seq_feat_handle.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: seq_feat_handle.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 19:25:42  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

#ifndef SEQ_FEAT_HANDLE__HPP
#define SEQ_FEAT_HANDLE__HPP

/*  $Id: seq_feat_handle.hpp,v 1000.0 2004/06/01 19:25:42 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: Aleksey Grichenko, Eugene Vasilchenko
*
* File Description:
*   Seq-feat handle
*
*/

#include <corelib/ncbiobj.hpp>
#include <objmgr/impl/heap_scope.hpp>
#include <util/range.hpp>
#include <objects/seqloc/Na_strand.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objmgr/impl/seq_annot_info.hpp>
#include <objmgr/impl/snp_annot_info.hpp>

BEGIN_NCBI_SCOPE

BEGIN_SCOPE(objects)

class CSeq_annot_Handle;

class CSeq_feat_Handle
{
public:
    CSeq_feat_Handle(void);
    CSeq_feat_Handle(CScope& scope,
                     const CSeq_annot_Info& annot_info,
                     size_t index);
    CSeq_feat_Handle(CScope& scope,
                     const CSeq_annot_SNP_Info& snp_info,
                     size_t index);
    ~CSeq_feat_Handle(void);

    CSeq_annot_Handle GetAnnot(void) const;

    CConstRef<CSeq_feat> GetSeq_feat(void) const;
    bool IsTableSNP(void) const;

    typedef CRange<TSeqPos> TRange;

    TRange GetRange(void) const;

    // Mappings for CSeq_feat methods
    bool IsSetId(void) const;
    const CFeat_id& GetId(void) const;
    const CSeqFeatData& GetData(void) const;
    bool IsSetPartial(void) const;
    bool GetPartial(void) const;
    bool IsSetExcept(void) const;
    bool GetExcept(void) const;
    bool IsSetComment(void) const;
    const string& GetComment(void) const;
    bool IsSetProduct(void) const;
    const CSeq_loc& GetProduct(void) const;
    const CSeq_loc& GetLocation(void) const;
    bool IsSetQual(void) const;
    const CSeq_feat::TQual& GetQual(void) const;
    bool IsSetTitle(void) const;
    const string& GetTitle(void) const;
    bool IsSetExt(void) const;
    const CUser_object& GetExt(void) const;
    bool IsSetCit(void) const;
    const CPub_set& GetCit(void) const;
    bool IsSetExp_ev(void) const;
    CSeq_feat::EExp_ev GetExp_ev(void) const;
    bool IsSetXref(void) const;
    const CSeq_feat::TXref& GetXref(void) const;
    bool IsSetDbxref(void) const;
    const CSeq_feat::TDbxref& GetDbxref(void) const;
    bool IsSetPseudo(void) const;
    bool GetPseudo(void) const;
    bool IsSetExcept_text(void) const;
    const string& GetExcept_text(void) const;

    // Access to some methods of CSeq_feat members
    CSeqFeatData::E_Choice GetFeatType(void) const;
    CSeqFeatData::ESubtype GetFeatSubtype(void) const;

    // Table SNP only types and methods
    typedef SSNP_Info::TSNPId TSNPId;
    typedef SSNP_Info::TWeight TWeight;

    TSNPId GetSNPId(void) const;
    CSeq_id::TGi GetGi(void) const;
    bool IsMinusStrand(void) const;
    TWeight GetWeight(void) const;
    size_t GetAllelesCount(void) const;
    string GetAllele(size_t index) const;

private:
    const SSNP_Info& x_GetSNP_Info(void) const;
    const CSeq_feat& x_GetSeq_feat(void) const;

    enum EAnnotInfoType {
        eType_null,
        eType_Seq_annot_Info,
        eType_Seq_annot_SNP_Info
    };

    CHeapScope                 m_Scope;
    CConstRef<CSeq_annot_Info> m_Annot;
    EAnnotInfoType             m_AnnotInfoType;
    size_t                     m_Index;
};


inline
bool CSeq_feat_Handle::IsTableSNP(void) const
{
    return m_AnnotInfoType == eType_Seq_annot_SNP_Info;
}


inline
bool CSeq_feat_Handle::IsMinusStrand(void) const
{
    return x_GetSNP_Info().MinusStrand();
}


inline
CSeq_feat_Handle::TSNPId CSeq_feat_Handle::GetSNPId(void) const
{
    return x_GetSNP_Info().m_SNP_Id;
}


inline
CSeq_feat_Handle::TWeight CSeq_feat_Handle::GetWeight(void) const
{
    return x_GetSNP_Info().m_Weight;
}


inline
bool CSeq_feat_Handle::IsSetId(void) const
{
    return x_GetSeq_feat().IsSetId();
}


