Seq_data_.hpp

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/* $Id$
 * ===========================================================================
 *
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 *               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
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 *  and reliability of the software and data, the NLM and the U.S.
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 *  warranties of performance, merchantability or fitness for any particular
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/// @file Seq_data_.hpp
/// Data storage class.
///
/// This file was generated by application DATATOOL
/// using the following specifications:
/// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seq/seq.asn">seq.asn</a>
/// and additional tune-up parameters:
/// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seq/seq.def">seq.def</a>
///
/// ATTENTION:
///   Don't edit or commit this file into CVS as this file will
///   be overridden (by DATATOOL) without warning!
 
#ifndef OBJECTS_SEQ_SEQ_DATA_BASE_HPP
#define OBJECTS_SEQ_SEQ_DATA_BASE_HPP
 
// standard includes
#include <serial/serialbase.hpp>
 
// generated includes
#include <objects/seq/IUPACaa.hpp>
#include <objects/seq/IUPACna.hpp>
#include <objects/seq/NCBI2na.hpp>
#include <objects/seq/NCBI4na.hpp>
#include <objects/seq/NCBI8aa.hpp>
#include <objects/seq/NCBI8na.hpp>
#include <objects/seq/NCBIeaa.hpp>
#include <objects/seq/NCBIpaa.hpp>
#include <objects/seq/NCBIpna.hpp>
#include <objects/seq/NCBIstdaa.hpp>
 
BEGIN_NCBI_SCOPE
 
#ifndef BEGIN_objects_SCOPE
#  define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
#  define END_objects_SCOPE END_SCOPE(objects)
#endif
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
 
// forward declarations
class CSeq_gap;
 
 
// generated classes
 
 
/** @addtogroup dataspec_NCBI_Sequence
 *
 * @{
 */
 
/////////////////////////////////////////////////////////////////////////////
///*** Various internal sequence representations ************
///*      all are controlled, fixed length forms
/// sequence representations
///
/// CSeq_data_Base --
///
 
class NCBI_SEQ_EXPORT CSeq_data_Base : public CSerialObject
{
    typedef CSerialObject Tparent;
public:
    // constructor
    CSeq_data_Base(void);
    // destructor
    virtual ~CSeq_data_Base(void);
 
    // type info
    DECLARE_INTERNAL_TYPE_INFO();
 
 
    /// Choice variants.
    enum E_Choice {
        e_not_set = 0,  ///< No variant selected
        e_Iupacna,      ///< IUPAC 1 letter nuc acid code
        e_Iupacaa,      ///< IUPAC 1 letter amino acid code
        e_Ncbi2na,      ///< 2 bit nucleic acid code
        e_Ncbi4na,      ///< 4 bit nucleic acid code
        e_Ncbi8na,      ///< 8 bit extended nucleic acid code
        e_Ncbipna,      ///< nucleic acid probabilities
        e_Ncbi8aa,      ///< 8 bit extended amino acid codes
        e_Ncbieaa,      ///< extended ASCII 1 letter aa codes
        e_Ncbipaa,      ///< amino acid probabilities
        e_Ncbistdaa,    ///< consecutive codes for std aas
        e_Gap           ///< gap types
    };
    /// Maximum+1 value of the choice variant enumerator.
    enum E_ChoiceStopper {
        e_MaxChoice = 12 ///< == e_Gap+1
    };
 
    /// Reset the whole object
    virtual void Reset(void);
 
    /// Reset the selection (set it to e_not_set).
    virtual void ResetSelection(void);
 
    /// Which variant is currently selected.
    ///
    /// @return
    ///   Choice state enumerator.
    E_Choice Which(void) const;
 
    /// Verify selection, throw exception if it differs from the expected.
    ///
    /// @param index
    ///   Expected selection.
    void CheckSelected(E_Choice index) const;
 
    /// Throw 'InvalidSelection' exception.
    ///
    /// @param index
    ///   Expected selection.
    NCBI_NORETURN void ThrowInvalidSelection(E_Choice index) const;
 
    /// Retrieve selection name (for diagnostic purposes).
    ///
    /// @param index
    ///   One of possible selection states.
    /// @return
    ///   Name string.
    static string SelectionName(E_Choice index);
 
