seq_vector.hpp

ncbi源码

{
    return m_Mol;
}


inline
bool CSeqVector::IsProtein(void) const
{
    return m_Mol == CSeq_inst::eMol_aa;
}


inline
bool CSeqVector::IsNucleotide(void) const
{
    return m_Mol != CSeq_inst::eMol_aa;
}


inline
void CSeqVector::GetSeqData(TSeqPos start, TSeqPos stop, string& buffer) const
{
    m_Iterator.GetSeqData(start, stop, buffer);
}


inline
void CSeqVector::GetSeqData(const const_iterator& start,
                            const const_iterator& stop,
                            string& buffer) const
{
    m_Iterator.GetSeqData(start.GetPos(), stop.GetPos(), buffer);
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_vector.hpp,v $
* Revision 1000.2  2004/04/12 17:28:00  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.50
*
* Revision 1.50  2004/04/12 16:49:16  vasilche
* Allow null scope in CSeqMap_CI and CSeqVector.
*
* Revision 1.49  2004/02/25 18:58:17  shomrat
* Added a new construtor based on Seq-loc in scope
*
* Revision 1.48  2003/12/02 18:28:07  grichenk
* Pass const_iterator to GetSeqData by reference.
*
* Revision 1.47  2003/12/02 16:42:49  grichenk
* Fixed GetSeqData to return empty string if start > stop.
* Added GetSeqData(const_iterator, const_iterator, string).
*
* Revision 1.46  2003/10/24 19:28:12  vasilche
* Added implementation of CSeqVector::empty().
*
* Revision 1.45  2003/10/08 14:16:54  vasilche
* Removed circular reference CSeqVector <-> CSeqVector_CI.
*
* Revision 1.44  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 1.43  2003/08/29 13:34:47  vasilche
* Rewrote CSeqVector/CSeqVector_CI code to allow better inlining.
* CSeqVector::operator[] made significantly faster.
* Added possibility to have platform dependent byte unpacking functions.
*
* Revision 1.42  2003/08/21 18:43:29  vasilche
* Added CSeqVector::IsProtein() and CSeqVector::IsNucleotide() methods.
*
* Revision 1.41  2003/08/21 13:32:04  vasilche
* Optimized CSeqVector iteration.
* Set some CSeqVector values (mol type, coding) in constructor instead of detecting them while iteration.
* Remove unsafe bit manipulations with coding.
*
* Revision 1.40  2003/07/17 19:10:27  grichenk
* Added methods for seq-map and seq-vector validation,
* updated demo.
*
* Revision 1.39  2003/06/24 19:46:41  grichenk
* Changed cache from vector<char> to char*. Made
* CSeqVector::operator[] inline.
*
* Revision 1.38  2003/06/13 19:40:14  grichenk
* Removed _ASSERT() from x_GetSeqMap()
*
* Revision 1.37  2003/06/13 17:22:26  grichenk
* Check if seq-map is not null before using it
*
* Revision 1.36  2003/06/12 18:38:47  vasilche
* Added default constructor of CSeqVector.
*
* Revision 1.35  2003/06/11 19:32:53  grichenk
* Added molecule type caching to CSeqMap, simplified
* coding and sequence type calculations in CSeqVector.
*
* Revision 1.34  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 1.33  2003/05/27 19:44:04  grichenk
* Added CSeqVector_CI class
*
* Revision 1.32  2003/05/20 15:44:37  vasilche
* Fixed interaction of CDataSource and CDataLoader in multithreaded app.
* Fixed some warnings on WorkShop.
* Added workaround for memory leak on WorkShop.
*
* Revision 1.31  2003/05/05 21:00:27  vasilche
* Fix assignment of empty CSeqVector.
*
* Revision 1.30  2003/04/29 19:51:12  vasilche
* Fixed interaction of Data Loader garbage collector and TSE locking mechanism.
* Made some typedefs more consistent.
*
* Revision 1.29  2003/04/24 16:12:37  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.28  2003/02/27 20:56:03  vasilche
* kTypeUnknown bit made fitting in 8 bit integer.
*
* Revision 1.27  2003/02/25 14:48:06  vasilche
* Added Win32 export modifier to object manager classes.
*
* Revision 1.26  2003/02/20 17:01:20  vasilche
* Changed value of kTypeUnknown to fit in 16 bit enums on Mac.
*
* Revision 1.25  2003/02/06 19:05:39  vasilche
* Fixed old cache data copying.
* Delayed sequence type (protein/dna) resolution.
*
* Revision 1.24  2003/01/23 19:33:57  vasilche
* Commented out obsolete methods.
* Use strand argument of CSeqVector instead of creation reversed seqmap.
* Fixed ordering operators of CBioseqHandle to be consistent.
*
* Revision 1.23  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 1.22  2003/01/03 19:45:44  dicuccio
* Replaced kPosUnknwon with kInvalidSeqPos (non-static variable; work-around for
* MSVC)
*
* Revision 1.21  2002/12/26 20:51:36  dicuccio
* Added Win32 export specifier
*
* Revision 1.20  2002/12/26 16:39:22  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.19  2002/10/03 13:45:37  grichenk
* CSeqVector::size() made const
*
* Revision 1.18  2002/09/03 21:26:58  grichenk
* Replaced bool arguments in CSeqVector constructor and getters
* with enums.
*
* Revision 1.17  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 1.16  2002/05/31 17:52:58  grichenk
* Optimized for better performance (CTSE_Info uses atomic counter,
* delayed annotations indexing, no location convertions in
* CAnnot_Types_CI if no references resolution is required etc.)
*
* Revision 1.15  2002/05/17 17:14:50  grichenk
* +GetSeqData() for getting a range of characters from a seq-vector
*
* Revision 1.14  2002/05/09 14:16:29  grichenk
* sm_SizeUnknown -> kPosUnknown, minor fixes for unsigned positions
*
* Revision 1.13  2002/05/06 03:30:36  vakatov
* OM/OM1 renaming
*
* Revision 1.12  2002/05/03 21:28:02  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.11  2002/05/03 18:36:13  grichenk
* Fixed members initialization
*
* Revision 1.10  2002/04/30 14:32:51  ucko
* Have size() return int in keeping with its actual behavior; should cut
* down on warnings about truncation of 64-bit integers.
*
* Revision 1.9  2002/04/29 16:23:25  grichenk
* GetSequenceView() reimplemented in CSeqVector.
* CSeqVector optimized for better performance.
*
* Revision 1.8  2002/04/25 16:37:19  grichenk
* Fixed gap coding, added GetGapChar() function
*
* Revision 1.7  2002/04/23 19:01:06  grichenk
* Added optional flag to GetSeqVector() and GetSequenceView()
* for switching to IUPAC encoding.
*
* 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  2002/01/28 19:45:34  gouriano
* changed the interface of BioseqHandle: two functions moved from Scope
*
* Revision 1.3  2002/01/23 21:59:29  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.2  2002/01/16 16:26:36  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:04:04  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/

#endif  // SEQ_VECTOR__HPP