genemark_loader.hpp

来自「ncbi源码」· HPP 代码 · 共 149 行

/*
 * ===========================================================================
 * 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.
 *
 * =========================================================================
 */