qualifiers.hpp

ncbi源码

private:
    CCdregion::TCode_break m_Value;
};


class CFlatCodonQVal : public IFlatQVal
{
public:
    CFlatCodonQVal(unsigned int codon, unsigned char aa, bool is_ascii = true);
    CFlatCodonQVal(const string& value); // for imports
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    string m_Codon, m_AA;
    bool   m_Checked;
};


class CFlatExpEvQVal : public IFlatQVal
{
public:
    CFlatExpEvQVal(CSeq_feat::TExp_ev value) : m_Value(value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CSeq_feat::TExp_ev m_Value;
};


class CFlatIllegalQVal : public IFlatQVal
{
public:
    CFlatIllegalQVal(const CGb_qual& value) : m_Value(&value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<CGb_qual> m_Value;
};


class CFlatLabelQVal : public CFlatStringQVal
{
public:
    CFlatLabelQVal(const string& value)
        : CFlatStringQVal(value, CFormatQual::eUnquoted) { }
    // XXX - should override Format to check syntax
};


class CFlatMolTypeQVal : public IFlatQVal
{
public:
    typedef CMolInfo::TBiomol TBiomol;
    typedef CSeq_inst::TMol   TMol;

    CFlatMolTypeQVal(TBiomol biomol, TMol mol) : m_Biomol(biomol), m_Mol(mol) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    TBiomol m_Biomol;
    TMol    m_Mol;
};


class CFlatOrgModQVal : public IFlatQVal
{
public:
    CFlatOrgModQVal(const COrgMod& value) : m_Value(&value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<COrgMod> m_Value;
};


class CFlatOrganelleQVal : public IFlatQVal
{
public:
    CFlatOrganelleQVal(CBioSource::TGenome value) : m_Value(value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CBioSource::TGenome m_Value;
};


class CFlatPubSetQVal : public IFlatQVal
{
public:
    CFlatPubSetQVal(const CPub_set& value) : m_Value(&value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<CPub_set> m_Value;
};


class CFlatSeqIdQVal : public IFlatQVal
{
public:
    CFlatSeqIdQVal(const CSeq_id& value, bool add_gi_prefix = false) 
        : m_Value(&value), m_GiPrefix(add_gi_prefix) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<CSeq_id> m_Value;
    bool               m_GiPrefix;
};


class CFlatSeqLocQVal : public IFlatQVal
{
public:
    CFlatSeqLocQVal(const CSeq_loc& value) : m_Value(&value) { }
    void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
                TFlags) const
        { x_AddFQ(q, n, CFlatSeqLoc(*m_Value, ctx).GetString()); }

private:
    CConstRef<CSeq_loc> m_Value;
};


class CFlatSubSourceQVal : public IFlatQVal
{
public:
    CFlatSubSourceQVal(const CSubSource& value) : m_Value(&value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<CSubSource> m_Value;
};


class CFlatXrefQVal : public IFlatQVal
{
public:
    typedef CSeq_feat::TDbxref                       TXref;
    typedef CQualContainer<EFeatureQualifier> TQuals;

    CFlatXrefQVal(const TXref& value, const TQuals* quals = 0) 
        :   m_Value(value), m_Quals(quals) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    bool x_XrefInGeneXref(const CDbtag& dbtag) const;

    TXref             m_Value;
    CConstRef<TQuals> m_Quals;
};


class CFlatModelEvQVal : public IFlatQVal
{
public:
    CFlatModelEvQVal(const CUser_object& value) : m_Value(&value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<CUser_object> m_Value;
};


class CFlatGoQVal : public IFlatQVal
{
public:
    CFlatGoQVal(const CUser_field& value) : m_Value(&value) { }
    void Format(TFlatQuals& quals, const string& name, CBioseqContext& ctx,
                TFlags flags) const;

private:
    CConstRef<CUser_field> m_Value;
};


class CFlatAnticodonQVal : public IFlatQVal
{
public:
    CFlatAnticodonQVal(const CSeq_loc& ac, const string& aa) :
        m_Anticodon(&ac), m_Aa(aa) { }
    void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
                TFlags) const;

private:
    CConstRef<CSeq_loc> m_Anticodon;
    string              m_Aa;
};


class CFlatTrnaCodonsQVal : public IFlatQVal
{
public:
    CFlatTrnaCodonsQVal(const CTrna_ext& trna) : m_Value(&trna) { }
    void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
                TFlags) const;

private:
    CConstRef<CTrna_ext> m_Value;
};


class CFlatProductQVal : public CFlatStringQVal
{
public:
    typedef CSeqFeatData::ESubtype  TSubtype;
    CFlatProductQVal(const string& value, TSubtype subtype) :
        CFlatStringQVal(value), m_Subtype(subtype)
    {}
    void Format(TFlatQuals& q, const string& n, CBioseqContext& ctx,
                TFlags) const;
private:
    TSubtype m_Subtype;
};

// ...

END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: qualifiers.hpp,v $
* Revision 1000.1  2004/06/01 19:39:59  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.12
*
* Revision 1.12  2004/05/19 14:44:38  shomrat
* + CQualContainer::Erase(..)
*
* Revision 1.11  2004/05/06 17:43:00  shomrat
* CFlatQual -> CFormatQual to prevent name collisions in ncbi_seqext lib
*
* Revision 1.10  2004/04/26 21:11:23  ucko
* Tweak previous fix so that it compiles with MSVC.
*
* Revision 1.9  2004/04/26 16:49:27  ucko
* Add an explicit "typename" annotation required by GCC 3.4.
*
* Revision 1.8  2004/04/22 15:39:05  shomrat
* Changes in context
*
* Revision 1.7  2004/03/31 15:57:49  ucko
* Add missing "typename"s in CQualContainer's typedefs.
*
* Revision 1.6  2004/03/30 20:25:26  shomrat
* + class CQualContainer
*
* Revision 1.5  2004/03/18 15:28:45  shomrat
* Fixes to quals formatting; + new Product qual
*
* Revision 1.4  2004/03/08 20:59:02  shomrat
* + GI prefix flag for Seq-id qualifiers
*
* Revision 1.3  2004/03/05 18:50:48  shomrat
* Added new qualifier classes
*
* Revision 1.2  2004/02/11 16:37:20  shomrat
* added CFlatStringListQVal class and an optional suffix to CFormatQual
*
* Revision 1.1  2003/12/17 19:49:19  shomrat
* Initial revision (adapted from flat lib)
*
*
* ===========================================================================
*/

#endif  /* OBJTOOLS_FORMAT_ITEMS___QUALIFIERS__HPP */