Packed_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.
 *  Government do not and cannot warrant the performance or results that
 *  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
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
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/// @file Packed_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_PACKED_SEG_BASE_HPP
#define OBJECTS_SEQALIGN_PACKED_SEG_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) global or partial alignments
///
/// CPacked_seg_Base --
///
 
class NCBI_SEQALIGN_EXPORT CPacked_seg_Base : public CSerialObject
{
    typedef CSerialObject Tparent;
public:
    // constructor
    CPacked_seg_Base(void);
    // destructor
    virtual ~CPacked_seg_Base(void);
 
    // type info
    DECLARE_INTERNAL_TYPE_INFO();
 
    // types
    typedef int TDim;
    typedef int TNumseg;
    typedef vector< CRef< CSeq_id > > TIds;
    typedef vector< TSeqPos > TStarts;
    typedef vector< char > TPresent;
    typedef vector< TSeqPos > TLens;
    typedef vector< ENa_strand > TStrands;
    typedef vector< CRef< CScore > > TScores;
 
    // member index
    enum class E_memberIndex {
        e__allMandatory = 0,
        e_dim,
        e_numseg,
        e_ids,
        e_starts,
        e_present,
        e_lens,
        e_strands,
        e_scores
    };
    typedef Tparent::CMemberIndex<E_memberIndex, 9> 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);
 
    /// number of segments here
    /// Check if a value has been assigned to Numseg data member.
    ///
    /// Data member Numseg is mandatory;
    /// its type is defined as 'typedef int TNumseg'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetNumseg(void) const;
 
    /// Check if it is safe to call GetNumseg method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetNumseg(void) const;
 
    /// Reset Numseg data member.
    void ResetNumseg(void);
 
    /// Get the Numseg member data.
    ///
    /// @return
    ///   Copy of the member data.
    TNumseg GetNumseg(void) const;
 
    /// Assign a value to Numseg data member.
    ///
    /// @param value
    ///   Value to assign
    void SetNumseg(TNumseg value);
 
    /// Assign a value to Numseg data member.
    ///
    /// @return
    ///   Reference to the data value.
    TNumseg& SetNumseg(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 for whole alignment
    /// 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);
 
    /// Boolean if each sequence present or absent in
    ///   each segment
    /// Check if a value has been assigned to Present data member.
    ///
    /// Data member Present is mandatory;
    /// its type is defined as 'typedef vector< char > TPresent'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetPresent(void) const;
 
    /// Check if it is safe to call GetPresent method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetPresent(void) const;
 
    /// Reset Present data member.
    void ResetPresent(void);
 
    /// Get the Present member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TPresent& GetPresent(void) const;
 
    /// Assign a value to Present data member.
    ///
    /// @return
    ///   Reference to the data value.
    TPresent& SetPresent(void);
 
    /// length of each segment
    /// Check if a value has been assigned to Lens data member.
    ///
    /// Data member Lens is mandatory;
    /// its type is defined as 'typedef vector< TSeqPos > TLens'
    /// @return
    ///   - true, if a value has been assigned.
    ///   - false, otherwise.
    bool IsSetLens(void) const;
 
    /// Check if it is safe to call GetLens method.
    ///
    /// @return
    ///   - true, if the data member is getatable.
    ///   - false, otherwise.
    bool CanGetLens(void) const;
 
    /// Reset Lens data member.
    void ResetLens(void);
 
    /// Get the Lens member data.
    ///
    /// @return
    ///   Reference to the member data.
    const TLens& GetLens(void) const;
 
    /// Assign a value to Lens data member.
    ///
    /// @return
    ///   Reference to the data value.
    TLens& SetLens(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);
 
    /// score for each segment
    /// 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
    CPacked_seg_Base(const CPacked_seg_Base&);
    CPacked_seg_Base& operator=(const CPacked_seg_Base&);
 
    // data
    Uint4 m_set_State[1];
    int m_Dim;
    int m_Numseg;
    vector< CRef< CSeq_id > > m_Ids;
    vector< TSeqPos > m_Starts;
    vector< char > m_Present;
    vector< TSeqPos > m_Lens;
    vector< ENa_strand > m_Strands;
    vector< CRef< CScore > > m_Scores;
};
 
/* @} */
 
 
 
 
 
