Sparse_seg_.hpp

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/* $Id$
 * ===========================================================================
 *
 *                            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.
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 *  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
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 *
 *  Please cite the author in any work or product based on this material.
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/// @file Sparse_seg_.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/seqalign/seqalign.asn">seqalign.asn</a>
/// and additional tune-up parameters:
/// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seqalign/seqalign.def">seqalign.def</a>
///
/// ATTENTION:
///   Don't edit or commit this file into CVS as this file will
///   be overridden (by DATATOOL) without warning!
 
#ifndef OBJECTS_SEQALIGN_SPARSE_SEG_BASE_HPP
#define OBJECTS_SEQALIGN_SPARSE_SEG_BASE_HPP
 
// standard includes
#include <serial/serialbase.hpp>
 
// generated includes
#include <vector>
 
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 CScore;
class CSeq_id;
class CSparse_align;
class CSparse_seg_ext;
 
 
// generated classes
 
 
/** @addtogroup dataspec_NCBI_Seqalign
 *
 * @{
 */
 
/////////////////////////////////////////////////////////////////////////////
/// ==========================================================================
///
/// Sparse-seg follows the semantics of dense-seg and is more optimal for
/// representing sparse multiple alignments
///
/// ==========================================================================
///
/// CSparse_seg_Base --
///
 
class NCBI_SEQALIGN_EXPORT CSparse_seg_Base : public CSerialObject
{
    typedef CSerialObject Tparent;
public:
    // constructor
    CSparse_seg_Base(void);
    // destructor
    virtual ~CSparse_seg_Base(void);
 
    // type info
    DECLARE_INTERNAL_TYPE_INFO();
 
    // types
    typedef CSeq_id TMaster_id;
    typedef vector< CRef< CSparse_align > > TRows;
    typedef vector< CRef< CScore > > TRow_scores;
    typedef vector< CRef< CSparse_seg_ext > > TExt;
 
    // member index
    enum class E_memberIndex {
        e__allMandatory = 0,
        e_master_id,
        e_rows,
        e_row_scores,
        e_ext
    };
    typedef Tparent::CMemberIndex<E_memberIndex, 5> TmemberIndex;
 
    // getters
    // setters
 
    /// Check if a value has been assigned to Master_id data member.
    ///
    /// Data member Master_id is optional;
    /// its type is defined as 'typedef CSeq_id TMaster_id'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetMaster_id(void) const;
 
    /// Check if it is safe to call GetMaster_id method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetMaster_id(void) const;
 
    /// Reset Master_id data member.
    void ResetMaster_id(void);
 
    /// Get the Master_id member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TMaster_id& GetMaster_id(void) const;
 
    /// Assign a value to Master_id data member.
    ///
    /// @param value
    ///   Reference to value.
    void SetMaster_id(TMaster_id& value);
 
    /// Assign a value to Master_id data member.
    ///
    /// @return
    ///   Reference to the data value.
    TMaster_id& SetMaster_id(void);
 
    /// pairwise alignments constituting this multiple alignment
    /// Check if a value has been assigned to Rows data member.
    ///
    /// Data member Rows is mandatory;
    /// its type is defined as 'typedef vector< CRef< CSparse_align > > TRows'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetRows(void) const;
 
    /// Check if it is safe to call GetRows method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetRows(void) const;
 
    /// Reset Rows data member.
    void ResetRows(void);
 
    /// Get the Rows member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TRows& GetRows(void) const;
 
    /// Assign a value to Rows data member.
    ///
    /// @return
    ///   Reference to the data value.
    TRows& SetRows(void);
 
    /// per-row scores
    /// Check if a value has been assigned to Row_scores data member.
    ///
    /// Data member Row_scores is optional;
    /// its type is defined as 'typedef vector< CRef< CScore > > TRow_scores'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetRow_scores(void) const;
 
    /// Check if it is safe to call GetRow_scores method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetRow_scores(void) const;
 
