flat_seqloc.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: flat_seqloc.hpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:39:38 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef OBJTOOLS_FORMAT_ITEMS___FLAT_SEQLOC__HPP
- #define OBJTOOLS_FORMAT_ITEMS___FLAT_SEQLOC__HPP
- /* $Id: flat_seqloc.hpp,v 1000.1 2004/06/01 19:39:38 gouriano Exp $
- * ===========================================================================
- *
- * 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
- *
- * File Description:
- * new (early 2003) flat-file generator -- location representation
- *
- */
- #include <corelib/ncbiobj.hpp>
- #include <util/range.hpp>
- #include <objects/seqloc/Seq_loc.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- // forward declarations
- class CInt_fuzz;
- class CSeq_id;
- class CSeq_interval;
- class CSeq_loc;
- class CBioseqContext;
- class CFlatGapLoc : public CSeq_loc
- {
- public:
- typedef TSeqPos TLength;
- CFlatGapLoc(TLength value) : m_Length(value) { SetNull(); }
- TLength GetLength(void) const { return m_Length; }
- void SetLength(const TLength& value) { m_Length = value; }
- private:
- TLength m_Length;
- };
- class CFlatSeqLoc : public CObject // derived from CObject to allow for caching
- {
- public:
- enum EType
- {
- eType_location, // Seq-loc
- eType_assembly // Genome assembly
- };
- typedef EType TType;
-
- CFlatSeqLoc(const CSeq_loc& loc, CBioseqContext& ctx,
- TType type = eType_location);
- const string& GetString(void) const { return m_String; }
-
- private:
- void x_Add(const CSeq_loc& loc, CNcbiOstrstream& oss,
- CBioseqContext& ctx, TType type, bool show_comp);
- void x_Add(const CSeq_interval& si, CNcbiOstrstream& oss,
- CBioseqContext& ctx, TType type, bool show_comp);
- void x_Add(const CSeq_point& pnt, CNcbiOstrstream& oss,
- CBioseqContext& ctx, TType type, bool show_comp);
- void x_Add(TSeqPos pnt, const CInt_fuzz* fuzz, CNcbiOstrstream& oss,
- bool html = false);
- void x_AddID(const CSeq_id& id, CNcbiOstrstream& oss,
- CBioseqContext& ctx, TType type);
- // data
- string m_String; // whole location, as a GB-style string
- };
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: flat_seqloc.hpp,v $
- * Revision 1000.1 2004/06/01 19:39:38 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
- *
- * Revision 1.4 2004/04/22 15:36:25 shomrat
- * Changes in context
- *
- * Revision 1.3 2004/03/05 18:50:25 shomrat
- * clean code
- *
- * Revision 1.2 2004/02/19 17:53:47 shomrat
- * add flag to differentiate between loaction and genome assembly formatting
- *
- * Revision 1.1 2003/12/17 19:47:33 shomrat
- * Initial revision (adapted from flat lib)
- *
- *
- * ===========================================================================
- */
- #endif /* OBJTOOLS_FORMAT_ITEMS___FLAT_SEQLOC__HPP */