context.hpp

ncbi源码

    CFlatFileContext(const CFlatFileConfig& cfg) : m_Cfg(cfg) {}
    // destructor
    ~CFlatFileContext(void) {}

    const CSeq_entry_Handle& GetEntry(void) const { return m_Entry;  }
    void SetEntry(const CSeq_entry_Handle& entry) { m_Entry = entry; }

    const CSubmit_block* GetSubmitBlock(void) const { return m_Submit; }
    void SetSubmit(const CSubmit_block& sub) { m_Submit = ⊂ }

    const CFlatFileConfig& GetConfig(void) const { return m_Cfg; }

    const SAnnotSelector* GetAnnotSelector(void) const;
    SAnnotSelector& SetAnnotSelector(void);
    void SetAnnotSelector(const SAnnotSelector&);

    const CSeq_loc* GetLocation(void) const { return m_Loc; }
    void SetLocation(const CSeq_loc* loc) { m_Loc.Reset(loc); }

    void AddSection(TSection& section) { m_Sections.push_back(section); }

    void Reset(void);

private:

    CFlatFileConfig             m_Cfg;
    CSeq_entry_Handle           m_Entry;
    TSections                   m_Sections;
    CConstRef<CSubmit_block>    m_Submit;
    auto_ptr<SAnnotSelector>    m_Selector;
    CConstRef<CSeq_loc>         m_Loc;
};


/////////////////////////////////////////////////////////////////////////////
// inline methods

// -------- CBioseqContext

inline
const CBioseq::TId& CBioseqContext::GetBioseqIds(void) const
{
    return m_Handle.GetBioseqCore()->GetId();
}

inline
SIZE_TYPE CBioseqContext::GetTotalNumParts(void) const
{
    return m_Master->GetNumParts();
}

inline
void CBioseqContext::SetMaster(CMasterContext& mctx) {
    m_Master.Reset(&mctx);
}

inline
bool CBioseqContext::IsRSCompleteGenomic(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_chromosome;  // NC_
}

inline
bool CBioseqContext::IsRSIncompleteGenomic(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_genomic;  // NG_
}

inline
bool CBioseqContext::IsRSMRna(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_mrna;  // NM_
}

inline
bool CBioseqContext::IsRSNonCodingRna(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_ncrna;  // NR_
}

inline
bool CBioseqContext::IsRSProtein(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_prot;  // NP_
}

inline
bool CBioseqContext::IsRSContig(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_contig;  // NT_
}

inline
bool CBioseqContext::IsRSIntermedWGS(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_wgs_intermed;  // NW_
}

inline
bool CBioseqContext::IsRSPredictedMRna(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_mrna_predicted;  // XM_
}

inline
bool CBioseqContext::IsRSPredictedNCRna(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_ncrna_predicted;  // XR_
}

inline
bool CBioseqContext::IsRSPredictedProtein(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_prot_predicted;  // XP_
}

inline
bool CBioseqContext::IsRSWGSNuc(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_wgs_nuc;  // NZ_
}

inline
bool CBioseqContext::IsRSWGSProt(void)  const
{
    return m_RefseqInfo == CSeq_id::eAcc_refseq_wgs_prot;  // ZP_
}

inline
const CFlatFileConfig& CBioseqContext::Config(void) const
{
    return m_FFCtx.GetConfig();
}

inline
const CSubmit_block* CBioseqContext::GetSubmitBlock(void) const
{
    return m_FFCtx.GetSubmitBlock();
}

inline
const CSeq_entry_Handle& CBioseqContext::GetEntry(void) const
{
    return m_FFCtx.GetEntry();
}

inline
const SAnnotSelector* CBioseqContext::GetAnnotSelector(void) const
{
    return m_FFCtx.GetAnnotSelector();
}

inline
const CSeq_loc* CBioseqContext::GetMasterLocation(void) const
{
    return m_FFCtx.GetLocation();
}


inline
CMolInfo::TTech CBioseqContext::GetTech(void) const
{
    return m_Molinfo ? m_Molinfo->GetTech() : CMolInfo::eTech_unknown;
}


inline
CMolInfo::TBiomol CBioseqContext::GetBiomol(void) const
{
    return m_Molinfo ? m_Molinfo->GetBiomol() : CMolInfo::eBiomol_unknown;
}


inline
bool CBioseqContext::IsGenbankFormat(void) const
{
    return (Config().IsFormatGenbank()  ||
            Config().IsFormatGBSeq()    ||
            Config().IsFormatDDBJ());
}


// -------- CFlatFileContext

inline
const SAnnotSelector* CFlatFileContext::GetAnnotSelector(void) const
{
    return m_Selector.get();
}

inline
SAnnotSelector& CFlatFileContext::SetAnnotSelector(void)
{
    if ( m_Selector.get() == 0 ) {
        m_Selector.reset(new SAnnotSelector);
    }

    return *m_Selector;
}


inline
void CFlatFileContext::SetAnnotSelector(const SAnnotSelector& sel)
{
    m_Selector.reset(new SAnnotSelector(sel));
}


inline
void CFlatFileContext::Reset(void)
{
    m_Entry.Reset();
    m_Sections.clear();
    m_Submit.Reset();
    m_Selector.reset();
    m_Loc.Reset();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: context.hpp,v $
* Revision 1000.1  2004/06/01 19:38:24  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.18
*
* Revision 1.18  2004/05/19 14:45:50  shomrat
* + CFlatFileContext::Reset
*
* Revision 1.17  2004/05/06 17:44:28  shomrat
* + IsEMBL and IsInNucProt
*
* Revision 1.16  2004/04/27 15:09:31  shomrat
* + IsGenbankFormat
*
* Revision 1.15  2004/04/22 16:11:24  ucko
* Move CBioseqContext::SetMaster's body to the end of the file, as some
* compilers insist on seeing CMasterContext's full definition first.
*
* Revision 1.14  2004/04/22 15:41:38  shomrat
* Refactoring of context
*
* Revision 1.13  2004/03/31 17:14:00  shomrat
* name changes
*
* Revision 1.12  2004/03/25 20:28:55  shomrat
* Use handle objects
*
* Revision 1.11  2004/03/18 15:29:38  shomrat
* + flag ShowFtableRefs
*
* Revision 1.10  2004/03/16 19:07:48  vasilche
* Include <memory> for auto_ptr<>.
*
* Revision 1.9  2004/03/16 15:40:21  vasilche
* Added required include
*
* Revision 1.8  2004/03/12 16:55:10  shomrat
* + ViewNuc(), ViewProt()
*
* Revision 1.7  2004/03/10 21:38:01  shomrat
* Fixed usage of m_RefseqInfo
*
* Revision 1.6  2004/03/05 18:53:34  shomrat
* added customization flags
*
* Revision 1.5  2004/02/19 17:56:21  shomrat
* add flag for skipping gathering of source features
*
* Revision 1.4  2004/02/11 22:47:41  shomrat
* using types in flag file
*
* Revision 1.3  2004/02/11 16:39:49  shomrat
* added more user customization flags
*
* Revision 1.2  2004/01/14 15:50:17  shomrat
* multiple changes (work in progress)
*
* Revision 1.1  2003/12/18 17:41:20  shomrat
* file was moved from src directory
*
* Revision 1.1  2003/12/17 20:18:54  shomrat
* Initial Revision (adapted from flat lib)
*
* ===========================================================================
*/

#endif  /* OBJTOOLS_FORMAT___CONTEXT__HPP */