seq_entry_info.cpp

来自「ncbi源码」· C++ 代码 · 共 630 行 · 第 1/2 页

    }
    x_DSUnmapObject(m_Object, ds);
    TParent::x_DSDetachContents(ds);
}


void CSeq_entry_Info::x_DSMapObject(CConstRef<TObject> obj, CDataSource& ds)
{
    ds.x_Map(obj, this);
}


void CSeq_entry_Info::x_DSUnmapObject(CConstRef<TObject> obj, CDataSource& ds)
{
    ds.x_Unmap(obj, this);
}


void CSeq_entry_Info::x_SetObject(TObject& obj)
{
    x_CheckWhich(CSeq_entry::e_not_set);
    _ASSERT(!m_Object);
    _ASSERT(!m_Contents);

    m_Object.Reset(&obj);
    switch ( (m_Which = obj.Which()) ) {
    case CSeq_entry::e_Seq:
        m_Contents.Reset(new CBioseq_Info(obj.SetSeq()));
        break;
    case CSeq_entry::e_Set:
        m_Contents.Reset(new CBioseq_set_Info(obj.SetSet()));
        break;
    default:
        break;
    }
    x_AttachContents();
}


void CSeq_entry_Info::x_SetObject(const CSeq_entry_Info& info)
{
    x_CheckWhich(CSeq_entry::e_not_set);
    _ASSERT(!m_Object);
    _ASSERT(!m_Contents);

    m_Which = info.m_Which;
    m_Object.Reset(new CSeq_entry);
    switch ( m_Which ) {
    case CSeq_entry::e_Seq:
    {
        CRef<CBioseq_Info> seq(new CBioseq_Info(info.GetSeq()));
        m_Contents.Reset(seq);
        x_AttachObjectVariant(seq->x_GetObject());
        break;
    }
    case CSeq_entry::e_Set:
    {
        CRef<CBioseq_set_Info> seqset(new CBioseq_set_Info(info.GetSet()));
        m_Contents.Reset(seqset);
        x_AttachObjectVariant(seqset->x_GetObject());
        break;
    }
    default:
        break;
    }
    x_AttachContents();
}


void CSeq_entry_Info::x_DetachObjectVariant(void)
{
    m_Object->Reset();
}


void CSeq_entry_Info::x_AttachObjectVariant(CBioseq_set& seqset)
{
    x_DetachObjectVariant();
    m_Object->SetSet(seqset);
}


void CSeq_entry_Info::x_AttachObjectVariant(CBioseq& seq)
{
    x_DetachObjectVariant();
    m_Object->SetSeq(seq);
}

/*
CRef<CSeq_entry> CSeq_entry_Info::x_CreateObject(void) const
{        
    CRef<TObject> obj(new TObject);
    switch ( Which() ) {
    case CSeq_entry::e_Set:
        obj->SetSet(const_cast<CBioseq_set&>
                    (*GetSet().GetCompleteBioseq_set()));
        break;
    case CSeq_entry::e_Seq:
        obj->SetSeq(const_cast<CBioseq&>
                    (*GetSeq().GetCompleteBioseq()));
        break;
    default:
        break;
    }
    return obj;
}
*/


void CSeq_entry_Info::x_AttachContents(void)
{
    if ( m_Contents ) {
        m_Contents->x_ParentAttach(*this);
        x_AttachObject(*m_Contents);
    }
}


void CSeq_entry_Info::x_DetachContents(void)
{
    if ( m_Contents ) {
        x_DetachObject(*m_Contents);
        m_Contents->x_ParentDetach(*this);
    }
}


void CSeq_entry_Info::UpdateAnnotIndex(void) const
{
    if ( x_DirtyAnnotIndex() ) {
        GetTSE_Info().UpdateAnnotIndex(*this);
        _ASSERT(!x_DirtyAnnotIndex());
    }
}


void CSeq_entry_Info::x_UpdateAnnotIndexContents(CTSE_Info& tse)
{
    m_Contents->x_UpdateAnnotIndex(tse);
    TParent::x_UpdateAnnotIndexContents(tse);
}


