genemark_loader.hpp
上传用户:yhdzpy8989
上传日期:2007-06-13
资源大小:13604k
文件大小:5k
- /*
- * ===========================================================================
- * PRODUCTION $Log: genemark_loader.hpp,v $
- * PRODUCTION Revision 1000.2 2004/04/12 19:32:45 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.15
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef GUI_CORE_DOC_BASIC___GENEMARK_LOADER__HPP
- #define GUI_CORE_DOC_BASIC___GENEMARK_LOADER__HPP
- /* $Id: genemark_loader.hpp,v 1000.2 2004/04/12 19:32:45 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: Dmitry Dernovoy
- *
- * File Description:
- * CGeneMarkLoader - Plugin to load GeneMark's predictions
- */
- #include <gui/core/doc_loader.hpp>
- #include <objects/seq/Seq_annot.hpp>
- BEGIN_NCBI_SCOPE
- USING_SCOPE(objects);
- class CGeneMarkLoader : public CDocLoader<CGeneMarkLoader>
- {
- public:
- CGeneMarkLoader();
- ~CGeneMarkLoader();
- // pure virtual requirement: load data into a document
- void Import(objects::CPluginMessage& msg);
- static void GetInfo(CPluginInfo& info);
- private:
- enum EFileFormat {
- fUnknownFormat = 0,
- fGeneMarkHMM = 1,
- fGeneMark = 2,
- fGlimmer2 = 3
- };
- CRef<CSeq_annot> x_LoadGeneMarkFile(const string& fname,
- const CSeq_id& id);
- CRef<CSeq_annot> x_LoadGeneMarkHmmFile(const string& fname,
- const CSeq_id& id);
- CRef<CSeq_annot> x_LoadGlimmer2File(const string& fname,
- const CSeq_id& id);
- EFileFormat x_RecognizeFormat(const string& fname);
- };
- END_NCBI_SCOPE
- #endif // GUI_CORE_DOC_BASIC___GENEMARK_LOADER__HPP
- /*
- * =========================================================================
- * $Log: genemark_loader.hpp,v $
- * Revision 1000.2 2004/04/12 19:32:45 gouriano
- * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.15
- *
- * Revision 1.15 2003/12/09 21:45:38 dernovoy
- * Glimmer2 output loader was added
- *
- * Revision 1.14 2003/11/04 17:49:25 dicuccio
- * Changed calling parameters for plugins - pass CPluginMessage instead of paired
- * CPluginCommand/CPluginReply
- *
- * Revision 1.13 2003/10/10 17:19:33 dicuccio
- * Added Import() interface. Removed dead Save() interfaces
- *
- * Revision 1.12 2003/09/29 15:45:48 dicuccio
- * Deprecated gui/scope.hpp
- *
- * Revision 1.11 2003/07/14 11:17:22 shomrat
- * Plugin messageing system related changes
- *
- * Revision 1.10 2003/06/25 17:02:59 dicuccio
- * Split CPluginHandle into a handle (pointer-to-implementation) and
- * implementation file. Lots of #include file clean-ups.
- *
- * Revision 1.9 2003/06/20 14:52:58 dicuccio
- * Revised plugin registration - moved GetInfo() into the plugin handler
- *
- * Revision 1.8 2003/04/24 16:39:29 dicuccio
- * Updated to reflect changes in plugin API
- *
- * Revision 1.7 2003/02/24 13:03:16 dicuccio
- * Renamed classes in plugin spec:
- * CArgSeg --> CPluginArgSet
- * CArgument --> CPluginArg
- * CPluginArgs --> CPluginCommand
- * CPluginCommands --> CPluginCommandSet
- *
- * Revision 1.6 2003/02/20 19:49:56 dicuccio
- * Created new plugin architecture, based on ASN.1 spec. Moved GBENCH frameowrk
- * over to use new plugin architecture.
- *
- * Revision 1.5 2003/01/13 13:10:07 dicuccio
- * Namespace clean-up. Retired namespace gui -> converted all to namespace ncbi.
- * Moved all FLUID-generated code into namespace ncbi.
- *
- * Revision 1.4 2003/01/08 21:19:48 dernovoy
- * m_SeqId added as private member - should contains gi for correct feature location
- *
- * Revision 1.3 2002/12/31 19:44:07 dernovoy
- * private methods added
- *
- * Revision 1.2 2002/12/30 17:55:42 dicuccio
- * Added new virtual requirement: Save() (not handled by some plugins; return
- * values should be obeyed)
- *
- * Revision 1.1 2002/12/26 17:12:39 dernovoy
- * Initial revision.
- *
- * =========================================================================
- */