basecount_item.hpp

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#ifndef OBJTOOLS_FORMAT_ITEMS___BASECOUNT_ITEM__HPP
#define OBJTOOLS_FORMAT_ITEMS___BASECOUNT_ITEM__HPP
 
/*  $Id: basecount_item.hpp 99549 2023-04-17 14:20:00Z gotvyans $
* ===========================================================================
*
*                            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.
*
* ===========================================================================
*
* Author:  Aaron Ucko, NCBI
*          Mati Shomrat
*
* File Description:
*   base count item for flat-file generator
*
*
*/
#include <corelib/ncbistd.hpp>
 
#include <list>
 
#include <objtools/format/items/item_base.hpp>
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
 
class CBioseqContext;
class IFormatter;
 
 
///////////////////////////////////////////////////////////////////////////
//
// Base Count
 
class NCBI_FORMAT_EXPORT CBaseCountItem : public CFlatItem
{
public:
    CBaseCountItem(CBioseqContext& ctx);
    void Format(IFormatter& formatter, IFlatTextOStream& text_os) const override;
 
    void GetCounts(SIZE_TYPE& a, SIZE_TYPE& c, SIZE_TYPE& g, SIZE_TYPE& t,
        SIZE_TYPE& other) const;
    SIZE_TYPE GetA(void) const { return m_A; }
    SIZE_TYPE GetC(void) const { return m_C; }
    SIZE_TYPE GetG(void) const { return m_G; }
    SIZE_TYPE GetT(void) const { return m_T; }
    SIZE_TYPE GetOther(void) const  { return m_Other; }
 
    EItem GetItemType() const override;
private:
    void x_GatherInfo(CBioseqContext& ctx) override;
 
    // data
    mutable TSeqPos     m_A, m_C, m_G, m_T, m_Other;
};
 
 
inline
void CBaseCountItem::GetCounts
(SIZE_TYPE& a,
 SIZE_TYPE& c,
 SIZE_TYPE& g,
 SIZE_TYPE& t,
 SIZE_TYPE& other) const
{
    a = m_A;
    c = m_C;
    g = m_G;
    t = m_T;
    other = m_Other;
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif  /* OBJTOOLS_FORMAT_ITEMS___BASECOUNT_ITEM__HPP */