file_loader.hpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: file_loader.hpp,v $
 * PRODUCTION Revision 1000.4  2004/06/01 20:57:40  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.23
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_PLUGINS_DOC_BASIC___FILE_LOADER__HPP
#define GUI_PLUGINS_DOC_BASIC___FILE_LOADER__HPP

/*  $Id: file_loader.hpp,v 1000.4 2004/06/01 20:57:40 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:
 *    CDataPlugin_FileLoader - load sequence information from a file.
 */

#include <gui/core/doc_loader.hpp>
#include <gui/plugin/MessageStatus.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <objmgr/scope.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/submit/Seq_submit.hpp>



BEGIN_NCBI_SCOPE

class IDocument;
class CObjectInfo;

class CDataPlugin_FileLoader : public CDocLoader<CDataPlugin_FileLoader>
{
public:

    /// enum defining the formats we support
    enum EFormat {
        ///< autodetect will try to guess which of the
        ///< following formats applies.
        eFormat_Autodetect,

        ///< force ASN binary
        eFormat_AsnBinary,

        ///< force ASN text
        eFormat_AsnText,

        ///< force XML
        eFormat_XML,

        ///< force FASTA
        eFormat_FastA,

        ///< force generic text alignment
        eFormat_TextAlign,

        ///< force Newick format phylogenetic tree
        eFormat_NewickTree
    };

    CDataPlugin_FileLoader();
    ~CDataPlugin_FileLoader();

    /// virtual hook: load a document
    void Load(objects::CPluginMessage& msg);

    /// virtual hook: import data into a document
    void Import(objects::CPluginMessage& msg);

    /// Subversion of Load called when any suspected object is read
    void Load(const CObjectInfo& info, IDocument* doc,
              objects::CPluginReply& reply);

    static void GetInfo(objects::CPluginInfo& info);

private:

    /// Internal version of load - here we iterate through the various file
    /// types looking for a match.
    void x_LoadFile(const string& fname, EFormat fmt, IDocument* doc,
                    objects::CPluginReply& reply);
    void x_LoadStream(CNcbiIstream& input, EFormat fmt, IDocument* doc,
                      objects::CPluginReply& reply);

    /// sub-versions of load, called for each object that is read
    void x_Load(objects::CSeq_entry& entry, IDocument* doc,
                objects::CPluginReply& reply);

    void x_Load(objects::CBioseq_set& bioseq_set, IDocument* doc,
                objects::CPluginReply& reply);

    void x_Load(objects::CBioseq& bioseq, IDocument* doc,
                objects::CPluginReply& reply);

    void x_Load(objects::CSeq_annot& annot, IDocument* doc,
                objects::CPluginReply& reply);

    void x_Load(objects::CSeq_align& align, IDocument* doc,
                objects::CPluginReply& reply);

    void x_Load(objects::CSeq_align_set& align, IDocument* doc,
                objects::CPluginReply& reply);

    void x_Load(objects::CSeq_submit& submit, IDocument* doc,
                objects::CPluginReply& reply);


    /// Convert a single Seq-entry to a single bioseq handle
    objects::CBioseq_Handle
    x_SeqEntryToBioseqHandle(objects::CSeq_entry& entry,
                             objects::CScope& scope);

    /// internal load-into function to add an annotation to a document
    objects::EMessageStatus
    x_LoadAnnotation(IDocument* doc, CRef<objects::CSeq_annot>& annot);
};


END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: file_loader.hpp,v $
 * Revision 1000.4  2004/06/01 20:57:40  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.23
 *
 * Revision 1.23  2004/05/25 17:21:59  dicuccio
 * Modified class names.  Fonts to 12 point
 *
 * Revision 1.22  2004/04/05 14:27:10  dicuccio
 * Added check to make sure the file exists before opening.  Added support for
 * seq-align-set conversions
 *
 * Revision 1.21  2004/03/23 22:09:01  jcherry
 * Isolate stream operations from file stuff
 *
 * Revision 1.20  2004/03/01 15:12:04  dicuccio
 * Added support for CLUSTAL alignments.  Added handling of type specification in
 * plugin args.  Added support for Newic format phylogenetic trees.
 *
 * Revision 1.19  2003/11/18 17:49:01  dicuccio
 * Added standard processing of return values
 *
 * Revision 1.18  2003/11/04 17:49:24  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.17  2003/10/10 17:17:28  dicuccio
 * Added Import() method - split out from Load()
 *
 * Revision 1.16  2003/09/29 15:39:10  dicuccio
 * Header file clean-up.  Deprecated gui/scope.hpp and gui/core/types.hpp.  Added
 * GenBank data loader management dialog
 *
 * Revision 1.15  2003/09/16 14:07:28  dicuccio
 * Removed Save function - split into separate plugin class
 *
 * Revision 1.14  2003/09/04 14:51:01  dicuccio
 * Use IDocument instead of CDocument
 *
 * Revision 1.13  2003/07/14 11:16:38  shomrat
 * Plugin messageing system related changes
 *
 * Revision 1.12  2003/06/20 14:52:57  dicuccio
 * Revised plugin registration - moved GetInfo() into the plugin handler
 *
 * Revision 1.11  2003/06/17 19:14:56  dicuccio
 * Cleaned up and re-enabled file importing
 *
 * Revision 1.10  2003/06/10 14:59:13  kuznets
 * File opening reimplemented using CObjectsSniffer(obj_sniff.hpp)
 *
 * Revision 1.9  2003/06/02 16:06:22  dicuccio
 * Rearranged src/objects/ subtree.  This includes the following shifts:
 *     - src/objects/asn2asn --> arc/app/asn2asn
 *     - src/objects/testmedline --> src/objects/ncbimime/test
 *     - src/objects/objmgr --> src/objmgr
 *     - src/objects/util --> src/objmgr/util
 *     - src/objects/alnmgr --> src/objtools/alnmgr
 *     - src/objects/flat --> src/objtools/flat
 *     - src/objects/validator --> src/objtools/validator
 *     - src/objects/cddalignview --> src/objtools/cddalignview
 * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
 * replaces the three libmmdb? libs.
 *
 * Revision 1.8  2003/04/24 16:39:08  dicuccio
 * Updated to reflect changes in plugin API.  Changed location of document marshal
 * from framework to plugin
 *
 * 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  2003/02/05 19:55:53  dicuccio
 * Reworked file loading to handle more types
 *
 * Revision 1.4  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 1.3  2002/12/30 17:55:42  dicuccio
 * Added new virtual requirement: Save() (not handled by some plugins; return
 * values should be obeyed)
 *
 * Revision 1.2  2002/12/09 20:35:59  dicuccio
 * Large revision to file loading code - added ability to read more object
 * types, added ability to import annotations into current document.
 *
 * Revision 1.1  2002/11/25 20:51:01  dicuccio
 * Initial revision.
 *
 * ===========================================================================
 */

#endif  /// GUI_PLUGINS_DOC_BASIC___FILE_LOADER__HPP