seq_annot_handle.cpp

来自「ncbi源码」· C++ 代码 · 共 182 行

/*
 * ===========================================================================
 * PRODUCTION $Log: seq_annot_handle.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:23:49  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: seq_annot_handle.cpp,v 1000.2 2004/06/01 19:23:49 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Aleksey Grichenko, Eugene Vasilchenko
*
* File Description:
*
*/

#include <ncbi_pch.hpp>
#include <objmgr/seq_annot_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/impl/scope_impl.hpp>
#include <objmgr/impl/seq_annot_info.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CSeq_annot_Handle::CSeq_annot_Handle(CScope& scope,
                                     const CSeq_annot_Info& info)
    : m_Scope(&scope), m_Info(&info)
{
}


CConstRef<CSeq_annot> CSeq_annot_Handle::GetCompleteSeq_annot(void) const
{
    return x_GetInfo().GetCompleteSeq_annot();
}


const CSeq_annot& CSeq_annot_Handle::GetSeq_annot(void) const
{
    ERR_POST_ONCE(Warning<<
                  "CSeq_annot_Handle::GetSeq_annot() is deprecated, "
                  "use GetCompleteSeq_annot().");
    return *GetCompleteSeq_annot();
}


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


CSeq_entry_Handle CSeq_annot_Handle::GetTopLevelEntry(void) const
{
    CSeq_entry_Handle ret;
    const CSeq_annot_Info& info = x_GetInfo();
    if ( info.HasTSE_Info() ) {
        ret = CSeq_entry_Handle(GetScope(), info.GetTSE_Info());
    }
    return ret;
}


CSeq_annot_EditHandle CSeq_annot_Handle::GetEditHandle(void) const
{
    return m_Scope->GetEditHandle(*this);
}


bool CSeq_annot_Handle::IsNamed(void) const
{
    return x_GetInfo().GetName().IsNamed();
}


const string& CSeq_annot_Handle::GetName(void) const
{
    return x_GetInfo().GetName().GetName();
}


CSeq_annot_Info& CSeq_annot_EditHandle::x_GetInfo(void) const
{
    return const_cast<CSeq_annot_Info&>(CSeq_annot_Handle::x_GetInfo());
}


CSeq_entry_EditHandle CSeq_annot_EditHandle::GetParentEntry(void) const
{
    return CSeq_entry_EditHandle(GetScope(),
                                 x_GetInfo().GetParentSeq_entry_Info());
}


void CSeq_annot_EditHandle::Remove(void) const
{
    m_Scope->RemoveAnnot(*this);
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_annot_handle.cpp,v $
* Revision 1000.2  2004/06/01 19:23:49  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
*
* Revision 1.9  2004/05/21 21:42:13  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.8  2004/04/29 15:44:30  grichenk
* Added GetTopLevelEntry()
*
* Revision 1.7  2004/03/24 18:30:30  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.6  2004/03/16 21:01:32  vasilche
* Added methods to move Bioseq withing Seq-entry
*
* Revision 1.5  2004/03/16 15:47:28  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.4  2003/10/08 17:55:53  vasilche
* Fixed null initialization of CHeapScope.
*
* Revision 1.3  2003/10/08 14:14:27  vasilche
* Use CHeapScope instead of CRef<CScope> internally.
*
* Revision 1.2  2003/10/07 13:43:23  vasilche
* Added proper handling of named Seq-annots.
* Added feature search from named Seq-annots.
* Added configurable adaptive annotation search (default: gene, cds, mrna).
* Fixed selection of blobs for loading from GenBank.
* Added debug checks to CSeq_id_Mapper for easier finding lost CSeq_id_Handles.
* Fixed leaked split chunks annotation stubs.
* Moved some classes definitions in separate *.cpp files.
*
* Revision 1.1  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.
*
* ===========================================================================
*/