bioseq_handle.cpp

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            seg_loc->SetInt().SetId(*id);
            seg_loc->SetInt().SetFrom(rit->first.GetFrom());
            seg_loc->SetInt().SetTo(rit->first.GetTo());
            view_loc->SetMix().Set().push_back(seg_loc);
        }
        ret = CSeqMap::CreateSeqMapForSeq_loc(*view_loc, &GetScope());
    }
    return ret;
}


CSeq_entry_Handle CBioseq_Handle::GetTopLevelEntry(void) const
{
    return CSeq_entry_Handle(GetScope(),
                             x_GetInfo().GetTSE_Info());
}


CSeq_entry_Handle CBioseq_Handle::GetParentEntry(void) const
{
    return CSeq_entry_Handle(m_Scope,
                             x_GetInfo().GetParentSeq_entry_Info());
}


CSeq_entry_Handle CBioseq_Handle::GetSeq_entry_Handle(void) const
{
    return GetParentEntry();
}



static int s_Complexity[] = {
    0, // not-set (0)
    3, // nuc-prot (1)
    2, // segset (2)
    2, // conset (3)
    1, // parts (4)
    1, // gibb (5)
    1, // gi (6)
    5, // genbank (7)
    3, // pir (8)
    4, // pub-set (9)
    4, // equiv (10)
    3, // swissprot (11)
    3, // pdb-entry (12)
    4, // mut-set (13)
    4, // pop-set (14)
    4, // phy-set (15)
    4, // eco-set (16)
    4, // gen-prod-set (17)
    4, // wgs-set (18)
    0, // other (255 - processed separately)
};


CSeq_entry_Handle
CBioseq_Handle::GetComplexityLevel(CBioseq_set::EClass cls) const
{
    if (cls == CBioseq_set::eClass_other) {
        // adjust 255 to the correct value
        cls = CBioseq_set::EClass(sizeof(s_Complexity) - 1);
    }
    CSeq_entry_Handle last = GetParentEntry();
    _ASSERT(last && last.IsSeq());
    CSeq_entry_Handle e = last.GetParentEntry();
    while ( e ) {
        _ASSERT(e.IsSet());
        // Found good level
        if ( last.IsSet()  &&
             s_Complexity[last.GetSet().GetClass()] == s_Complexity[cls] )
            break;
        // Gone too high
        if ( s_Complexity[e.GetSet().GetClass()] > s_Complexity[cls] ) {
            break;
        }
        // Go up one level
        last = e;
        e = e.GetParentEntry();
    }
    return last;
}


CSeq_entry_Handle
CBioseq_Handle::GetExactComplexityLevel(CBioseq_set::EClass cls) const
{
    CSeq_entry_Handle ret = GetComplexityLevel(cls);
    if ( ret  &&  
         (!ret.IsSet()  ||  !ret.GetSet().IsSetClass()  ||
         ret.GetSet().GetClass() != cls) ) {
        ret.Reset();
    }
    return ret;
}


CRef<CSeq_loc> CBioseq_Handle::MapLocation(const CSeq_loc& loc) const
{
    CSeq_loc_Mapper mapper(*this);
    return mapper.Map(loc);
}


CBioseq_EditHandle
CBioseq_Handle::CopyTo(const CSeq_entry_EditHandle& entry,
                       int index) const
{
    return entry.CopyBioseq(*this, index);
}


CBioseq_EditHandle
CBioseq_Handle::CopyTo(const CBioseq_set_EditHandle& seqset,
                       int index) const
{
    return seqset.CopyBioseq(*this, index);
}


CBioseq_EditHandle
CBioseq_Handle::CopyToSeq(const CSeq_entry_EditHandle& entry) const
{
    return entry.CopySeq(*this);
}


/////////////////////////////////////////////////////////////////////////////
// CBioseq_EditHandle
/////////////////////////////////////////////////////////////////////////////

CBioseq_EditHandle::CBioseq_EditHandle(void)
{
}


CBioseq_EditHandle::CBioseq_EditHandle(const CBioseq_Handle& h)
    : CBioseq_Handle(h)
{
}


CSeq_entry_EditHandle CBioseq_EditHandle::GetParentEntry(void) const
{
    return CSeq_entry_EditHandle(m_Scope,
                                 x_GetInfo().GetParentSeq_entry_Info());
}


CSeq_annot_EditHandle
CBioseq_EditHandle::AttachAnnot(const CSeq_annot& annot) const
{
    return GetParentEntry().AttachAnnot(annot);
}


CSeq_annot_EditHandle
CBioseq_EditHandle::CopyAnnot(const CSeq_annot_Handle& annot) const
{
    return GetParentEntry().CopyAnnot(annot);
}


CSeq_annot_EditHandle
CBioseq_EditHandle::TakeAnnot(const CSeq_annot_EditHandle& annot) const
{
    return GetParentEntry().TakeAnnot(annot);
}


CBioseq_EditHandle
CBioseq_EditHandle::MoveTo(const CSeq_entry_EditHandle& entry,
                           int index) const
{
    return entry.TakeBioseq(*this, index);
}