    /// Reset Row_scores data member.
    void ResetRow_scores(void);
 
    /// Get the Row_scores member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TRow_scores& GetRow_scores(void) const;
 
    /// Assign a value to Row_scores data member.
    ///
    /// @return
    ///   Reference to the data value.
    TRow_scores& SetRow_scores(void);
 
    /// index of extra items
    /// Check if a value has been assigned to Ext data member.
    ///
    /// Data member Ext is optional;
    /// its type is defined as 'typedef vector< CRef< CSparse_seg_ext > > TExt'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetExt(void) const;
 
    /// Check if it is safe to call GetExt method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetExt(void) const;
 
    /// Reset Ext data member.
    void ResetExt(void);
 
    /// Get the Ext member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TExt& GetExt(void) const;
 
    /// Assign a value to Ext data member.
    ///
    /// @return
    ///   Reference to the data value.
    TExt& SetExt(void);
 
    /// Reset the whole object
    virtual void Reset(void);
 
 
private:
    // Prohibit copy constructor and assignment operator
    CSparse_seg_Base(const CSparse_seg_Base&);
    CSparse_seg_Base& operator=(const CSparse_seg_Base&);
 
    // data
    Uint4 m_set_State[1];
    CRef< TMaster_id > m_Master_id;
    vector< CRef< CSparse_align > > m_Rows;
    vector< CRef< CScore > > m_Row_scores;
    vector< CRef< CSparse_seg_ext > > m_Ext;
};
 
/* @} */
 
 
 
 
 
///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////
inline
bool CSparse_seg_Base::IsSetMaster_id(void) const
{
    return m_Master_id.NotEmpty();
}
 
inline
bool CSparse_seg_Base::CanGetMaster_id(void) const
{
    return IsSetMaster_id();
}
 
inline
const CSparse_seg_Base::TMaster_id& CSparse_seg_Base::GetMaster_id(void) const
{
    if (!CanGetMaster_id()) {
        ThrowUnassigned(0);
    }
    return (*m_Master_id);
}
 
inline
bool CSparse_seg_Base::IsSetRows(void) const
{
    return ((m_set_State[0] & 0xc) != 0);
}
 
inline
bool CSparse_seg_Base::CanGetRows(void) const
{
    return true;
}
 
inline
const CSparse_seg_Base::TRows& CSparse_seg_Base::GetRows(void) const
{
    return m_Rows;
}
 
inline
CSparse_seg_Base::TRows& CSparse_seg_Base::SetRows(void)
{
    m_set_State[0] |= 0x4;
    return m_Rows;
}
 
inline
bool CSparse_seg_Base::IsSetRow_scores(void) const
{
    return ((m_set_State[0] & 0x30) != 0);
}
 
inline
bool CSparse_seg_Base::CanGetRow_scores(void) const
{
    return true;
}
 
inline
const CSparse_seg_Base::TRow_scores& CSparse_seg_Base::GetRow_scores(void) const
{
    return m_Row_scores;
}
 
inline
CSparse_seg_Base::TRow_scores& CSparse_seg_Base::SetRow_scores(void)
{
    m_set_State[0] |= 0x10;
    return m_Row_scores;
}
 
inline
bool CSparse_seg_Base::IsSetExt(void) const
{
    return ((m_set_State[0] & 0xc0) != 0);
}
 
inline
bool CSparse_seg_Base::CanGetExt(void) const
{
    return true;
}
 
inline
const CSparse_seg_Base::TExt& CSparse_seg_Base::GetExt(void) const
{
    return m_Ext;
}
 
inline
CSparse_seg_Base::TExt& CSparse_seg_Base::SetExt(void)
{
    m_set_State[0] |= 0x40;
    return m_Ext;
}
 
///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////
 
 
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
 
#endif // OBJECTS_SEQALIGN_SPARSE_SEG_BASE_HPP