
- cout << "map time/iter: " << (e2) / double(iters) << endl;
- cout << endl;
-
- sw.Start();
-
- CDensityMap<int> new_bins(handle, window);
- for (i = 0; i < iters; ++i ) {
- new_bins.Clear();
- new_bins.AddFeatures(handle, sel);
- }
- double e3 = sw.Elapsed();
-
- cout << "new bins: " << new_bins.GetBins() << endl;
- cout << "new bins max: " << new_bins.GetMax() << endl;
- cout << "new bins time: " << e3 << " seconds" << endl;
- cout << "new time/iter: " << (e3) / double(iters) << endl;
-
- return 0;
- }
- int main(int argc, const char* argv[])
- {
- return CTestDensityMap().AppMain(argc, argv, 0, eDS_Default, 0);
- }
- /*
- * ===========================================================================
- * $Log: test_density_map.cpp,v $
- * Revision 1000.0 2004/06/01 21:22:02 gouriano
- * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
- *
- * Revision 1.2 2004/05/21 22:27:44 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.1 2004/05/09 23:59:55 dicuccio
- * Standardized names of demo and test applications. Cleaned up LIB
- * specifications to eliminate unneeded libraries after splitting libgui_utils
- * into libgui_utils and libgui_objutils
- *
- * Revision 1.6 2004/05/06 18:00:11 gorelenk
- * Fixed include to density_map.hpp
- *
- * Revision 1.5 2004/04/13 17:38:46 grichenk
- * Fixed enumerator usage.
- *
- * Revision 1.4 2004/03/23 21:07:55 gorelenk
- * Corrected compilation errors.
- *
- * Revision 1.3 2004/02/09 21:02:46 rsmith
- * compare new and old CDensityMap implementations.
- *
- * Revision 1.2 2004/01/07 17:39:03 vasilche
- * Fixed include path to genbank loader.
- *
- * Revision 1.1 2003/08/15 19:05:42 dicuccio
- * Initial revision
- *
- * ===========================================================================
- */