    /// Select the requested variant if needed.
    ///
    /// @param index
    ///   New selection state.
    /// @param reset
    ///   Flag that defines the resetting of the variant data. The data will
    ///   be reset if either the current selection differs from the new one,
    ///   or the flag is set to eDoResetVariant.
    void Select(E_Choice index, EResetVariant reset = eDoResetVariant);
    /// Select the requested variant if needed,
    /// allocating CObject variants from memory pool.
    void Select(E_Choice index,
                EResetVariant reset,
                CObjectMemoryPool* pool);
 
    // types
    typedef CIUPACna TIupacna;
    typedef CIUPACaa TIupacaa;
    typedef CNCBI2na TNcbi2na;
    typedef CNCBI4na TNcbi4na;
    typedef CNCBI8na TNcbi8na;
    typedef CNCBIpna TNcbipna;
    typedef CNCBI8aa TNcbi8aa;
    typedef CNCBIeaa TNcbieaa;
    typedef CNCBIpaa TNcbipaa;
    typedef CNCBIstdaa TNcbistdaa;
    typedef CSeq_gap TGap;
 
    // getters
    // setters
 
 
    /// Check if variant Iupacna is selected.
    ///
    /// Iupacna type is defined as 'typedef CIUPACna TIupacna'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsIupacna(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TIupacna& GetIupacna(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TIupacna& SetIupacna(void);
 
    /// Select the variant and set its data.
    ///
    /// @param value
    ///   Variant data.
    void SetIupacna(const TIupacna& value);
 
 
    /// Check if variant Iupacaa is selected.
    ///
    /// Iupacaa type is defined as 'typedef CIUPACaa TIupacaa'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsIupacaa(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TIupacaa& GetIupacaa(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TIupacaa& SetIupacaa(void);
 
    /// Select the variant and set its data.
    ///
    /// @param value
    ///   Variant data.
    void SetIupacaa(const TIupacaa& value);
 
 
    /// Check if variant Ncbi2na is selected.
    ///
    /// Ncbi2na type is defined as 'typedef CNCBI2na TNcbi2na'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbi2na(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbi2na& GetNcbi2na(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbi2na& SetNcbi2na(void);
 
 
    /// Check if variant Ncbi4na is selected.
    ///
    /// Ncbi4na type is defined as 'typedef CNCBI4na TNcbi4na'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbi4na(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbi4na& GetNcbi4na(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbi4na& SetNcbi4na(void);
 
 
    /// Check if variant Ncbi8na is selected.
    ///
    /// Ncbi8na type is defined as 'typedef CNCBI8na TNcbi8na'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbi8na(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbi8na& GetNcbi8na(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbi8na& SetNcbi8na(void);
 
 
    /// Check if variant Ncbipna is selected.
    ///
    /// Ncbipna type is defined as 'typedef CNCBIpna TNcbipna'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbipna(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbipna& GetNcbipna(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbipna& SetNcbipna(void);
 
 
    /// Check if variant Ncbi8aa is selected.
    ///
    /// Ncbi8aa type is defined as 'typedef CNCBI8aa TNcbi8aa'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbi8aa(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbi8aa& GetNcbi8aa(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbi8aa& SetNcbi8aa(void);
 
 
    /// Check if variant Ncbieaa is selected.
    ///
    /// Ncbieaa type is defined as 'typedef CNCBIeaa TNcbieaa'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbieaa(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbieaa& GetNcbieaa(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbieaa& SetNcbieaa(void);
 
    /// Select the variant and set its data.
    ///
    /// @param value
    ///   Variant data.
    void SetNcbieaa(const TNcbieaa& value);
 
 
    /// Check if variant Ncbipaa is selected.
    ///
    /// Ncbipaa type is defined as 'typedef CNCBIpaa TNcbipaa'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbipaa(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbipaa& GetNcbipaa(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbipaa& SetNcbipaa(void);
 
 
    /// Check if variant Ncbistdaa is selected.
    ///
    /// Ncbistdaa type is defined as 'typedef CNCBIstdaa TNcbistdaa'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsNcbistdaa(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TNcbistdaa& GetNcbistdaa(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TNcbistdaa& SetNcbistdaa(void);
 
