/* $Id: Spliced_exon.hpp 393364 2013-03-25 14:10:03Z mozese2 $
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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
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 *  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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/// @file Spliced_exon.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_exon_.hpp


#ifndef OBJECTS_SEQALIGN_SPLICED_EXON_HPP
#define OBJECTS_SEQALIGN_SPLICED_EXON_HPP


// generated includes
#include <objects/seqalign/Spliced_exon_.hpp>
#include <objects/seqalign/Seq_align.hpp>

#include <util/range_coll.hpp>

// generated classes

BEGIN_NCBI_SCOPE

BEGIN_objects_SCOPE // namespace ncbi::objects::

class CSeq_interval;
class CSpliced_seg;

/////////////////////////////////////////////////////////////////////////////
class NCBI_SEQALIGN_EXPORT CSpliced_exon : public CSpliced_exon_Base
{
    typedef CSpliced_exon_Base Tparent;
public:
    // constructor
    CSpliced_exon(void);
    // destructor
    ~CSpliced_exon(void);

    CRef<CSeq_interval> CreateRowSeq_interval(CSeq_align::TDim    row,
                                              const CSpliced_seg& seg) const;

    /// Return exon's range within this row
    ///
    /// @param row
    ///   0 for product, 1 for genomic
    /// @param always_as_nuc
    ///   If true, row is 0 and product is a protein, return range as a nucleic
    ///   acid sequence; be default for a protein return range over amino acids
    TSeqRange GetRowSeq_range(CSeq_align::TDim    row,
                              bool always_as_nuc) const;

    /// Return insertions within exon
    ///
    /// @param row
    ///   return gaps in this row; 0 for product, 1 for genomic
    /// @param seg
    ///   Parent SPliced-seg object
    CRangeCollection<TSeqPos> GetRowSeq_insertions(CSeq_align::TDim    row,
                                             const CSpliced_seg& seg) const;

    /// Return insertions within exon
    ///
    /// @param row
    ///   return gaps in this row; 0 for product, 1 for genomic
    /// @param seg
    ///   Parent SPliced-seg object
    /// @param within_product_ranges
    ///   Only return insertions within these ranges on the product. If row is
    /// 1, return genomic insertions aligned to a position within these ranges
    CRangeCollection<TSeqPos> GetRowSeq_insertions(
        CSeq_align::TDim    row,
        const CSpliced_seg& seg,
        const CRangeCollection<TSeqPos> &within_product_ranges) const;

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

};

/////////////////// CSpliced_exon inline methods

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


/////////////////// end of CSpliced_exon inline methods


END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE


#endif // OBJECTS_SEQALIGN_SPLICED_EXON_HPP
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