seq_map.hpp

ncbi源码

    CSegment& x_Add(const CPacked_seqpnt& seq);
    CSegment& x_Add(const CSeq_loc_mix& seq);
    CSegment& x_Add(const CSeq_loc_equiv& seq);
    CSegment& x_Add(const CSeq_literal& seq);
    CSegment& x_Add(const CDelta_seq& seq);
    CSegment& x_Add(const CSeq_loc& seq);
    CSegment& x_Add(const CSeq_id& seq);
    CSegment& x_Add(const CSeq_point& seq);
    CSegment& x_Add(const CSeq_interval& seq);
    CSegment& x_AddUnloadedSubMap(TSeqPos len);
    CSegment& x_AddUnloadedSeq_data(TSeqPos len);

private:
    void ResolveAll(void) const;
    
private:
    // Prohibit copy operator and constructor
    CSeqMap(const CSeqMap&);
    CSeqMap& operator= (const CSeqMap&);
    
protected:    
    // interface for iterators
    size_t x_GetSegmentsCount(void) const;
    const CSegment& x_GetSegment(size_t index) const;
    void x_GetSegmentException(size_t index) const;
    CSegment& x_SetSegment(size_t index);
    size_t x_FindSegment(TSeqPos position, CScope* scope) const;
    
    TSeqPos x_GetSegmentLength(size_t index, CScope* scope) const;
    TSeqPos x_GetSegmentPosition(size_t index, CScope* scope) const;
    TSeqPos x_ResolveSegmentLength(size_t index, CScope* scope) const;
    TSeqPos x_ResolveSegmentPosition(size_t index, CScope* scope) const;
    CBioseq_Handle x_GetBioseqHandle(const CSegment& seg, CScope* scope) const;

    CConstRef<CSeqMap> x_GetSubSeqMap(const CSegment& seg, CScope* scope,
                                      bool resolveExternal = false) const;
    virtual const CSeq_data& x_GetSeq_data(const CSegment& seg) const;
    virtual const CSeq_id& x_GetRefSeqid(const CSegment& seg) const;
    virtual TSeqPos x_GetRefPosition(const CSegment& seg) const;
    virtual bool x_GetRefMinusStrand(const CSegment& seg) const;
    
    void x_LoadObject(const CSegment& seg) const;
    const CObject* x_GetObject(const CSegment& seg) const;
    CObject* x_GetObject(CSegment& seg);
    virtual void x_SetSeq_data(size_t index, CSeq_data& data);
    virtual void x_SetSubSeqMap(size_t index, CSeqMap_Delta_seqs* subMap);

    typedef vector<CSegment> TSegments;
    
    // segments in this seqmap
    vector<CSegment> m_Segments;
    
    // index of last resolved segment position
    mutable size_t   m_Resolved;
    
    CRef<CObject>    m_Delta;

    // Molecule type from seq-inst
    TMol    m_Mol;
    // Sequence length
    mutable TSeqPos m_SeqLength;

    // MT-protection
    mutable CFastMutex   m_SeqMap_Mtx;
    
    friend class CSeqMap_CI;
    friend class CSeqMap_CI_SegmentInfo;
};