 
    /// Check if variant Gap is selected.
    ///
    /// Gap type is defined as 'typedef CSeq_gap TGap'.
    /// @return
    ///   - true, if the variant is selected.
    ///   - false, otherwise.
    bool IsGap(void) const;
 
    /// Get the variant data.
    ///
    /// @return
    ///   Reference to the data.
    const TGap& GetGap(void) const;
 
    /// Select the variant.
    ///
    /// @return
    ///   Reference to the variant data.
    TGap& SetGap(void);
    /// Select the variant and set its data.
    ///
    /// @param value
    ///   Reference to the data.
    void SetGap(TGap& value);
 
 
private:
    // copy constructor and assignment operator
    CSeq_data_Base(const CSeq_data_Base& );
    CSeq_data_Base& operator=(const CSeq_data_Base& );
    // choice state
    E_Choice m_choice;
    // helper methods
    void DoSelect(E_Choice index, CObjectMemoryPool* pool = 0);
 
    static const char* const sm_SelectionNames[];
    // data
    union {
        NCBI_NS_NCBI::CUnionBuffer<TIupacna> m_Iupacna;
        NCBI_NS_NCBI::CUnionBuffer<TIupacaa> m_Iupacaa;
        NCBI_NS_NCBI::CUnionBuffer<TNcbi2na> m_Ncbi2na;
        NCBI_NS_NCBI::CUnionBuffer<TNcbi4na> m_Ncbi4na;
        NCBI_NS_NCBI::CUnionBuffer<TNcbi8na> m_Ncbi8na;
        NCBI_NS_NCBI::CUnionBuffer<TNcbipna> m_Ncbipna;
        NCBI_NS_NCBI::CUnionBuffer<TNcbi8aa> m_Ncbi8aa;
        NCBI_NS_NCBI::CUnionBuffer<TNcbieaa> m_Ncbieaa;
        NCBI_NS_NCBI::CUnionBuffer<TNcbipaa> m_Ncbipaa;
        NCBI_NS_NCBI::CUnionBuffer<TNcbistdaa> m_Ncbistdaa;
        NCBI_NS_NCBI::CSerialObject *m_object;
    };
};
 
/* @} */
 
 
 
 
 
///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////
inline
CSeq_data_Base::E_Choice CSeq_data_Base::Which(void) const
{
    return m_choice;
}
 
inline
void CSeq_data_Base::CheckSelected(E_Choice index) const
{
    if ( m_choice != index )
        ThrowInvalidSelection(index);
}
 
inline
void CSeq_data_Base::Select(E_Choice index, NCBI_NS_NCBI::EResetVariant reset, NCBI_NS_NCBI::CObjectMemoryPool* pool)
{
    if ( reset == NCBI_NS_NCBI::eDoResetVariant || m_choice != index ) {
        if ( m_choice != e_not_set )
            ResetSelection();
        DoSelect(index, pool);
    }
}
 
inline
void CSeq_data_Base::Select(E_Choice index, NCBI_NS_NCBI::EResetVariant reset)
{
    Select(index, reset, 0);
}
 
inline
bool CSeq_data_Base::IsIupacna(void) const
{
    return m_choice == e_Iupacna;
}
 
inline
const CSeq_data_Base::TIupacna& CSeq_data_Base::GetIupacna(void) const
{
    CheckSelected(e_Iupacna);
    return *m_Iupacna;
}
 
inline
CSeq_data_Base::TIupacna& CSeq_data_Base::SetIupacna(void)
{
    Select(e_Iupacna, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Iupacna;
}
 
inline
bool CSeq_data_Base::IsIupacaa(void) const
{
    return m_choice == e_Iupacaa;
}
 
inline
const CSeq_data_Base::TIupacaa& CSeq_data_Base::GetIupacaa(void) const
{
    CheckSelected(e_Iupacaa);
    return *m_Iupacaa;
}
 
inline
CSeq_data_Base::TIupacaa& CSeq_data_Base::SetIupacaa(void)
{
    Select(e_Iupacaa, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Iupacaa;
}
 
inline
bool CSeq_data_Base::IsNcbi2na(void) const
{
    return m_choice == e_Ncbi2na;
}
 
inline
const CSeq_data_Base::TNcbi2na& CSeq_data_Base::GetNcbi2na(void) const
{
    CheckSelected(e_Ncbi2na);
    return *m_Ncbi2na;
}
 
