Dense_diag_.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.
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 *
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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 Dense_diag_.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_DENSE_DIAG_BASE_HPP
#define OBJECTS_SEQALIGN_DENSE_DIAG_BASE_HPP
 
// standard includes
#include <serial/serialbase.hpp>
 
// generated includes
#include <vector>
#include <objects/seqloc/Na_strand.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 CScore;
class CSeq_id;
 
 
// generated classes
 
 
/** @addtogroup dataspec_NCBI_Seqalign
 *
 * @{
 */
 
/////////////////////////////////////////////////////////////////////////////
/// for (multiway) diagonals
///
/// CDense_diag_Base --
///
 
class NCBI_SEQALIGN_EXPORT CDense_diag_Base : public CSerialObject
{
    typedef CSerialObject Tparent;
public:
    // constructor
    CDense_diag_Base(void);
    // destructor
    virtual ~CDense_diag_Base(void);
 
    // type info
    DECLARE_INTERNAL_TYPE_INFO();
 
    // types
    typedef int TDim;
    typedef vector< CRef< CSeq_id > > TIds;
    typedef vector< TSeqPos > TStarts;
    typedef TSeqPos TLen;
    typedef vector< ENa_strand > TStrands;
    typedef vector< CRef< CScore > > TScores;
 
    // member index
    enum class E_memberIndex {
        e__allMandatory = 0,
        e_dim,
        e_ids,
        e_starts,
        e_len,
        e_strands,
        e_scores
    };
    typedef Tparent::CMemberIndex<E_memberIndex, 7> TmemberIndex;
 
    // getters
    // setters
 
    /// dimensionality
    /// Check if a value has been assigned to Dim data member.
    ///
    /// Data member Dim is optional with default 2;
    /// its type is defined as 'typedef int TDim'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetDim(void) const;
 
    /// Check if it is safe to call GetDim method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetDim(void) const;
 
    /// Reset Dim data member.
    void ResetDim(void);
 
    /// Assign default value to Dim data member.
    void SetDefaultDim(void);
 
    /// Get the Dim member data.
    ///
    /// @return
    ///   Copy of the member data.
    TDim GetDim(void) const;
 
    /// Assign a value to Dim data member.
    ///
    /// @param value
    ///   Value to assign
    void SetDim(TDim value);
 
    /// Assign a value to Dim data member.
    ///
    /// @return
    ///   Reference to the data value.
    TDim& SetDim(void);
 
    /// sequences in order
    /// Check if a value has been assigned to Ids data member.
    ///
    /// Data member Ids is mandatory;
    /// its type is defined as 'typedef vector< CRef< CSeq_id > > TIds'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetIds(void) const;
 
    /// Check if it is safe to call GetIds method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetIds(void) const;
 
    /// Reset Ids data member.
    void ResetIds(void);
 
    /// Get the Ids member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TIds& GetIds(void) const;
 
    /// Assign a value to Ids data member.
    ///
    /// @return
    ///   Reference to the data value.
    TIds& SetIds(void);
 
    /// start OFFSETS in ids order
    /// Check if a value has been assigned to Starts data member.
    ///
    /// Data member Starts is mandatory;
    /// its type is defined as 'typedef vector< TSeqPos > TStarts'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetStarts(void) const;
 
    /// Check if it is safe to call GetStarts method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetStarts(void) const;
 
    /// Reset Starts data member.
    void ResetStarts(void);
 
    /// Get the Starts member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TStarts& GetStarts(void) const;
 
    /// Assign a value to Starts data member.
    ///
    /// @return
    ///   Reference to the data value.
    TStarts& SetStarts(void);
 
    /// len of aligned segments
    /// Check if a value has been assigned to Len data member.
    ///
    /// Data member Len is mandatory;
    /// its type is defined as 'typedef TSeqPos TLen'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetLen(void) const;
 
    /// Check if it is safe to call GetLen method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetLen(void) const;
 
    /// Reset Len data member.
    void ResetLen(void);
 
    /// Get the Len member data.
    ///
    /// @return
    ///   Copy of the member data.
    TLen GetLen(void) const;
 
    /// Assign a value to Len data member.
    ///
    /// @param value
    ///   Value to assign
    void SetLen(TLen value);
 
    /// Assign a value to Len data member.
    ///
    /// @return
    ///   Reference to the data value.
    TLen& SetLen(void);
 
    /// Check if a value has been assigned to Strands data member.
    ///
    /// Data member Strands is optional;
    /// its type is defined as 'typedef vector< ENa_strand > TStrands'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetStrands(void) const;
 
    /// Check if it is safe to call GetStrands method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetStrands(void) const;
 
    /// Reset Strands data member.
    void ResetStrands(void);
 
    /// Get the Strands member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TStrands& GetStrands(void) const;
 
    /// Assign a value to Strands data member.
    ///
    /// @return
    ///   Reference to the data value.
    TStrands& SetStrands(void);
 
    /// Check if a value has been assigned to Scores data member.
    ///
    /// Data member Scores is optional;
    /// its type is defined as 'typedef vector< CRef< CScore > > TScores'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetScores(void) const;
 
    /// Check if it is safe to call GetScores method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetScores(void) const;
 
    /// Reset Scores data member.
    void ResetScores(void);
 
