/* $Id: Spliced_seg.hpp 692825 2025-01-29 19:07:49Z ivanov $
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 *               National Center for Biotechnology Information
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 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
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/// @file Spliced_seg.hpp
/// User-defined methods of the data storage class.
///
/// This file was originally generated by application DATATOOL
/// using the following specifications:
/// 'seqalign.asn'.
///
/// New methods or data members can be added to it if needed.
/// See also: Spliced_seg_.hpp


#ifndef OBJECTS_SEQALIGN_SPLICED_SEG_HPP
#define OBJECTS_SEQALIGN_SPLICED_SEG_HPP


// generated includes
#include <objects/seqalign/Spliced_seg_.hpp>
#include <util/range.hpp>

// generated classes

BEGIN_NCBI_SCOPE

BEGIN_objects_SCOPE // namespace ncbi::objects::

class CSeq_align;

/////////////////////////////////////////////////////////////////////////////
class NCBI_SEQALIGN_EXPORT CSpliced_seg : public CSpliced_seg_Base
{
    typedef CSpliced_seg_Base Tparent;
public:
    // constructor
    CSpliced_seg(void);
    // destructor
    ~CSpliced_seg(void);

    /// types
    typedef int TDim;

    /// Validators
    void Validate    (bool full_test = false) const;
    TDim CheckNumRows(void)                   const {
        return 2;
    }
    bool IsConsistentBiologicalOrder(void) const;

    TSeqPos InternalUnaligned(void) const;

    /// GetSeqRange
    /// NB: In case the product-type is protein, these only return the
    /// amin part of Prot-pos.  The frame is ignored.
    CRange<TSeqPos> GetSeqRange(TDim row) const;
    TSeqPos         GetSeqStart(TDim row) const;
    TSeqPos         GetSeqStop (TDim row) const;

    /// Get strand (the first one if segments have different strands).
    ENa_strand      GetSeqStrand(TDim row) const;

    /// Convert this alignment to a discontinuous segment
    CRef<CSeq_align> AsDiscSeg() const;

private:
    // Prohibit copy constructor and assignment operator
    CSpliced_seg(const CSpliced_seg& value);
    CSpliced_seg& operator=(const CSpliced_seg& value);

};

/////////////////// CSpliced_seg inline methods

// constructor
inline
CSpliced_seg::CSpliced_seg(void)
{
}


/////////////////// end of CSpliced_seg inline methods


END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE


#endif // OBJECTS_SEQALIGN_SPLICED_SEG_HPP
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