lds_object.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: lds_object.hpp,v $
 * PRODUCTION Revision 1000.0  2003/10/29 21:01:30  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

#ifndef LDS_OBJECT_HPP__
#define LDS_OBJECT_HPP__
/*  $Id: lds_object.hpp,v 1000.0 2003/10/29 21:01:30 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.
 *
 * ===========================================================================
 *
 * Author: Anatoliy Kuznetsov
 *
 * File Description: Different operations on LDS Object table
 *
 */

#include <corelib/ncbistd.hpp>
#include <util/format_guess.hpp>

#include <objtools/lds/lds_db.hpp>
#include <objtools/lds/lds_set.hpp>
#include <objtools/lds/lds_expt.hpp>
#include <objtools/lds/admin/lds_coreobjreader.hpp>


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

class CObjectManager;
class CScope;

//////////////////////////////////////////////////////////////////
//
// SLDS_ObjectDB and SLDS_AnnotDB related methods.
//

class NCBI_LDS_EXPORT CLDS_Object
{
public:
    CLDS_Object(SLDS_TablesCollection& db, const map<string, int>& obj_map);
    ~CLDS_Object();

    // Delete all objects living in the specified set of files.
    // All deleted ids are added to deleted set.
    void DeleteCascadeFiles(const CLDS_Set& file_ids, 
                            CLDS_Set* objects_deleted,
                            CLDS_Set* annotations_deleted);

    // Reload all objects in given set of files
    void UpdateCascadeFiles(const CLDS_Set& file_ids);

    void UpdateFileObjects(int file_id,
                           const string& file_name,
                           CFormatGuess::EFormat format);

    // Return max record id in "object" and "annotation" tables. 
    // Both tables share the same objects sequence numbering.
    // Function returns 0 if no record were found.
    int FindMaxObjRecId();

protected:

    // Checks if parsed object is a "bio object" (returns TRUE) 
    // or an annotation. if applicable object_str_id parameter receives
    // objject or annotation id. (fasta format).
    // If possible function extracts objects' title and molecule type
    // (0 - unknown, 1 - NA, 2 - protein)
    bool IsObject(const CLDS_CoreObjectsReader::SObjectDetails& parse_info,
                  string* object_str_id, 
                  string* object_title);

    // Save object to the database, return record id.
    // NOTE: This function recursively finds all objects' parents and saves
    // the whole genealogy tree (not only the immediate argument).
    int SaveObject(int file_id, 
                   CLDS_CoreObjectsReader* sniffer,
                   CLDS_CoreObjectsReader::SObjectDetails* obj_info);

    // Save object information, return record id. This function is specific 
    // for fasta format.
    int SaveObject(int file_id,
                   const string& seq_id,
                   const string& description,
                   size_t offset,
                   int type_id);

private:
    CLDS_Object(const CLDS_Object&);
    CLDS_Object& operator=(const CLDS_Object&);

private:
    SLDS_TablesCollection&  m_db;
    const map<string, int>& m_ObjTypeMap;

    // Max. id in "object" and "annotation" table
    int                     m_MaxObjRecId;
    CRef<CObjectManager>    m_TSE_Manager;  // OM for top level seq entry
    CRef<CScope>            m_Scope;        // OM Scope
};



END_SCOPE(objects)
END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: lds_object.hpp,v $
 * Revision 1000.0  2003/10/29 21:01:30  gouriano
 * PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.9
 *
 * Revision 1.9  2003/07/29 19:50:30  kuznets
 * Replaced bare pointers with CRef<>
 *
 * Revision 1.8  2003/07/09 19:30:18  kuznets
 * Implemented collection of sequence ids from alignments.
 *
 * Revision 1.7  2003/06/16 16:24:16  kuznets
 * Fixed #include paths (lds <-> lds_admin separation)
 *
 * Revision 1.6  2003/06/04 16:34:42  kuznets
 * Added forward declaration of "ObjectManager & Co".
 *
 * Revision 1.5  2003/06/03 19:14:02  kuznets
 * Added lds dll export/import specifications
 *
 * Revision 1.4  2003/06/03 14:07:46  kuznets
 * Include paths changed to reflect the new directory structure
 *
 * Revision 1.3  2003/05/30 20:29:39  kuznets
 * Implemented annotations loading
 *
 * Revision 1.2  2003/05/23 20:33:33  kuznets
 * Bulk changes in lds library, code reorganizations, implemented top level
 * objects read, metainformation persistance implemented for top level objects...
 *
 * Revision 1.1  2003/05/22 21:01:02  kuznets
 * Initial revision
 *
 * ===========================================================================
 */

#endif