bioseq_info.cpp

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bool CBioseq_Info::CanGetInst_Fuzz(void) const
{
    return CanGetInst() && GetInst().CanGetFuzz();
}


const CBioseq_Info::TInst_Fuzz& CBioseq_Info::GetInst_Fuzz(void) const
{
    return GetInst().GetFuzz();
}


bool CBioseq_Info::IsSetInst_Topology(void) const
{
    return IsSetInst() && GetInst().IsSetTopology();
}


bool CBioseq_Info::CanGetInst_Topology(void) const
{
    return CanGetInst() && GetInst().CanGetTopology();
}


CBioseq_Info::TInst_Topology CBioseq_Info::GetInst_Topology(void) const
{
    return GetInst().GetTopology();
}


bool CBioseq_Info::IsSetInst_Strand(void) const
{
    return IsSetInst() && GetInst().IsSetStrand();
}


bool CBioseq_Info::CanGetInst_Strand(void) const
{
    return CanGetInst() && GetInst().CanGetStrand();
}


CBioseq_Info::TInst_Strand CBioseq_Info::GetInst_Strand(void) const
{
    return GetInst().GetStrand();
}


bool CBioseq_Info::IsSetInst_Seq_data(void) const
{
    return IsSetInst() && GetInst().IsSetSeq_data();
}


bool CBioseq_Info::CanGetInst_Seq_data(void) const
{
    return CanGetInst() && GetInst().CanGetSeq_data();
}


const CBioseq_Info::TInst_Seq_data& CBioseq_Info::GetInst_Seq_data(void) const
{
    return GetInst().GetSeq_data();
}


bool CBioseq_Info::IsSetInst_Ext(void) const
{
    return IsSetInst() && GetInst().IsSetExt();
}


bool CBioseq_Info::CanGetInst_Ext(void) const
{
    return CanGetInst() && GetInst().CanGetExt();
}


const CBioseq_Info::TInst_Ext& CBioseq_Info::GetInst_Ext(void) const
{
    return GetInst().GetExt();
}


bool CBioseq_Info::IsSetInst_Hist(void) const
{
    return IsSetInst() && GetInst().IsSetHist();
}


bool CBioseq_Info::CanGetInst_Hist(void) const
{
    return CanGetInst() && GetInst().CanGetHist();
}


const CBioseq_Info::TInst_Hist& CBioseq_Info::GetInst_Hist(void) const
{
    return GetInst().GetHist();
}


void CBioseq_Info::SetInst(TInst& v)
{
    m_Object->SetInst(v);
}


void CBioseq_Info::SetInst_Repr(TInst_Repr v)
{
    m_Object->SetInst().SetRepr(v);;
}


void CBioseq_Info::SetInst_Mol(TInst_Mol v)
{
    m_Object->SetInst().SetMol(v);;
}


void CBioseq_Info::SetInst_Length(TInst_Length v)
{
    m_Object->SetInst().SetLength(v);;
}


void CBioseq_Info::SetInst_Fuzz(TInst_Fuzz& v)
{
    m_Object->SetInst().SetFuzz(v);;
}


void CBioseq_Info::SetInst_Topology(TInst_Topology v)
{
    m_Object->SetInst().SetTopology(v);;
}


void CBioseq_Info::SetInst_Strand(TInst_Strand v)
{
    m_Object->SetInst().SetStrand(v);;
}


void CBioseq_Info::SetInst_Seq_data(TInst_Seq_data& v)
{
    m_Object->SetInst().SetSeq_data(v);;
}


void CBioseq_Info::SetInst_Ext(TInst_Ext& v)
{
    m_Object->SetInst().SetExt(v);
}


void CBioseq_Info::SetInst_Hist(TInst_Hist& v)
{
    m_Object->SetInst().SetHist(v);;
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(void) const
{
    return x_CalcBioseqLength(GetInst());
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CSeq_inst& inst) const
{
    if ( !inst.IsSetExt() ) {
        NCBI_THROW(CObjMgrException, eOtherError,
                   "CBioseq_Info::x_CalcBioseqLength: "
                   "failed: Seq-inst.ext is not set");
    }
    switch ( inst.GetExt().Which() ) {
    case CSeq_ext::e_Seg:
        return x_CalcBioseqLength(inst.GetExt().GetSeg());
    case CSeq_ext::e_Ref:
        return x_CalcBioseqLength(inst.GetExt().GetRef().Get());
    case CSeq_ext::e_Delta:
        return x_CalcBioseqLength(inst.GetExt().GetDelta());
    default:
        NCBI_THROW(CObjMgrException, eOtherError,
                   "CBioseq_Info::x_CalcBioseqLength: "
                   "failed: bad Seg-ext type");
    }
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CSeq_id& whole) const
{
    CConstRef<CBioseq_Info> ref =
        GetTSE_Info().FindBioseq(CSeq_id_Handle::GetHandle(whole));
    if ( !ref ) {
        NCBI_THROW(CObjMgrException, eOtherError,
                   "CBioseq_Info::x_CalcBioseqLength: "
                   "failed: external whole reference");
    }
    return ref->GetBioseqLength();
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CPacked_seqint& ints) const
{
    TSeqPos ret = 0;
    ITERATE ( CPacked_seqint::Tdata, it, ints.Get() ) {
        ret += (*it)->GetLength();
    }
    return ret;
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CSeq_loc& seq_loc) const
{
    switch ( seq_loc.Which() ) {
    case CSeq_loc::e_not_set:
    case CSeq_loc::e_Null:
    case CSeq_loc::e_Empty:
        return 0;
    case CSeq_loc::e_Whole:
        return x_CalcBioseqLength(seq_loc.GetWhole());
    case CSeq_loc::e_Int:
        return seq_loc.GetInt().GetLength();
    case CSeq_loc::e_Pnt:
        return 1;
    case CSeq_loc::e_Packed_int:
        return x_CalcBioseqLength(seq_loc.GetPacked_int());
    case CSeq_loc::e_Packed_pnt:
        return seq_loc.GetPacked_pnt().GetPoints().size();
    case CSeq_loc::e_Mix:
        return x_CalcBioseqLength(seq_loc.GetMix());
    case CSeq_loc::e_Equiv:
        return x_CalcBioseqLength(seq_loc.GetEquiv());
    default:
        NCBI_THROW(CObjMgrException, eOtherError,
                   "CBioseq_Info::x_CalcBioseqLength: "
                   "failed: bad Seq-loc type");
    }
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CSeq_loc_mix& seq_mix) const
{
    TSeqPos ret = 0;
    ITERATE ( CSeq_loc_mix::Tdata, it, seq_mix.Get() ) {
        ret += x_CalcBioseqLength(**it);
    }
    return ret;
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CSeq_loc_equiv& seq_equiv) const
{
    TSeqPos ret = 0;
    ITERATE ( CSeq_loc_equiv::Tdata, it, seq_equiv.Get() ) {
        ret += x_CalcBioseqLength(**it);
    }
    return ret;
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CSeg_ext& seg_ext) const
{
    TSeqPos ret = 0;
    ITERATE ( CSeg_ext::Tdata, it, seg_ext.Get() ) {
        ret += x_CalcBioseqLength(**it);
    }
    return ret;
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CDelta_ext& delta) const
{
    TSeqPos ret = 0;
    ITERATE ( CDelta_ext::Tdata, it, delta.Get() ) {
        ret += x_CalcBioseqLength(**it);
    }
    return ret;
}


