bioseq_set_handle.cpp

来自「ncbi源码」· C++ 代码 · 共 457 行

/*
 * ===========================================================================
 * PRODUCTION $Log: bioseq_set_handle.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:23:00  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: bioseq_set_handle.cpp,v 1000.1 2004/06/01 19:23:00 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:
*    Handle to Seq-entry object
*
*/

#include <ncbi_pch.hpp>
#include <objmgr/bioseq_set_handle.hpp>

#include <objmgr/scope.hpp>

#include <objmgr/impl/scope_impl.hpp>
#include <objmgr/impl/bioseq_set_info.hpp>

#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqset/Seq_entry.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CBioseq_set_Handle::CBioseq_set_Handle(CScope& scope,
                                       const CBioseq_set_Info& info)
    : m_Scope(&scope), m_Info(&info)
{
}


CConstRef<CBioseq_set> CBioseq_set_Handle::GetCompleteBioseq_set(void) const
{
    return x_GetInfo().GetCompleteBioseq_set();
}


CConstRef<CBioseq_set> CBioseq_set_Handle::GetBioseq_setCore(void) const
{
    return x_GetInfo().GetBioseq_setCore();
}


CSeq_entry_Handle CBioseq_set_Handle::GetParentEntry(void) const
{
    CSeq_entry_Handle ret;
    const CBioseq_set_Info& info = x_GetInfo();
    if ( info.HasParent_Info() ) {
        ret = CSeq_entry_Handle(GetScope(), info.GetParentSeq_entry_Info());
    }
    return ret;
}


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


CBioseq_set_EditHandle CBioseq_set_Handle::GetEditHandle(void) const
{
    return m_Scope->GetEditHandle(*this);
}


bool CBioseq_set_Handle::IsSetId(void) const
{
    return x_GetInfo().IsSetId();
}


bool CBioseq_set_Handle::CanGetId(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetId();
}


const CBioseq_set::TId& CBioseq_set_Handle::GetId(void) const
{
    return x_GetInfo().GetId();
}


bool CBioseq_set_Handle::IsSetColl(void) const
{
    return x_GetInfo().IsSetColl();
}


bool CBioseq_set_Handle::CanGetColl(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetColl();
}


const CBioseq_set::TColl& CBioseq_set_Handle::GetColl(void) const
{
    return x_GetInfo().GetColl();
}


bool CBioseq_set_Handle::IsSetLevel(void) const
{
    return x_GetInfo().IsSetLevel();
}


bool CBioseq_set_Handle::CanGetLevel(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetLevel();
}


CBioseq_set::TLevel CBioseq_set_Handle::GetLevel(void) const
{
    return x_GetInfo().GetLevel();
}


bool CBioseq_set_Handle::IsSetClass(void) const
{
    return x_GetInfo().IsSetClass();
}


bool CBioseq_set_Handle::CanGetClass(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetClass();
}


CBioseq_set::TClass CBioseq_set_Handle::GetClass(void) const
{
    return x_GetInfo().GetClass();
}


bool CBioseq_set_Handle::IsSetRelease(void) const
{
    return x_GetInfo().IsSetRelease();
}


bool CBioseq_set_Handle::CanGetRelease(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetRelease();
}


const CBioseq_set::TRelease& CBioseq_set_Handle::GetRelease(void) const
{
    return x_GetInfo().GetRelease();
}


bool CBioseq_set_Handle::IsSetDate(void) const
{
    return x_GetInfo().IsSetDate();
}


bool CBioseq_set_Handle::CanGetDate(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetDate();
}


const CBioseq_set::TDate& CBioseq_set_Handle::GetDate(void) const
{
    return x_GetInfo().GetDate();
}


bool CBioseq_set_Handle::IsSetDescr(void) const
{
    return x_GetInfo().IsSetDescr();
}


bool CBioseq_set_Handle::CanGetDescr(void) const
{
    return bool(m_Info)  &&  x_GetInfo().CanGetDescr();
}


const CBioseq_set::TDescr& CBioseq_set_Handle::GetDescr(void) const
{
    return x_GetInfo().GetDescr();
}


/////////////////////////////////////////////////////////////////////////////
// CBioseq_set_EditHandle