inline
CSeq_data_Base::TNcbi2na& CSeq_data_Base::SetNcbi2na(void)
{
    Select(e_Ncbi2na, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbi2na;
}
 
inline
bool CSeq_data_Base::IsNcbi4na(void) const
{
    return m_choice == e_Ncbi4na;
}
 
inline
const CSeq_data_Base::TNcbi4na& CSeq_data_Base::GetNcbi4na(void) const
{
    CheckSelected(e_Ncbi4na);
    return *m_Ncbi4na;
}
 
inline
CSeq_data_Base::TNcbi4na& CSeq_data_Base::SetNcbi4na(void)
{
    Select(e_Ncbi4na, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbi4na;
}
 
inline
bool CSeq_data_Base::IsNcbi8na(void) const
{
    return m_choice == e_Ncbi8na;
}
 
inline
const CSeq_data_Base::TNcbi8na& CSeq_data_Base::GetNcbi8na(void) const
{
    CheckSelected(e_Ncbi8na);
    return *m_Ncbi8na;
}
 
inline
CSeq_data_Base::TNcbi8na& CSeq_data_Base::SetNcbi8na(void)
{
    Select(e_Ncbi8na, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbi8na;
}
 
inline
bool CSeq_data_Base::IsNcbipna(void) const
{
    return m_choice == e_Ncbipna;
}
 
inline
const CSeq_data_Base::TNcbipna& CSeq_data_Base::GetNcbipna(void) const
{
    CheckSelected(e_Ncbipna);
    return *m_Ncbipna;
}
 
inline
CSeq_data_Base::TNcbipna& CSeq_data_Base::SetNcbipna(void)
{
    Select(e_Ncbipna, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbipna;
}
 
inline
bool CSeq_data_Base::IsNcbi8aa(void) const
{
    return m_choice == e_Ncbi8aa;
}
 
inline
const CSeq_data_Base::TNcbi8aa& CSeq_data_Base::GetNcbi8aa(void) const
{
    CheckSelected(e_Ncbi8aa);
    return *m_Ncbi8aa;
}
 
inline
CSeq_data_Base::TNcbi8aa& CSeq_data_Base::SetNcbi8aa(void)
{
    Select(e_Ncbi8aa, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbi8aa;
}
 
inline
bool CSeq_data_Base::IsNcbieaa(void) const
{
    return m_choice == e_Ncbieaa;
}
 
inline
const CSeq_data_Base::TNcbieaa& CSeq_data_Base::GetNcbieaa(void) const
{
    CheckSelected(e_Ncbieaa);
    return *m_Ncbieaa;
}
 
inline
CSeq_data_Base::TNcbieaa& CSeq_data_Base::SetNcbieaa(void)
{
    Select(e_Ncbieaa, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbieaa;
}
 
inline
bool CSeq_data_Base::IsNcbipaa(void) const
{
    return m_choice == e_Ncbipaa;
}
 
inline
const CSeq_data_Base::TNcbipaa& CSeq_data_Base::GetNcbipaa(void) const
{
    CheckSelected(e_Ncbipaa);
    return *m_Ncbipaa;
}
 
inline
CSeq_data_Base::TNcbipaa& CSeq_data_Base::SetNcbipaa(void)
{
    Select(e_Ncbipaa, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbipaa;
}
 
inline
bool CSeq_data_Base::IsNcbistdaa(void) const
{
    return m_choice == e_Ncbistdaa;
}
 
inline
const CSeq_data_Base::TNcbistdaa& CSeq_data_Base::GetNcbistdaa(void) const
{
    CheckSelected(e_Ncbistdaa);
    return *m_Ncbistdaa;
}
 
inline
CSeq_data_Base::TNcbistdaa& CSeq_data_Base::SetNcbistdaa(void)
{
    Select(e_Ncbistdaa, NCBI_NS_NCBI::eDoNotResetVariant);
    return *m_Ncbistdaa;
}
 
inline
bool CSeq_data_Base::IsGap(void) const
{
    return m_choice == e_Gap;
}
 
///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////
 
 
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
 
#endif // OBJECTS_SEQ_SEQ_DATA_BASE_HPP