seq_align_mapper.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: seq_align_mapper.hpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:22:07 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef SEQ_ALIGN_MAPPER__HPP
- #define SEQ_ALIGN_MAPPER__HPP
- /* $Id: seq_align_mapper.hpp,v 1000.1 2004/06/01 19:22:07 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: Aleksey Grichenko
- *
- * File Description:
- * Alignment mapper
- *
- */
- #include <objmgr/seq_id_handle.hpp>
- #include <objmgr/impl/seq_loc_cvt.hpp>
- #include <objects/seqloc/Na_strand.hpp>
- #include <objects/seqalign/Seq_align.hpp>
- #include <objects/seqalign/Score.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- class CDense_seg;
- class CPacked_seg;
- class CSeq_align_set;
- class CMappingRange;
- class CSeq_loc_Mapper;
- struct SAlignment_Segment
- {
- struct SAlignment_Row
- {
- SAlignment_Row(void);
- void SetMapped(void);
- int GetSegStart(void) const;
- bool SameStrand(const SAlignment_Row& r) const;
- CSeq_id_Handle m_Id;
- TSeqPos m_Start; ///< kInvalidSeqPos means skipped segment
- bool m_IsSetStrand;
- ENa_strand m_Strand;
- int m_Width; ///< not stored in ASN.1, width of a character
- bool m_Mapped;
- };
- typedef vector<SAlignment_Row> TRows;
- SAlignment_Segment(int len, size_t dim);
- SAlignment_Row& GetRow(size_t idx);
- SAlignment_Row& CopyRow(size_t idx, const SAlignment_Row& src_row);
- SAlignment_Row& AddRow(size_t idx,
- const CSeq_id& id,
- int start,
- bool is_set_strand,
- ENa_strand strand,
- int width);
- SAlignment_Row& AddRow(size_t idx,
- const CSeq_id_Handle& id,
- int start,
- bool is_set_strand,
- ENa_strand strand,
- int width);
- typedef vector< CRef<CScore> > TScores;
- void SetScores(const TScores& scores);
- int m_Len;
- TRows m_Rows;
- bool m_HaveStrands;
- TScores m_Scores;
- };
- class CSeq_align_Mapper : public CObject
- {
- public:
- typedef CSeq_align::C_Segs::TDendiag TDendiag;
- typedef CSeq_align::C_Segs::TStd TStd;
- CSeq_align_Mapper(const CSeq_align& align);
- ~CSeq_align_Mapper(void) {}
- void Convert(CSeq_loc_Conversion_Set& cvts,
- unsigned int loc_index_shift = 0);
- void Convert(CSeq_loc_Mapper& mapper);
- CRef<CSeq_align> GetDstAlign(void) const;
- private:
- typedef list<SAlignment_Segment> TSegments;
- // Segment insertion functions
- SAlignment_Segment& x_PushSeg(int len, size_t dim);
- SAlignment_Segment& x_InsertSeg(TSegments::iterator& where,
- int len,
- size_t dim);
- void x_Init(const TDendiag& diags);
- void x_Init(const CDense_seg& denseg);
- void x_Init(const TStd& sseg);
- void x_Init(const CPacked_seg& pseg);
- void x_Init(const CSeq_align_set& align_set);
- typedef CSeq_loc_Conversion_Set::TRange TRange;
- typedef CSeq_loc_Conversion_Set::TRangeMap TRangeMap;
- typedef CSeq_loc_Conversion_Set::TIdMap TIdMap;
- typedef CSeq_loc_Conversion_Set::TConvByIndex TConvByIndex;
- // Mapping through CSeq_loc_Conversion
- void x_ConvertAlign(CSeq_loc_Conversion_Set& cvts,
- unsigned int loc_index_shift);
- void x_ConvertRow(CSeq_loc_Conversion& cvt,
- size_t row);
- void x_ConvertRow(TIdMap& cvts,
- size_t row);
- CSeq_id_Handle x_ConvertSegment(TSegments::iterator& seg_it,