#include <objmgr/seq_map.inl>


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_map.hpp,v $
* Revision 1000.2  2004/04/12 17:27:48  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.44
*
* Revision 1.44  2004/03/16 15:47:26  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.43  2003/11/12 16:53:16  grichenk
* Modified CSeqMap to work with const objects (CBioseq, CSeq_loc etc.)
*
* Revision 1.42  2003/09/30 16:21:59  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.41  2003/09/05 17:29:39  grichenk
* Structurized Object Manager exceptions
*
* Revision 1.40  2003/07/17 19:10:27  grichenk
* Added methods for seq-map and seq-vector validation,
* updated demo.
*
* Revision 1.39  2003/06/26 19:47:25  grichenk
* Added sequence length cache
*
* Revision 1.38  2003/06/24 14:22:46  vasilche
* Fixed CSeqMap constructor from CSeq_loc.
*
* Revision 1.37  2003/06/11 19:32:53  grichenk
* Added molecule type caching to CSeqMap, simplified
* coding and sequence type calculations in CSeqVector.
*
* Revision 1.36  2003/06/10 19:06:34  vasilche
* Simplified CSeq_id_Mapper and CSeq_id_Handle.
*
* Revision 1.35  2003/06/02 16:01:36  dicuccio
* Rearranged include/objects/ subtree.  This includes the following shifts:
*     - include/objects/alnmgr --> include/objtools/alnmgr
*     - include/objects/cddalignview --> include/objtools/cddalignview
*     - include/objects/flat --> include/objtools/flat
*     - include/objects/objmgr/ --> include/objmgr/
*     - include/objects/util/ --> include/objmgr/util/
*     - include/objects/validator --> include/objtools/validator
*
* Revision 1.34  2003/05/20 20:36:13  vasilche
* Added FindResolved() with strand argument.
*
* Revision 1.33  2003/02/24 18:57:21  vasilche
* Make feature gathering in one linear pass using CSeqMap iterator.
* Do not use feture index by sub locations.
* Sort features at the end of gathering in one vector.
* Extracted some internal structures and classes in separate header.
* Delay creation of mapped features.
*
* Revision 1.32  2003/02/05 15:55:26  vasilche
* Added eSeqEnd segment at the beginning of seq map.
* Added flags to CSeqMap_CI to stop on data, gap, or references.
*
* Revision 1.31  2003/01/28 17:16:22  vasilche
* Added CSeqMap::ResolvedRangeIterator with strand coordinate translation.
*
* Revision 1.30  2003/01/22 20:11:53  vasilche
* Merged functionality of CSeqMapResolved_CI to CSeqMap_CI.
* CSeqMap_CI now supports resolution and iteration over sequence range.
* Added several caches to CScope.
* Optimized CSeqVector().
* Added serveral variants of CBioseqHandle::GetSeqVector().
* Tried to optimize annotations iterator (not much success).
* Rewritten CHandleRange and CHandleRangeMap classes to avoid sorting of list.
*
* Revision 1.29  2002/12/30 19:35:47  vasilche
* Removed redundant friend declarations.
*
* Revision 1.28  2002/12/27 21:11:09  kuznets
* Fixed Windows specific syntax problem in class CSeqMap::CSegment member
* m_Iterator was an unnamed structure. For correct MSVC compilation must have
* a type name.
*
* Revision 1.27  2002/12/27 19:32:46  ucko
* Add forward declarations for nested classes so they can stay protected.
*
* Revision 1.26  2002/12/27 19:29:41  vasilche
* Fixed access to protected class on WorkShop.
*
* Revision 1.25  2002/12/27 19:04:46  vasilche
* Fixed segmentation fault on 64 bit platforms.
*
* Revision 1.24  2002/12/26 20:49:28  dicuccio
* Wrapped previous unimplemented ctor in #ifdef for MSWIN only
*
* Revision 1.22  2002/12/26 16:39:21  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.21  2002/10/18 19:12:39  grichenk
* Removed mutex pools, converted most static mutexes to non-static.
* Protected CSeqMap::x_Resolve() with mutex. Modified code to prevent
* dead-locks.
*
* Revision 1.20  2002/07/08 20:50:56  grichenk
* Moved log to the end of file
* Replaced static mutex (in CScope, CDataSource) with the mutex
* pool. Redesigned CDataSource data locking.
*
* Revision 1.19  2002/06/30 03:27:38  vakatov
* Get rid of warnings, ident the code, move CVS logs to the end of file
*
* Revision 1.18  2002/05/29 21:19:57  gouriano
* added debug dump
*
* Revision 1.17  2002/05/21 18:40:15  grichenk
* Prohibited copy constructor and operator =()
*
* Revision 1.16  2002/05/06 03:30:36  vakatov
* OM/OM1 renaming
*
* Revision 1.15  2002/05/03 21:28:02  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.14  2002/04/30 18:54:50  gouriano
* added GetRefSeqid function
*
* Revision 1.13  2002/04/11 12:07:28  grichenk
* Redesigned CAnnotTypes_CI to resolve segmented sequences correctly.
*
* Revision 1.12  2002/04/05 21:26:17  grichenk
* Enabled iteration over annotations defined on segments of a
* delta-sequence.
*
* Revision 1.11  2002/04/02 16:40:53  grichenk
* Fixed literal segments handling
*
* Revision 1.10  2002/03/27 15:07:53  grichenk
* Fixed CSeqMap::CSegmentInfo::operator==()
*
* Revision 1.9  2002/03/15 18:10:05  grichenk
* Removed CRef<CSeq_id> from CSeq_id_Handle, added
* key to seq-id map th CSeq_id_Mapper
*
* Revision 1.8  2002/03/08 21:25:30  gouriano
* fixed errors with unresolvable references
*
* Revision 1.7  2002/02/25 21:05:26  grichenk
* Removed seq-data references caching. Increased MT-safety. Fixed typos.
*
* Revision 1.6  2002/02/21 19:27:00  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.5  2002/02/15 20:36:29  gouriano
* changed implementation of HandleRangeMap
*
* Revision 1.4  2002/01/30 22:08:47  gouriano
* changed CSeqMap interface
*
* Revision 1.3  2002/01/23 21:59:29  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.2  2002/01/16 16:26:37  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:04:04  gouriano
* restructured objmgr
*
* ===========================================================================
*/

#endif  // OBJECTS_OBJMGR___SEQ_MAP__HPP