entrez_db.hpp

来自「ncbi源码」· HPP 代码 · 共 170 行

/*
 * ===========================================================================
 * PRODUCTION $Log: entrez_db.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 21:26:35  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.1
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_PLUGINS_DOC_BASIC___ENTREZ_DB__HPP
#define GUI_PLUGINS_DOC_BASIC___ENTREZ_DB__HPP

/*  $Id: entrez_db.hpp,v 1000.0 2004/06/01 21:26:35 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:
 *    CEntrezDBCache -- cache of Entrez database handlers
 */

#include <corelib/ncbistd.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/entrez2/entrez2_client.hpp>
#include <objects/entrez2/Entrez2_docsum.hpp>
#include <objects/entrez2/Entrez2_docsum_list.hpp>

BEGIN_NCBI_SCOPE

class IEntrezDBHandler
{
public:
    struct SHeaderInfo {
        string name;
        float rel_width;

        SHeaderInfo() {}
        SHeaderInfo(const string& n, float w)
            : name(n)
            , rel_width(w) { }
    };

    virtual ~IEntrezDBHandler() { }

    // get the name of the database as Entrez knows it
    virtual string GetDbName() const = 0;

    // get a copy of the name that is nice to print
    virtual string GetVisibleDbName() const = 0;

    // perform a query in the handled database
    virtual CRef<objects::CEntrez2_docsum_list> Query(const string& terms,
                                                      size_t& total_uids,
                                                      size_t offs = 0,
                                                      size_t count = 0) = 0;

    // return the list of column headers to be used when displaying
    // results for this database
    virtual void GetHeaders(vector<SHeaderInfo>& headers) const = 0;

    // return a vector<string> representing the values for a single docsum
    virtual void Format(const objects::CEntrez2_docsum& ds,
                        vector<string>& cols) const = 0;

    // how to resolve to seq-ids when a seq-id is not immediately obvious
    enum ESeqIdFlags {
        // favor nucleotides (proteins favored otherwise)
        fFavorNucleotide    = 0x1,

        // return only the "best" id
        fFavorBest          = 0x2,

        // return only the RefSeq id(s)
        fFavorRefSeq        = 0x4,

        fDefaults           = 0
    };
    typedef int TSeqIdFlags;

    // retrieve seq-ids for a given set of docsums
    typedef list< CRef<objects::CSeq_id> > TIds;
    virtual TIds GetSeqIds(const objects::CEntrez2_docsum_list& ds_list,
                           TSeqIdFlags flags = fDefaults) = 0;
    virtual TIds GetSeqIds(const objects::CEntrez2_docsum& ds,
                           TSeqIdFlags flags = fDefaults) = 0;

};


//
// derived class providing basic query functions
//

class CEntrezDBHandler : public IEntrezDBHandler, public CObject
{
public:
    virtual CRef<objects::CEntrez2_docsum_list> Query(const string& terms,
                                                      size_t& total_uids,
                                                      size_t offs = 0,
                                                      size_t count = 0);

protected:
    objects::CEntrez2Client& x_GetClient();

private:
    CRef<objects::CEntrez2Client> m_Client;
};


//
// manager for instances
class CEntrezDBManager : public CObject
{
public:
    CEntrezDBManager();
    void RegisterHandler(CEntrezDBHandler& handler);
    IEntrezDBHandler& GetHandler(const string& db) const;

    struct SDbEntry {
        string db_name;
        string visible_db_name;
    };
    typedef list<SDbEntry> TEntries;
    void GetDatabases(TEntries& entries);

private:
    typedef map<string, CRef<CEntrezDBHandler> > THandlers;
    THandlers m_Handlers;
};

END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: entrez_db.hpp,v $
 * Revision 1000.0  2004/06/01 21:26:35  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.1
 *
 * Revision 1.1  2004/05/25 17:15:39  dicuccio
 * Initial revision - moved over from old GenBank search
 *
 * ===========================================================================
 */


#endif  // GUI_PLUGINS_DOC_BASIC___ENTREZ_DB__HPP