CBioseq_EditHandle
CBioseq_EditHandle::MoveTo(const CBioseq_set_EditHandle& seqset,
                                int index) const
{
    return seqset.TakeBioseq(*this, index);
}


CBioseq_EditHandle
CBioseq_EditHandle::MoveToSeq(const CSeq_entry_EditHandle& entry) const
{
    return entry.TakeSeq(*this);
}


void CBioseq_EditHandle::Remove(void) const
{
    m_Scope->RemoveBioseq(*this);
}


/////////////////////////////////////////////////////////////////////////////
// Bioseq members

void CBioseq_EditHandle::SetDescr(TDescr& v) const
{
    x_GetInfo().SetDescr(v);
}


void CBioseq_EditHandle::SetInst(TInst& v) const
{
    x_GetInfo().SetInst(v);
}


void CBioseq_EditHandle::SetInst_Repr(TInst_Repr v) const
{
    x_GetInfo().SetInst_Repr(v);
}


void CBioseq_EditHandle::SetInst_Mol(TInst_Mol v) const
{
    x_GetInfo().SetInst_Mol(v);
}


void CBioseq_EditHandle::SetInst_Length(TInst_Length v) const
{
    x_GetInfo().SetInst_Length(v);
}


void CBioseq_EditHandle::SetInst_Fuzz(TInst_Fuzz& v) const
{
    x_GetInfo().SetInst_Fuzz(v);
}


void CBioseq_EditHandle::SetInst_Topology(TInst_Topology v) const
{
    x_GetInfo().SetInst_Topology(v);
}


void CBioseq_EditHandle::SetInst_Strand(TInst_Strand v) const
{
    x_GetInfo().SetInst_Strand(v);
}


void CBioseq_EditHandle::SetInst_Seq_data(TInst_Seq_data& v) const
{
    x_GetInfo().SetInst_Seq_data(v);
}


void CBioseq_EditHandle::SetInst_Ext(TInst_Ext& v) const
{
    x_GetInfo().SetInst_Ext(v);
}


void CBioseq_EditHandle::SetInst_Hist(TInst_Hist& v) const
{
    x_GetInfo().SetInst_Hist(v);
}



// end of Bioseq members
/////////////////////////////////////////////////////////////////////////////