bool CSeq_entry_Info::IsSetDescr(void) const
{
    return bool(m_Contents) && m_Contents->IsSetDescr();
}


const CSeq_descr& CSeq_entry_Info::GetDescr(void) const
{
    return m_Contents->GetDescr();
}


void CSeq_entry_Info::SetDescr(TDescr& v)
{
    m_Contents->SetDescr(v);
}


void CSeq_entry_Info::ResetDescr(void)
{
    m_Contents->ResetDescr();
}


bool CSeq_entry_Info::AddSeqdesc(CSeqdesc& d)
{
    return m_Contents->AddSeqdesc(d);
}


bool CSeq_entry_Info::RemoveSeqdesc(const CSeqdesc& d)
{
    return m_Contents->RemoveSeqdesc(d);
}


void CSeq_entry_Info::AddDescr(CSeq_entry_Info& src)
{
    if ( src.IsSetDescr() ) {
        m_Contents->AddSeq_descr(src.m_Contents->x_SetDescr());
    }
}


CRef<CSeq_annot_Info> CSeq_entry_Info::AddAnnot(const CSeq_annot& annot)
{
    return m_Contents->AddAnnot(annot);
}


void CSeq_entry_Info::AddAnnot(CRef<CSeq_annot_Info> annot)
{
    m_Contents->AddAnnot(annot);
}


void CSeq_entry_Info::RemoveAnnot(CRef<CSeq_annot_Info> annot)
{
    m_Contents->RemoveAnnot(annot);
}


CRef<CSeq_entry_Info> CSeq_entry_Info::AddEntry(CSeq_entry& entry,
                                                  int index)
{
    x_CheckWhich(CSeq_entry::e_Set);
    return SetSet().AddEntry(entry, index);
}


void CSeq_entry_Info::AddEntry(CRef<CSeq_entry_Info> entry, int index)
{
    x_CheckWhich(CSeq_entry::e_Set);
    SetSet().AddEntry(entry, index);
}


void CSeq_entry_Info::RemoveEntry(CRef<CSeq_entry_Info> entry)
{
    x_CheckWhich(CSeq_entry::e_Set);
    SetSet().RemoveEntry(entry);
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: seq_entry_info.cpp,v $
 * Revision 1000.3  2004/06/01 19:24:00  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 *
 * Revision 1.15  2004/05/21 21:42:13  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.14  2004/03/31 17:08:07  vasilche
 * Implemented ConvertSeqToSet and ConvertSetToSeq.
 *
 * Revision 1.13  2004/03/25 19:27:44  vasilche
 * Implemented MoveTo and CopyTo methods of handles.
 *
 * Revision 1.12  2004/03/24 18:30:30  vasilche
 * Fixed edit API.
 * Every *_Info object has its own shallow copy of original object.
 *
 * Revision 1.11  2004/03/16 15:47:28  vasilche
 * Added CBioseq_set_Handle and set of EditHandles
 *
 * Revision 1.10  2004/02/03 19:02:18  vasilche
 * Fixed broken 'dirty annot index' state after RemoveEntry().
 *
 * Revision 1.9  2004/02/02 14:46:44  vasilche
 * Several performance fixed - do not iterate whole tse set in CDataSource.
 *
 * Revision 1.8  2004/01/29 19:33:07  vasilche
 * Fixed coredump on WorkShop when invalid Seq-entry is added to CScope.
 *
 * Revision 1.7  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 1.6  2003/12/18 16:38:07  grichenk
 * Added CScope::RemoveEntry()
 *
 * Revision 1.5  2003/12/11 17:02:50  grichenk
 * Fixed CRef resetting in constructors.
 *
 * Revision 1.4  2003/11/19 22:18:03  grichenk
 * All exceptions are now CException-derived. Catch "exception" rather
 * than "runtime_error".
 *
 * Revision 1.3  2003/09/30 16:22:03  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 1.2  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 1.1  2003/04/24 16:12:38  vasilche
 * Object manager internal structures are splitted more straightforward.
 * Removed excessive header dependencies.
 *
 *
 * ===========================================================================
 */