seq_map.cpp

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CSeqMap::CSegment& CSeqMap::x_AddUnloadedSubMap(TSeqPos len)
{
    return x_AddSegment(eSeqSubMap, len);
}


CSeqMap::CSegment& CSeqMap::x_AddUnloadedSeq_data(TSeqPos len)
{
    return x_AddSegment(eSeqData, len);
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_data& data, TSeqPos len)
{
    return x_AddSegment(eSeqData, len, &data);
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_point& ref)
{
    return x_AddSegment(eSeqRef, &ref.GetId(),
                        ref.GetPoint(), 1,
                        ref.IsSetStrand()? ref.GetStrand(): eNa_strand_unknown);
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_interval& ref)
{
    return x_AddSegment(eSeqRef, &ref.GetId(),
                        ref.GetFrom(), ref.GetLength(),
                        ref.IsSetStrand()? ref.GetStrand(): eNa_strand_unknown);
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_id& ref)
{
    return x_AddSegment(eSeqRef, &ref, 0, kInvalidSeqPos);
}


CSeqMap::CSegment& CSeqMap::x_Add(CSeqMap* submap)
{
    return x_AddSegment(eSeqSubMap, kInvalidSeqPos, submap);
}


CSeqMap::CSegment& CSeqMap::x_Add(const CPacked_seqint& seq)
{
    return x_Add(new CSeqMap_Seq_intervals(seq));
}


CSeqMap::CSegment& CSeqMap::x_Add(const CPacked_seqpnt& seq)
{
    return x_Add(new CSeqMap_SeqPoss(seq));
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_loc_mix& seq)
{
    return x_Add(new CSeqMap_Seq_locs(seq, seq.Get()));
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_loc_equiv& seq)
{
    return x_Add(new CSeqMap_Seq_locs(seq, seq.Get()));
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_literal& seq)
{
    if ( seq.IsSetSeq_data() ) {
        return x_Add(seq.GetSeq_data(), seq.GetLength());
    }
    else {
        // No data exist - treat it like a gap
        return x_AddGap(seq.GetLength()); //???
    }
}


CSeqMap::CSegment& CSeqMap::x_Add(const CSeq_loc& loc)
{
    switch ( loc.Which() ) {
    case CSeq_loc::e_not_set:
    case CSeq_loc::e_Null:
    case CSeq_loc::e_Empty:
        return x_AddGap(0); // Add gap ???
    case CSeq_loc::e_Whole:
        return x_Add(loc.GetWhole());
    case CSeq_loc::e_Int:
        return x_Add(loc.GetInt());
    case CSeq_loc::e_Pnt:
        return x_Add(loc.GetPnt());
    case CSeq_loc::e_Packed_int:
        return x_Add(loc.GetPacked_int());
    case CSeq_loc::e_Packed_pnt:
        return x_Add(loc.GetPacked_pnt());
    case CSeq_loc::e_Mix:
        return x_Add(loc.GetMix());
    case CSeq_loc::e_Equiv:
        return x_Add(loc.GetEquiv());
    case CSeq_loc::e_Bond:
        NCBI_THROW(CSeqMapException, eDataError,
                   "e_Bond is not allowed as a reference type");
    case CSeq_loc::e_Feat:
        NCBI_THROW(CSeqMapException, eDataError,
                   "e_Feat is not allowed as a reference type");
    default:
        NCBI_THROW(CSeqMapException, eDataError,
                   "invalid reference type");
    }
}


