user_feature_dload.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: user_feature_dload.hpp,v $
 * PRODUCTION Revision 1000.1  2003/12/02 20:32:21  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: user_feature_dload.hpp,v 1000.1 2003/12/02 20:32:21 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:  Josh Cherry
 *
 * File Description:  Data loader for user features in tabular form
 *
 */

#ifndef OBJTOOLS_DATA_LOADERS_TABLE___USER_FEATURE_DLOAD__HPP
#define OBJTOOLS_DATA_LOADERS_TABLE___USER_FEATURE_DLOAD__HPP

#include <objmgr/data_loader.hpp>
#include <objtools/data_loaders/table/sqlite_table.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seq/Seq_annot.hpp>

BEGIN_NCBI_SCOPE

//
// class CFeatureDataLoader interprets a text-file database 
// as a set of features
//
class NCBI_XLOADER_TABLE_EXPORT CUsrFeatDataLoader
    : public objects::CDataLoader
{
public:
    /// Whether file uses zero-based or one-based numbering
    //  MUST equal 0 and 1
    typedef enum {
        eBeginIsZero = 0,
        eBeginIsOne = 1
    } EOffset;

    CUsrFeatDataLoader(const string& input_file,
                       const string& temp_file,
                       bool delete_file,
                       EOffset offset,
                       const string& type = string(),
                       const objects::CSeq_id* given_id = 0);
    
    // Request features from our database corresponding to a given
    // CSeq_id_Handle
    virtual void GetRecords(const objects::CSeq_id_Handle& handle,
                            EChoice choice);
    // Request an annot by CSeq_id_Handle
    CRef<objects::CSeq_annot> GetAnnot(const objects::CSeq_id_Handle& idh);
private:
    enum {
        eUnknown = -1,
        eAccession = 0,
        eStrand,
        eFrom,
        eTo,
        eType,

        eMaxKnownCol
    };

    // Whether file uses zero-based or one-based numbering
    EOffset m_Offset;

    // The 'type' field of the user feature; if this string
    // is non-empty, it is used, even if there's a 'type'
    // column in the file
    string m_Type;

    // mapping of column idx -> meaning
    vector<int> m_ColAssign;

    // mapping of col meaning -> column idx
    int m_ColIdx[eMaxKnownCol];

    // a seq. id, if it's not coming from the file
    CConstRef<objects::CSeq_id> m_SeqId;

    // reference to the table reader we use
    CRef<CSQLiteTable> m_Table;

    // the list of column names we have
    vector<string> m_Cols;

    // struct for sorting CSeq_id_Handle objects by their contents
    struct SIdHandleByContent
    {
        bool operator()(const objects::CSeq_id_Handle& h1,
                        const objects::CSeq_id_Handle& h2) const;
    };

    // the list of IDs we support
    typedef multimap<objects::CSeq_id_Handle, string,
                        SIdHandleByContent> TIdMap;
    TIdMap m_Ids;

    // the map of items we've already loaded
    typedef map<objects::CSeq_id_Handle, CRef<objects::CSeq_entry>,
                SIdHandleByContent> TEntries;
    TEntries m_Entries;
};


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: user_feature_dload.hpp,v $
 * Revision 1000.1  2003/12/02 20:32:21  gouriano
 * PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.2
 *
 * Revision 1.2  2003/11/28 13:40:40  dicuccio
 * Fixed to match new API in CDataLoader
 *
 * Revision 1.1  2003/11/14 19:09:16  jcherry
 * Initial version
 *
 * ===========================================================================
 */

#endif  // OBJTOOLS_DATA_LOADERS_TABLE___USER_FEATURE_DLOAD__HPP