- CSeq_loc_Conversion& cvt,
- size_t row);
- CSeq_id_Handle x_ConvertSegment(TSegments::iterator& seg_it,
- TIdMap& id_map,
- size_t row);
- // Mapping through CSeq_loc_Mapper
- void x_ConvertAlign(CSeq_loc_Mapper& mapper);
- void x_ConvertRow(CSeq_loc_Mapper& mapper,
- size_t row);
- CSeq_id_Handle x_ConvertSegment(TSegments::iterator& seg_it,
- CSeq_loc_Mapper& mapper,
- size_t row);
- void x_GetDstDendiag(CRef<CSeq_align>& dst) const;
- void x_GetDstDenseg(CRef<CSeq_align>& dst) const;
- void x_GetDstStd(CRef<CSeq_align>& dst) const;
- void x_GetDstPacked(CRef<CSeq_align>& dst) const;
- void x_GetDstDisc(CRef<CSeq_align>& dst) const;
- // Used for e_Disc alignments
- typedef vector<CSeq_align_Mapper> TSubAligns;
- // Flags to indicate possible destination alignment types:
- // multi-dim or multi-id alignments can be packed into std-seg
- // or dense-diag only.
- enum EAlignFlags {
- eAlign_Normal, // Normal alignment, may be packed into any type
- eAlign_Empty, // Empty alignment
- eAlign_MultiId, // A row contains different IDs
- eAlign_MultiDim // Segments have different number of rows
- };
- CConstRef<CSeq_align> m_OrigAlign;
- mutable CRef<CSeq_align> m_DstAlign;
- TSegments m_Segs;
- TSubAligns m_SubAligns;
- bool m_HaveStrands;
- bool m_HaveWidths;
- size_t m_Dim;
- EAlignFlags m_AlignFlags;
- };
- inline
- SAlignment_Segment::SAlignment_Row::SAlignment_Row(void)
- : m_Start(kInvalidSeqPos),
- m_IsSetStrand(false),
- m_Strand(eNa_strand_unknown),
- m_Width(0),
- m_Mapped(false)
- {
- return;
- }
- inline
- void SAlignment_Segment::SAlignment_Row::SetMapped(void)
- {
- m_Mapped = true;
- }
- inline
- bool SAlignment_Segment::SAlignment_Row::
- SameStrand(const SAlignment_Row& r) const
- {
- return m_IsSetStrand && SameOrientation(m_Strand, r.m_Strand);
- }
- inline
- int SAlignment_Segment::SAlignment_Row::GetSegStart(void) const
- {
- return m_Start != kInvalidSeqPos ? m_Start : -1;
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ---------------------------------------------------------------------------
- * $Log: seq_align_mapper.hpp,v $
- * Revision 1000.1 2004/06/01 19:22:07 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
- *
- * Revision 1.7 2004/05/26 14:57:36 ucko
- * Change CSeq_align_Mapper::m_Dim's type from unsigned int to size_t
- * for consistency with STL containers' size() methods.
- *
- * Revision 1.6 2004/05/26 14:29:20 grichenk
- * Redesigned CSeq_align_Mapper: preserve non-mapping intervals,
- * fixed strands handling, improved performance.
- *
- * Revision 1.5 2004/05/13 19:10:57 grichenk
- * Preserve scores in mapped alignments
- *
- * Revision 1.4 2004/05/10 20:22:24 grichenk
- * Fixed more warnings (removed inlines)
- *
- * Revision 1.3 2004/04/12 14:35:59 grichenk
- * Fixed mapping of alignments between nucleotides and proteins
- *
- * Revision 1.2 2004/04/07 18:36:12 grichenk
- * Fixed std-seg mapping
- *
- * Revision 1.1 2004/03/30 15:40:34 grichenk
- * Initial revision
- *
- *
- * ===========================================================================
- */
- #endif // SEQ_ALIGN_MAPPER__HPP
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