TSeqPos CBioseq_Info::x_CalcBioseqLength(const CDelta_seq& delta_seq) const
{
    switch ( delta_seq.Which() ) {
    case CDelta_seq::e_Loc:
        return x_CalcBioseqLength(delta_seq.GetLoc());
    case CDelta_seq::e_Literal:
        return delta_seq.GetLiteral().GetLength();
    default:
        NCBI_THROW(CObjMgrException, eOtherError,
                   "CBioseq_Info::x_CalcBioseqLength: "
                   "failed: bad Delta-seq type");
    }
}


string CBioseq_Info::IdString(void) const
{
    CNcbiOstrstream os;
    ITERATE ( TId, it, m_Id ) {
        if ( it != m_Id.begin() )
            os << " | ";
        os << it->AsString();
    }
    return CNcbiOstrstreamToString(os);
}


void CBioseq_Info::x_AttachMap(CSeqMap& seq_map)
{
    CFastMutexGuard guard(m_SeqMap_Mtx);
    if ( m_SeqMap ) {
        NCBI_THROW(CObjMgrException, eAddDataError,
                     "CBioseq_Info::AttachMap: bioseq already has SeqMap");
    }
    m_SeqMap.Reset(&seq_map);
}


const CSeqMap& CBioseq_Info::GetSeqMap(void) const
{
    const CSeqMap* ret = m_SeqMap.GetPointer();
    if ( !ret ) {
        CFastMutexGuard guard(m_SeqMap_Mtx);
        ret = m_SeqMap.GetPointer();
        if ( !ret ) {
            m_SeqMap = CSeqMap::CreateSeqMapForBioseq(*m_Object);
            ret = m_SeqMap.GetPointer();
            _ASSERT(ret);
        }
    }
    return *ret;
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: bioseq_info.cpp,v $
* Revision 1000.4  2004/06/01 19:22:57  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.22
*
* Revision 1.22  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.21  2004/05/11 18:05:03  grichenk
* include algorithm
*
* Revision 1.20  2004/05/11 17:45:51  grichenk
* Implemented HasId(), AddId() and RemoveId()
*
* Revision 1.19  2004/05/06 17:32:37  grichenk
* Added CanGetXXXX() methods
*
* Revision 1.18  2004/03/31 17:08:07  vasilche
* Implemented ConvertSeqToSet and ConvertSetToSeq.
*
* Revision 1.17  2004/03/24 18:30:29  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.16  2004/03/16 15:47:27  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.15  2003/12/11 17:02:50  grichenk
* Fixed CRef resetting in constructors.
*
* Revision 1.14  2003/11/19 22:18:02  grichenk
* All exceptions are now CException-derived. Catch "exception" rather
* than "runtime_error".
*
* Revision 1.13  2003/11/12 16:53:17  grichenk
* Modified CSeqMap to work with const objects (CBioseq, CSeq_loc etc.)
*
* Revision 1.12  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 1.11  2003/06/02 16:06:37  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 1.10  2003/04/24 16:12:38  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.9  2003/03/14 19:10:41  grichenk
* + SAnnotSelector::EIdResolving; fixed operator=() for several classes
*
* Revision 1.8  2003/03/11 15:51:06  kuznets
* iterate -> ITERATE
*
* Revision 1.7  2003/02/05 17:59:17  dicuccio
* Moved formerly private headers into include/objects/objmgr/impl
*
* Revision 1.6  2002/12/26 20:55:17  dicuccio
* Moved seq_id_mapper.hpp, tse_info.hpp, and bioseq_info.hpp -> include/ tree
*
* Revision 1.5  2002/11/04 21:29:12  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.4  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 1.3  2002/05/29 21:21:13  gouriano
* added debug dump
*
* Revision 1.2  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 1.1  2002/02/07 21:25:05  grichenk
* Initial revision
*
*
* ===========================================================================
*/