    /// Get the Scores member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TScores& GetScores(void) const;
 
    /// Assign a value to Scores data member.
    ///
    /// @return
    ///   Reference to the data value.
    TScores& SetScores(void);
 
    /// Reset the whole object
    virtual void Reset(void);
 
 
private:
    // Prohibit copy constructor and assignment operator
    CDense_diag_Base(const CDense_diag_Base&);
    CDense_diag_Base& operator=(const CDense_diag_Base&);
 
    // data
    Uint4 m_set_State[1];
    int m_Dim;
    vector< CRef< CSeq_id > > m_Ids;
    vector< TSeqPos > m_Starts;
    TSeqPos m_Len;
    vector< ENa_strand > m_Strands;
    vector< CRef< CScore > > m_Scores;
};
 
/* @} */
 
 
 
 
 
///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////
inline
bool CDense_diag_Base::IsSetDim(void) const
{
    return ((m_set_State[0] & 0x3) != 0);
}
 
inline
bool CDense_diag_Base::CanGetDim(void) const
{
    return true;
}
 
inline
void CDense_diag_Base::ResetDim(void)
{
    m_Dim = 2;
    m_set_State[0] &= ~0x3;
}
 
inline
void CDense_diag_Base::SetDefaultDim(void)
{
    ResetDim();
}
 
inline
CDense_diag_Base::TDim CDense_diag_Base::GetDim(void) const
{
    return m_Dim;
}
 
inline
void CDense_diag_Base::SetDim(CDense_diag_Base::TDim value)
{
    m_Dim = value;
    m_set_State[0] |= 0x3;
}
 
inline
CDense_diag_Base::TDim& CDense_diag_Base::SetDim(void)
{
#ifdef _DEBUG
    if (!IsSetDim()) {
        memset(&m_Dim,UnassignedByte(),sizeof(m_Dim));
    }
#endif
    m_set_State[0] |= 0x1;
    return m_Dim;
}
 
inline
bool CDense_diag_Base::IsSetIds(void) const
{
    return ((m_set_State[0] & 0xc) != 0);
}
 
inline
bool CDense_diag_Base::CanGetIds(void) const
{
    return true;
}
 
inline
const CDense_diag_Base::TIds& CDense_diag_Base::GetIds(void) const
{
    return m_Ids;
}
 
inline
CDense_diag_Base::TIds& CDense_diag_Base::SetIds(void)
{
    m_set_State[0] |= 0x4;
    return m_Ids;
}
 
inline
bool CDense_diag_Base::IsSetStarts(void) const
{
    return ((m_set_State[0] & 0x30) != 0);
}
 
inline
bool CDense_diag_Base::CanGetStarts(void) const
{
    return true;
}
 
inline
const CDense_diag_Base::TStarts& CDense_diag_Base::GetStarts(void) const
{
    return m_Starts;
}
 
inline
CDense_diag_Base::TStarts& CDense_diag_Base::SetStarts(void)
{
    m_set_State[0] |= 0x10;
    return m_Starts;
}
 
inline
bool CDense_diag_Base::IsSetLen(void) const
{
    return ((m_set_State[0] & 0xc0) != 0);
}
 
inline
bool CDense_diag_Base::CanGetLen(void) const
{
    return IsSetLen();
}
 
inline
void CDense_diag_Base::ResetLen(void)
{
    m_Len = 0;
    m_set_State[0] &= ~0xc0;
}
 
inline
CDense_diag_Base::TLen CDense_diag_Base::GetLen(void) const
{
    if (!CanGetLen()) {
        ThrowUnassigned(3);
    }
    return m_Len;
}
 
inline
void CDense_diag_Base::SetLen(CDense_diag_Base::TLen value)
{
    m_Len = value;
    m_set_State[0] |= 0xc0;
}
 
inline
CDense_diag_Base::TLen& CDense_diag_Base::SetLen(void)
{
#ifdef _DEBUG
    if (!IsSetLen()) {
        memset(&m_Len,UnassignedByte(),sizeof(m_Len));
    }
#endif
    m_set_State[0] |= 0x40;
    return m_Len;
}
 
inline
bool CDense_diag_Base::IsSetStrands(void) const
{
    return ((m_set_State[0] & 0x300) != 0);
}
 
inline
bool CDense_diag_Base::CanGetStrands(void) const
{
    return true;
}
 
inline
const CDense_diag_Base::TStrands& CDense_diag_Base::GetStrands(void) const
{
    return m_Strands;
}
 
inline
CDense_diag_Base::TStrands& CDense_diag_Base::SetStrands(void)
{
    m_set_State[0] |= 0x100;
    return m_Strands;
}
 
inline
bool CDense_diag_Base::IsSetScores(void) const
{
    return ((m_set_State[0] & 0xc00) != 0);
}
 
inline
bool CDense_diag_Base::CanGetScores(void) const
{
    return true;
}
 
inline
const CDense_diag_Base::TScores& CDense_diag_Base::GetScores(void) const
{
    return m_Scores;
}
 
inline
CDense_diag_Base::TScores& CDense_diag_Base::SetScores(void)
{
    m_set_State[0] |= 0x400;
    return m_Scores;
}
 
///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////
 
 
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
 
#endif // OBJECTS_SEQALIGN_DENSE_DIAG_BASE_HPP