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: bioseq_handle.cpp,v $
* Revision 1000.5  2004/06/01 19:22:54  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.66
*
* Revision 1.66  2004/05/27 14:59:49  shomrat
* Added CBioseq_EditHandle constructor implementation
*
* Revision 1.65  2004/05/26 14:29:20  grichenk
* Redesigned CSeq_align_Mapper: preserve non-mapping intervals,
* fixed strands handling, improved performance.
*
* Revision 1.64  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.63  2004/05/10 18:26:37  grichenk
* Fixed 'not used' warnings
*
* Revision 1.62  2004/05/06 17:32:37  grichenk
* Added CanGetXXXX() methods
*
* Revision 1.61  2004/04/20 20:34:40  shomrat
* fix GetExactComplexityLevel
*
* Revision 1.60  2004/03/31 19:54:08  vasilche
* Fixed removal of bioseqs and bioseq-sets.
*
* Revision 1.59  2004/03/31 19:23:13  vasilche
* Fixed scope in CBioseq_Handle::GetEditHandle().
*
* Revision 1.58  2004/03/29 20:13:06  vasilche
* Implemented whole set of methods to modify Seq-entry object tree.
* Added CBioseq_Handle::GetExactComplexityLevel().
*
* Revision 1.57  2004/03/25 19:27:44  vasilche
* Implemented MoveTo and CopyTo methods of handles.
*
* Revision 1.56  2004/03/24 18:30:29  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.55  2004/03/16 21:01:32  vasilche
* Added methods to move Bioseq withing Seq-entry
*
* Revision 1.54  2004/03/16 15:47:27  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.53  2004/02/06 16:07:27  grichenk
* Added CBioseq_Handle::GetSeq_entry_Handle()
* Fixed MapLocation()
*
* Revision 1.52  2004/01/28 22:10:10  grichenk
* Removed extra seq-loc initialization in MapLocation
*
* Revision 1.51  2004/01/23 16:14:47  grichenk
* Implemented alignment mapping
*
* Revision 1.50  2004/01/22 20:10:40  vasilche
* 1. Splitted ID2 specs to two parts.
* ID2 now specifies only protocol.
* Specification of ID2 split data is moved to seqsplit ASN module.
* For now they are still reside in one resulting library as before - libid2.
* As the result split specific headers are now in objects/seqsplit.
* 2. Moved ID2 and ID1 specific code out of object manager.
* Protocol is processed by corresponding readers.
* ID2 split parsing is processed by ncbi_xreader library - used by all readers.
* 3. Updated OBJMGR_LIBS correspondingly.
*
* Revision 1.49  2003/11/28 15:13:26  grichenk
* Added CSeq_entry_Handle
*
* Revision 1.48  2003/11/26 17:55:57  vasilche
* Implemented ID2 split in ID1 cache.
* Fixed loading of splitted annotations.
*
* Revision 1.47  2003/11/10 18:12:43  grichenk
* Added MapLocation()
*
* Revision 1.46  2003/09/30 16:22:02  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 1.45  2003/09/05 17:29:40  grichenk
* Structurized Object Manager exceptions
*
* Revision 1.44  2003/08/27 14:27:19  vasilche
* Use Reverse(ENa_strand) function.
*
* Revision 1.43  2003/07/15 16:14:08  grichenk
* CBioseqHandle::IsSynonym() made public
*
* Revision 1.42  2003/06/24 14:22:46  vasilche
* Fixed CSeqMap constructor from CSeq_loc.
*
* Revision 1.41  2003/06/19 18:23:45  vasilche
* Added several CXxx_ScopeInfo classes for CScope related information.
* CBioseq_Handle now uses reference to CBioseq_ScopeInfo.
* Some fine tuning of locking in CScope.
*
* Revision 1.38  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 1.37  2003/04/29 19:51:13  vasilche
* Fixed interaction of Data Loader garbage collector and TSE locking mechanism.
* Made some typedefs more consistent.
*
* Revision 1.36  2003/04/24 16:12:38  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.35  2003/03/27 19:39:36  grichenk
* +CBioseq_Handle::GetComplexityLevel()
*
* Revision 1.34  2003/03/18 14:52:59  grichenk
* Removed obsolete methods, replaced seq-id with seq-id handle
* where possible. Added argument to limit annotations update to
* a single seq-entry.
*
* Revision 1.33  2003/03/12 20:09:33  grichenk
* Redistributed members between CBioseq_Handle, CBioseq_Info and CTSE_Info
*
* Revision 1.32  2003/03/11 15:51:06  kuznets
* iterate -> ITERATE
*
* Revision 1.31  2003/02/05 17:59:17  dicuccio
* Moved formerly private headers into include/objects/objmgr/impl
*
* Revision 1.30  2003/01/29 22:03:46  grichenk
* Use single static CSeq_id_Mapper instead of per-OM model.
*
* Revision 1.29  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 1.28  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 20:55:17  dicuccio
* Moved seq_id_mapper.hpp, tse_info.hpp, and bioseq_info.hpp -> include/ tree
*
* Revision 1.26  2002/12/26 16:39:24  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.25  2002/12/06 15:36:00  grichenk
* Added overlap type for annot-iterators
*
* Revision 1.24  2002/11/08 22:15:51  grichenk
* Added methods for removing/replacing annotations
*
* Revision 1.23  2002/11/08 19:43:35  grichenk
* CConstRef<> constructor made explicit
*
* Revision 1.22  2002/09/03 21:27:01  grichenk
* Replaced bool arguments in CSeqVector constructor and getters
* with enums.
*
* Revision 1.21  2002/07/10 16:49:29  grichenk
* Removed commented reference to old CDataSource mutex
*
* Revision 1.20  2002/07/08 20:51:01  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  2002/06/12 14:39:02  grichenk
* Renamed enumerators
*
* Revision 1.18  2002/06/06 21:00:42  clausen
* Added include for scope.hpp
*
* Revision 1.17  2002/05/31 17:53:00  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 1.16  2002/05/24 14:57:12  grichenk
* SerialAssign<>() -> CSerialObject::Assign()
*
* Revision 1.15  2002/05/21 18:39:30  grichenk
* CBioseq_Handle::GetResolvedSeqMap() -> CreateResolvedSeqMap()
*
* Revision 1.14  2002/05/06 03:28:46  vakatov
* OM/OM1 renaming
*
* Revision 1.13  2002/05/03 21:28:08  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.12  2002/04/29 16:23:28  grichenk
* GetSequenceView() reimplemented in CSeqVector.
* CSeqVector optimized for better performance.
*
* Revision 1.11  2002/04/23 19:01:07  grichenk
* Added optional flag to GetSeqVector() and GetSequenceView()
* for switching to IUPAC encoding.
*
* Revision 1.10  2002/04/22 20:06:59  grichenk
* +GetSequenceView(), +x_IsSynonym()
*
* Revision 1.9  2002/04/11 12:07:30  grichenk
* Redesigned CAnnotTypes_CI to resolve segmented sequences correctly.
*
* Revision 1.8  2002/03/19 19:16:28  gouriano
* added const qualifier to GetTitle and GetSeqVector
*
* Revision 1.7  2002/03/15 18:10:07  grichenk
* Removed CRef<CSeq_id> from CSeq_id_Handle, added
* key to seq-id map th CSeq_id_Mapper
*
* Revision 1.6  2002/03/04 15:08:44  grichenk
* Improved CTSE_Info locks
*
* Revision 1.5  2002/02/21 19:27:05  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.4  2002/01/28 19:44:49  gouriano
* changed the interface of BioseqHandle: two functions moved from Scope
*
* Revision 1.3  2002/01/23 21:59:31  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 19:06:17  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/