///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////
inline
bool CPacked_seg_Base::IsSetDim(void) const
{
    return ((m_set_State[0] & 0x3) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetDim(void) const
{
    return true;
}
 
inline
void CPacked_seg_Base::ResetDim(void)
{
    m_Dim = 2;
    m_set_State[0] &= ~0x3;
}
 
inline
void CPacked_seg_Base::SetDefaultDim(void)
{
    ResetDim();
}
 
inline
CPacked_seg_Base::TDim CPacked_seg_Base::GetDim(void) const
{
    return m_Dim;
}
 
inline
void CPacked_seg_Base::SetDim(CPacked_seg_Base::TDim value)
{
    m_Dim = value;
    m_set_State[0] |= 0x3;
}
 
inline
CPacked_seg_Base::TDim& CPacked_seg_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 CPacked_seg_Base::IsSetNumseg(void) const
{
    return ((m_set_State[0] & 0xc) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetNumseg(void) const
{
    return IsSetNumseg();
}
 
inline
void CPacked_seg_Base::ResetNumseg(void)
{
    m_Numseg = 0;
    m_set_State[0] &= ~0xc;
}
 
inline
CPacked_seg_Base::TNumseg CPacked_seg_Base::GetNumseg(void) const
{
    if (!CanGetNumseg()) {
        ThrowUnassigned(1);
    }
    return m_Numseg;
}
 
inline
void CPacked_seg_Base::SetNumseg(CPacked_seg_Base::TNumseg value)
{
    m_Numseg = value;
    m_set_State[0] |= 0xc;
}
 
inline
CPacked_seg_Base::TNumseg& CPacked_seg_Base::SetNumseg(void)
{
#ifdef _DEBUG
    if (!IsSetNumseg()) {
        memset(&m_Numseg,UnassignedByte(),sizeof(m_Numseg));
    }
#endif
    m_set_State[0] |= 0x4;
    return m_Numseg;
}
 
inline
bool CPacked_seg_Base::IsSetIds(void) const
{
    return ((m_set_State[0] & 0x30) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetIds(void) const
{
    return true;
}
 
inline
const CPacked_seg_Base::TIds& CPacked_seg_Base::GetIds(void) const
{
    return m_Ids;
}
 
inline
CPacked_seg_Base::TIds& CPacked_seg_Base::SetIds(void)
{
    m_set_State[0] |= 0x10;
    return m_Ids;
}
 
inline
bool CPacked_seg_Base::IsSetStarts(void) const
{
    return ((m_set_State[0] & 0xc0) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetStarts(void) const
{
    return true;
}
 
inline
const CPacked_seg_Base::TStarts& CPacked_seg_Base::GetStarts(void) const
{
    return m_Starts;
}
 
inline
CPacked_seg_Base::TStarts& CPacked_seg_Base::SetStarts(void)
{
    m_set_State[0] |= 0x40;
    return m_Starts;
}
 
inline
bool CPacked_seg_Base::IsSetPresent(void) const
{
    return ((m_set_State[0] & 0x300) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetPresent(void) const
{
    return IsSetPresent();
}
 
inline
const CPacked_seg_Base::TPresent& CPacked_seg_Base::GetPresent(void) const
{
    if (!CanGetPresent()) {
        ThrowUnassigned(4);
    }
    return m_Present;
}
 
inline
CPacked_seg_Base::TPresent& CPacked_seg_Base::SetPresent(void)
{
    m_set_State[0] |= 0x100;
    return m_Present;
}
 
inline
bool CPacked_seg_Base::IsSetLens(void) const
{
    return ((m_set_State[0] & 0xc00) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetLens(void) const
{
    return true;
}
 
inline
const CPacked_seg_Base::TLens& CPacked_seg_Base::GetLens(void) const
{
    return m_Lens;
}
 
inline
CPacked_seg_Base::TLens& CPacked_seg_Base::SetLens(void)
{
    m_set_State[0] |= 0x400;
    return m_Lens;
}
 
inline
bool CPacked_seg_Base::IsSetStrands(void) const
{
    return ((m_set_State[0] & 0x3000) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetStrands(void) const
{
    return true;
}
 
inline
const CPacked_seg_Base::TStrands& CPacked_seg_Base::GetStrands(void) const
{
    return m_Strands;
}
 
inline
CPacked_seg_Base::TStrands& CPacked_seg_Base::SetStrands(void)
{
    m_set_State[0] |= 0x1000;
    return m_Strands;
}
 
inline
bool CPacked_seg_Base::IsSetScores(void) const
{
    return ((m_set_State[0] & 0xc000) != 0);
}
 
inline
bool CPacked_seg_Base::CanGetScores(void) const
{
    return true;
}
 
inline
const CPacked_seg_Base::TScores& CPacked_seg_Base::GetScores(void) const
{
    return m_Scores;
}
 
inline
CPacked_seg_Base::TScores& CPacked_seg_Base::SetScores(void)
{
    m_set_State[0] |= 0x4000;
    return m_Scores;
}
 
///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////
 
 
 
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE
 
 
#endif // OBJECTS_SEQALIGN_PACKED_SEG_BASE_HPP