seq_annot_info.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: seq_annot_info.cpp,v $
 * PRODUCTION Revision 1000.4  2004/06/01 19:23:51  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.16
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: seq_annot_info.cpp,v 1000.4 2004/06/01 19:23:51 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: Eugene Vasilchenko
*
* File Description:
*   CSeq_annot_Info info -- entry for data source information about Seq-annot
*
*/


#include <ncbi_pch.hpp>
#include <objmgr/impl/seq_annot_info.hpp>
#include <objmgr/impl/seq_entry_info.hpp>
#include <objmgr/impl/bioseq_base_info.hpp>
#include <objmgr/impl/tse_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/annot_object.hpp>
#include <objmgr/impl/handle_range_map.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/snp_annot_info.hpp>
#include <objmgr/objmgr_exception.hpp>

#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seq/Annot_descr.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CSeq_annot_Info::CSeq_annot_Info(const CSeq_annot& annot)
{
    x_SetObject(annot);
}


CSeq_annot_Info::CSeq_annot_Info(CSeq_annot_SNP_Info& snp_annot)
{
    x_SetSNP_annot_Info(snp_annot);
}


CSeq_annot_Info::CSeq_annot_Info(const CSeq_annot_Info& info)
{
    x_SetObject(info);
}


CSeq_annot_Info::~CSeq_annot_Info(void)
{
}


const CBioseq_Base_Info& CSeq_annot_Info::GetParentBioseq_Base_Info(void) const
{
    return static_cast<const CBioseq_Base_Info&>(GetBaseParent_Info());
}


CBioseq_Base_Info& CSeq_annot_Info::GetParentBioseq_Base_Info(void)
{
    return static_cast<CBioseq_Base_Info&>(GetBaseParent_Info());
}


const CSeq_entry_Info& CSeq_annot_Info::GetParentSeq_entry_Info(void) const
{
    return GetParentBioseq_Base_Info().GetParentSeq_entry_Info();
}


CSeq_entry_Info& CSeq_annot_Info::GetParentSeq_entry_Info(void)
{
    return GetParentBioseq_Base_Info().GetParentSeq_entry_Info();
}


void CSeq_annot_Info::x_ParentAttach(CBioseq_Base_Info& parent)
{
    x_BaseParentAttach(parent);
}


void CSeq_annot_Info::x_ParentDetach(CBioseq_Base_Info& parent)
{
    x_BaseParentDetach(parent);
}


void CSeq_annot_Info::x_DSAttachContents(CDataSource& ds)
{
    TParent::x_DSAttachContents(ds);
    x_DSMapObject(m_Object, ds);
    if ( m_SNP_Info ) {
        m_SNP_Info->x_DSAttach(ds);
    }
}


void CSeq_annot_Info::x_DSDetachContents(CDataSource& ds)
{
    if ( m_SNP_Info ) {
        m_SNP_Info->x_DSDetach(ds);
    }
    ITERATE ( TDSMappedObjects, it, m_DSMappedObjects ) {
        x_DSUnmapObject(*it, ds);
    }
    m_DSMappedObjects.clear();
    TParent::x_DSDetachContents(ds);
}


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


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


void CSeq_annot_Info::x_TSEAttachContents(CTSE_Info& tse)
{
    TParent::x_TSEAttachContents(tse);
    if ( m_SNP_Info ) {
        m_SNP_Info->x_TSEAttach(tse);
    }
}


void CSeq_annot_Info::x_TSEDetachContents(CTSE_Info& tse)
{
    if ( m_SNP_Info ) {
        m_SNP_Info->x_TSEDetach(tse);
    }
    x_UnmapAnnotObjects(tse);
    TParent::x_TSEDetachContents(tse);
}


size_t
CSeq_annot_Info::GetAnnotObjectIndex(const CAnnotObject_Info& info) const
{
    _ASSERT(&info.GetSeq_annot_Info() == this);
    return m_ObjectInfos.GetIndex(info);
}


const CAnnotName& CSeq_annot_Info::GetName(void) const
{
    return m_Name.IsNamed()? m_Name: GetTSE_Info().GetName();
}


void CSeq_annot_Info::x_UpdateName(void)
{
    if ( m_Object->IsSetDesc() ) {
        string name;
        ITERATE( CSeq_annot::TDesc::Tdata, it, m_Object->GetDesc().Get() ) {
            const CAnnotdesc& desc = **it;
            if ( desc.Which() == CAnnotdesc::e_Name ) {
                name = desc.GetName();
                break;
            }
        }
        m_Name.SetNamed(name);
    }
    else {
        m_Name.SetUnnamed();
    }
}


CConstRef<CSeq_annot> CSeq_annot_Info::GetCompleteSeq_annot(void) const
{
    return GetSeq_annotCore();
}


CConstRef<CSeq_annot> CSeq_annot_Info::GetSeq_annotCore(void) const
{
    x_UpdateObject();
    return m_Object;
}


void CSeq_annot_Info::x_SetObject(const TObject& obj)
{
    _ASSERT(!m_SNP_Info && !m_Object);
    m_Object.Reset(&obj);
    x_UpdateName();
}


void CSeq_annot_Info::x_SetObject(const CSeq_annot_Info& info)
{
    _ASSERT(!m_SNP_Info && !m_Object);
    m_Object = info.m_Object;
    m_Name = info.m_Name;
    if ( info.m_SNP_Info ) {
        m_SNP_Info.Reset(new CSeq_annot_SNP_Info(*info.m_SNP_Info));
        m_SNP_Info->x_ParentAttach(*this);
        x_AttachObject(*m_SNP_Info);
    }
}


void CSeq_annot_Info::x_SetSNP_annot_Info(CSeq_annot_SNP_Info& snp_info)
{
    _ASSERT(!m_SNP_Info && !m_Object && !snp_info.HasParent_Info());
    x_SetObject(snp_info.GetRemainingSeq_annot());
    m_SNP_Info.Reset(&snp_info);
    snp_info.x_ParentAttach(*this);
    _ASSERT(&snp_info.GetParentSeq_annot_Info() == this);
    x_AttachObject(snp_info);
}


void CSeq_annot_Info::x_DoUpdateObject(void)
{
    NCBI_THROW(CObjMgrException, eNotImplemented,
               "CSeq_annot_Info::x_DoUpdateObject: unimplemented");
}


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