inline
const CFeat_id& CSeq_feat_Handle::GetId(void) const
{
    return x_GetSeq_feat().GetId();
}


inline
const CSeqFeatData& CSeq_feat_Handle::GetData(void) const
{
    return x_GetSeq_feat().GetData();
}


inline
bool CSeq_feat_Handle::IsSetPartial(void) const
{
    return x_GetSeq_feat().IsSetPartial();
}


inline
bool CSeq_feat_Handle::GetPartial(void) const
{
    return x_GetSeq_feat().GetPartial();
}


inline
bool CSeq_feat_Handle::IsSetExcept(void) const
{
    return x_GetSeq_feat().IsSetExcept();
}


inline
bool CSeq_feat_Handle::GetExcept(void) const
{
    return x_GetSeq_feat().GetExcept();
}


inline
bool CSeq_feat_Handle::IsSetComment(void) const
{
    return x_GetSeq_feat().IsSetComment();
}


inline
const string& CSeq_feat_Handle::GetComment(void) const
{
    return x_GetSeq_feat().GetComment();
}


inline
bool CSeq_feat_Handle::IsSetProduct(void) const
{
    return x_GetSeq_feat().IsSetProduct();
}


inline
const CSeq_loc& CSeq_feat_Handle::GetProduct(void) const
{
    return x_GetSeq_feat().GetProduct();
}


inline
const CSeq_loc& CSeq_feat_Handle::GetLocation(void) const
{
    return x_GetSeq_feat().GetLocation();
}


inline
bool CSeq_feat_Handle::IsSetQual(void) const
{
    return x_GetSeq_feat().IsSetQual();
}


inline
const CSeq_feat::TQual& CSeq_feat_Handle::GetQual(void) const
{
    return x_GetSeq_feat().GetQual();
}


inline
bool CSeq_feat_Handle::IsSetTitle(void) const
{
    return x_GetSeq_feat().IsSetTitle();
}


inline
const string& CSeq_feat_Handle::GetTitle(void) const
{
    return x_GetSeq_feat().GetTitle();
}


inline
bool CSeq_feat_Handle::IsSetExt(void) const
{
    return x_GetSeq_feat().IsSetExt();
}


inline
const CUser_object& CSeq_feat_Handle::GetExt(void) const
{
    return x_GetSeq_feat().GetExt();
}


inline
bool CSeq_feat_Handle::IsSetCit(void) const
{
    return x_GetSeq_feat().IsSetCit();
}


inline
const CPub_set& CSeq_feat_Handle::GetCit(void) const
{
    return x_GetSeq_feat().GetCit();
}


inline
bool CSeq_feat_Handle::IsSetExp_ev(void) const
{
    return x_GetSeq_feat().IsSetExp_ev();
}


inline
CSeq_feat::EExp_ev CSeq_feat_Handle::GetExp_ev(void) const
{
    return x_GetSeq_feat().GetExp_ev();
}


inline
bool CSeq_feat_Handle::IsSetXref(void) const
{
    return x_GetSeq_feat().IsSetXref();
}


inline
const CSeq_feat::TXref& CSeq_feat_Handle::GetXref(void) const
{
    return x_GetSeq_feat().GetXref();
}


inline
bool CSeq_feat_Handle::IsSetDbxref(void) const
{
    return x_GetSeq_feat().IsSetDbxref();
}


inline
const CSeq_feat::TDbxref& CSeq_feat_Handle::GetDbxref(void) const
{
    return x_GetSeq_feat().GetDbxref();
}


inline
bool CSeq_feat_Handle::IsSetPseudo(void) const
{
    return x_GetSeq_feat().IsSetPseudo();
}


inline
bool CSeq_feat_Handle::GetPseudo(void) const
{
    return x_GetSeq_feat().GetPseudo();
}


inline
bool CSeq_feat_Handle::IsSetExcept_text(void) const
{
    return x_GetSeq_feat().IsSetExcept_text();
}


inline
const string& CSeq_feat_Handle::GetExcept_text(void) const
{
    return x_GetSeq_feat().GetExcept_text();
}


inline
CSeqFeatData::E_Choice CSeq_feat_Handle::GetFeatType(void) const
{
    return x_GetSeq_feat().GetData().Which();
}


inline
CSeqFeatData::ESubtype CSeq_feat_Handle::GetFeatSubtype(void) const
{
    return x_GetSeq_feat().GetData().GetSubtype();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_feat_handle.hpp,v $
* Revision 1000.0  2004/06/01 19:25:42  gouriano
* PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
*
* Revision 1.2  2004/05/06 17:32:37  grichenk
* Added CanGetXXXX() methods
*
* Revision 1.1  2004/05/04 18:06:06  grichenk
* Initial revision
*
*
* ===========================================================================
*/

#endif  // SEQ_FEAT_HANDLE__HPP