CSeqMap::CSegment& CSeqMap::x_Add(const CDelta_seq& seq)
{
    switch ( seq.Which() ) {
    case CDelta_seq::e_Loc:
        return x_Add(seq.GetLoc());
    case CDelta_seq::e_Literal:
        return x_Add(seq.GetLiteral());
    default:
        NCBI_THROW(CSeqMapException, eDataError,
                   "Can not add empty Delta-seq");
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_map.cpp,v $
* Revision 1000.4  2004/06/01 19:24:15  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.53
*
* Revision 1.53  2004/05/21 21:42:13  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.52  2004/03/16 15:47:28  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.51  2004/02/19 17:19:10  vasilche
* Removed 'unused argument' warning.
*
* Revision 1.50  2003/11/19 22:18:04  grichenk
* All exceptions are now CException-derived. Catch "exception" rather
* than "runtime_error".
*
* Revision 1.49  2003/11/12 16:53:17  grichenk
* Modified CSeqMap to work with const objects (CBioseq, CSeq_loc etc.)
*
* Revision 1.48  2003/09/30 16:22:04  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 1.47  2003/09/05 17:29:40  grichenk
* Structurized Object Manager exceptions
*
* Revision 1.46  2003/08/27 14:27:19  vasilche
* Use Reverse(ENa_strand) function.
*
* Revision 1.45  2003/07/17 19:10:28  grichenk
* Added methods for seq-map and seq-vector validation,
* updated demo.
*
* Revision 1.44  2003/07/14 21:13:26  grichenk
* Added possibility to resolve seq-map iterator withing a single TSE
* and to skip intermediate references during this resolving.
*
* Revision 1.43  2003/06/30 18:39:18  vasilche
* Fixed access to uninitialized member.
*
* Revision 1.42  2003/06/27 19:09:02  grichenk
* Fixed problem with unset sequence length.
*
* Revision 1.41  2003/06/26 19:47:27  grichenk
* Added sequence length cache
*
* Revision 1.40  2003/06/24 14:22:46  vasilche
* Fixed CSeqMap constructor from CSeq_loc.
*
* Revision 1.39  2003/06/12 17:04:55  vasilche
* Fixed creation of CSeqMap for sequences with repr == not_set.
*
* Revision 1.38  2003/06/11 19:32:55  grichenk
* Added molecule type caching to CSeqMap, simplified
* coding and sequence type calculations in CSeqVector.
*
* Revision 1.37  2003/06/02 16:06:38  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.36  2003/05/21 16:03:08  vasilche
* Fixed access to uninitialized optional members.
* Added initialization of mandatory members.
*
* Revision 1.35  2003/05/20 20:36:14  vasilche
* Added FindResolved() with strand argument.
*
* Revision 1.34  2003/05/20 15:44:38  vasilche
* Fixed interaction of CDataSource and CDataLoader in multithreaded app.
* Fixed some warnings on WorkShop.
* Added workaround for memory leak on WorkShop.
*
* Revision 1.33  2003/04/24 16:12:38  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.32  2003/02/24 18:57:22  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 1.31  2003/02/05 17:59:17  dicuccio
* Moved formerly private headers into include/objects/objmgr/impl
*
* Revision 1.30  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 1.29  2003/01/28 17:16:06  vasilche
* Added CSeqMap::ResolvedRangeIterator with strand coordinate translation.
*
* Revision 1.28  2003/01/22 20:11:54  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 1.27  2002/12/26 20:55:18  dicuccio
* Moved seq_id_mapper.hpp, tse_info.hpp, and bioseq_info.hpp -> include/ tree
*
* Revision 1.26  2002/12/26 20:35:14  ucko
* #include <algorithm> for upper_bound<>
*
* Revision 1.25  2002/12/26 16:39:24  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.24  2002/11/04 21:29:12  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.23  2002/10/18 19:12:40  grichenk
* Removed mutex pools, converted most static mutexes to non-static.
* Protected CSeqMap::x_Resolve() with mutex. Modified code to prevent
* dead-locks.
*
* Revision 1.22  2002/07/08 20:51:02  grichenk
* Moved log to the end of file
* Replaced static mutex (in CScope, CDataSource) with the mutex
* pool. Redesigned CDataSource data locking.
*
* Revision 1.21  2002/05/29 21:21:13  gouriano
* added debug dump
*
* Revision 1.20  2002/05/06 17:43:06  ivanov
* ssize_t changed to long
*
* Revision 1.19  2002/05/06 17:03:49  ivanov
* Sorry. Rollback to R1.17
*
* Revision 1.18  2002/05/06 16:56:23  ivanov
* Fixed typo ssize_t -> size_t
*
* Revision 1.17  2002/05/06 03:28:47  vakatov
* OM/OM1 renaming
*
* Revision 1.16  2002/05/03 21:28:10  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.15  2002/05/02 20:42:38  grichenk
* throw -> THROW1_TRACE
*
* Revision 1.14  2002/04/30 18:55:41  gouriano
* added GetRefSeqid function
*
* Revision 1.13  2002/04/11 12:07:30  grichenk
* Redesigned CAnnotTypes_CI to resolve segmented sequences correctly.
*
* Revision 1.12  2002/04/04 21:33:55  grichenk
* Fixed x_FindSegment() for sequences with unresolved segments
*
* Revision 1.11  2002/04/03 18:06:48  grichenk
* Fixed segmented sequence bugs (invalid positioning of literals
* and gaps). Improved CSeqVector performance.
*
* Revision 1.9  2002/03/08 21:36:21  gouriano
* *** empty log message ***
*
* Revision 1.8  2002/03/08 21:24:35  gouriano
* fixed errors with unresolvable references
*
* Revision 1.7  2002/02/25 21:05:29  grichenk
* Removed seq-data references caching. Increased MT-safety. Fixed typos.
*
* Revision 1.6  2002/02/21 19:27:06  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.5  2002/02/01 21:49:38  gouriano
* minor changes to make it compilable and run on Solaris Workshop
*
* Revision 1.4  2002/01/30 22:09:28  gouriano
* changed CSeqMap interface
*
* Revision 1.3  2002/01/23 21:59:32  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.2  2002/01/16 16:25:56  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:06:24  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/