Dense_seg.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: Dense_seg.hpp,v $
- * PRODUCTION Revision 1000.3 2004/06/01 19:30:36 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: Dense_seg.hpp,v 1000.3 2004/06/01 19:30:36 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: .......
- *
- * File Description:
- * .......
- *
- * Remark:
- * This code was originally generated by application DATATOOL
- * using specifications from the data definition file
- * 'seqalign.asn'.
- */
- #ifndef OBJECTS_SEQALIGN_DENSE_SEG_HPP
- #define OBJECTS_SEQALIGN_DENSE_SEG_HPP
- // generated includes
- #include <objects/seqalign/Dense_seg_.hpp>
- #include <objects/seqalign/seqalign_exception.hpp>
- #include <util/range.hpp>
- // generated classes
- BEGIN_NCBI_SCOPE
- BEGIN_objects_SCOPE // namespace ncbi::objects::
- // forward declarations
- class CSeq_loc;
- class NCBI_SEQALIGN_EXPORT CDense_seg : public CDense_seg_Base
- {
- typedef CDense_seg_Base Tparent;
- public:
- // constructor
- CDense_seg(void);
- // destructor
- ~CDense_seg(void);
- typedef vector<int> TWidths;
- // optional
- // typedef vector<int> TWidths
- bool IsSetWidths(void) const;
- bool CanGetWidths(void) const;
- void ResetWidths(void);
- const TWidths& GetWidths(void) const;
- TWidths& SetWidths(void);
- // Validators
- TDim CheckNumRows(void) const;
- TNumseg CheckNumSegs(void) const;
- void Validate (bool full_test = false) const;
- // GetSeqRange
- CRange<TSeqPos> GetSeqRange(TDim row) const;
- TSeqPos GetSeqStart(TDim row) const;
- TSeqPos GetSeqStop(TDim row) const;
- /// Reverse the segments' orientation
- void Reverse(void);
- /// Swap two rows (changing *order*, not content)
- void SwapRows(TDim row1, TDim row2);
- /// Remap row coords according to a given seq-loc
- /// Optionally, ignore the strand of the loc
- void RemapToLoc(TDim row, const CSeq_loc& loc,
- bool ignore_strand = false);
- private:
- // Prohibit copy constructor and assignment operator
- CDense_seg(const CDense_seg& value);
- CDense_seg& operator=(const CDense_seg& value);
- // data
- Uint4 m_set_State1[1];
- TWidths m_Widths;
- };
- /////////////////// CDense_seg inline methods
- // constructor
- inline
- CDense_seg::CDense_seg(void)
- {
- memset(m_set_State1,0,sizeof(m_set_State1));
- }
- inline
- bool CDense_seg::IsSetWidths(void) const
- {
- return ((m_set_State1[0] & 0x3) != 0);
- }
- inline
- bool CDense_seg::CanGetWidths(void) const
- {
- return true;
- }
- inline
- const vector<int>& CDense_seg::GetWidths(void) const
- {
- return m_Widths;
- }
- inline
- vector<int>& CDense_seg::SetWidths(void)
- {
- m_set_State1[0] |= 0x1;
- return m_Widths;
- }
- inline
- void CDense_seg::ResetWidths(void)
- {
- m_Widths.clear();
- m_set_State1[0] &= ~0x3;
- }
- inline
- CRange<TSeqPos> CDense_seg::GetSeqRange(TDim row) const
- {
- return CRange<TSeqPos>(GetSeqStart(row), GetSeqStop(row));
- }
- inline
- CDense_seg::TDim CDense_seg::CheckNumRows() const
- {
- const size_t& dim = GetDim();
- if (dim != GetIds().size()) {
- NCBI_THROW(CSeqalignException, eInvalidAlignment,
- "CDense_seg::CheckNumRows()"
- " ids.size is inconsistent with dim");
- }
- return dim;
- }
- /////////////////// end of CDense_seg inline methods
- END_objects_SCOPE // namespace ncbi::objects::
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: Dense_seg.hpp,v $
- * Revision 1000.3 2004/06/01 19:30:36 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
- *
- * Revision 1.8 2004/05/06 18:23:35 todorov
- * + optional ignore_strand param to RemapToLoc
- *
- * Revision 1.7 2004/04/09 14:31:35 dicuccio
- * Back out previous commit - don't automatically set bit 1 and 2 in Set()
- *
- * Revision 1.6 2004/04/09 14:26:46 dicuccio
- * FIxed bug in SetWidths(): use the correct bit to indicate set state
- *
- * Revision 1.5 2003/11/04 14:46:16 todorov
- * +RemapToLoc
- *
- * Revision 1.4 2003/09/16 15:31:59 todorov
- * Added validation methods. Added seq range methods
- *
- * Revision 1.3 2003/08/26 20:28:38 johnson
- * added 'SwapRows' method
- *
- * Revision 1.2 2003/08/14 19:52:53 todorov
- * Added m_Widths to support nuc2prot aligns
- *
- * Revision 1.1 2003/08/13 18:11:35 johnson
- * added 'Reverse' method
- *
- *
- * ===========================================================================
- */
- #endif // OBJECTS_SEQALIGN_DENSE_SEG_HPP
- /* Original file checksum: lines: 93, chars: 2426, CRC32: 48766ca1 */
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