CSeq_entry_EditHandle CBioseq_set_EditHandle::GetParentEntry(void) const
{
    CSeq_entry_EditHandle ret;
    CBioseq_set_Info& info = x_GetInfo();
    if ( info.HasParent_Info() ) {
        ret = CSeq_entry_EditHandle(GetScope(),
                                    info.GetParentSeq_entry_Info());
    }
    return ret;
}


void CBioseq_set_EditHandle::ResetId(void) const
{
    x_GetInfo().ResetId();
}


void CBioseq_set_EditHandle::SetId(TId& v) const
{
    x_GetInfo().SetId(v);
}


void CBioseq_set_EditHandle::ResetColl(void) const
{
    x_GetInfo().ResetColl();
}


void CBioseq_set_EditHandle::SetColl(TColl& v) const
{
    x_GetInfo().SetColl(v);
}


void CBioseq_set_EditHandle::ResetLevel(void) const
{
    x_GetInfo().ResetLevel();
}


void CBioseq_set_EditHandle::SetLevel(TLevel v) const
{
    x_GetInfo().SetLevel(v);
}


void CBioseq_set_EditHandle::ResetClass(void) const
{
    x_GetInfo().ResetClass();
}


void CBioseq_set_EditHandle::SetClass(TClass v) const
{
    x_GetInfo().SetClass(v);
}


void CBioseq_set_EditHandle::ResetRelease(void) const
{
    x_GetInfo().ResetRelease();
}


void CBioseq_set_EditHandle::SetRelease(TRelease& v) const
{
    x_GetInfo().SetRelease(v);
}


void CBioseq_set_EditHandle::ResetDate(void) const
{
    x_GetInfo().ResetDate();
}


void CBioseq_set_EditHandle::SetDate(TDate& v) const
{
    x_GetInfo().SetDate(v);
}


void CBioseq_set_EditHandle::ResetDescr(void) const
{
    x_GetInfo().ResetDescr();
}


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


CSeq_entry_EditHandle CBioseq_set_EditHandle::AddNewEntry(int index) const
{
    return AttachEntry(*new CSeq_entry, index);
}


CBioseq_EditHandle
CBioseq_set_EditHandle::AttachBioseq(CBioseq& seq, int index) const
{
    return AddNewEntry(index).SelectSeq(seq);
}


CBioseq_EditHandle
CBioseq_set_EditHandle::CopyBioseq(const CBioseq_Handle& seq, int index) const
{
    return AddNewEntry(index).CopySeq(seq);
}


CBioseq_EditHandle
CBioseq_set_EditHandle::TakeBioseq(const CBioseq_EditHandle& seq, int index) const
{
    return AddNewEntry(index).TakeSeq(seq);
}


CSeq_entry_EditHandle
CBioseq_set_EditHandle::AttachEntry(CSeq_entry& entry, int index) const
{
    return m_Scope->AttachEntry(*this, entry, index);
}


CSeq_entry_EditHandle
CBioseq_set_EditHandle::CopyEntry(const CSeq_entry_Handle& entry,
                                  int index) const
{
    return m_Scope->CopyEntry(*this, entry, index);
}


CSeq_entry_EditHandle
CBioseq_set_EditHandle::TakeEntry(const CSeq_entry_EditHandle& entry,
                                  int index) const
{
    return m_Scope->TakeEntry(*this, entry, index);
}


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


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


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


void CBioseq_set_EditHandle::Remove(void) const
{
    m_Scope->RemoveBioseq_set(*this);
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: bioseq_set_handle.cpp,v $
* Revision 1000.1  2004/06/01 19:23:00  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.9
*
* Revision 1.9  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.8  2004/05/06 17:32:37  grichenk
* Added CanGetXXXX() methods
*
* Revision 1.7  2004/04/29 15:44:30  grichenk
* Added GetTopLevelEntry()
*
* Revision 1.6  2004/03/31 19:54:08  vasilche
* Fixed removal of bioseqs and bioseq-sets.
*
* Revision 1.5  2004/03/31 17:08:07  vasilche
* Implemented ConvertSeqToSet and ConvertSetToSeq.
*
* Revision 1.4  2004/03/29 20:13:06  vasilche
* Implemented whole set of methods to modify Seq-entry object tree.
* Added CBioseq_Handle::GetExactComplexityLevel().
*
* Revision 1.3  2004/03/24 18:30:29  vasilche
* Fixed edit API.
* Every *_Info object has its own shallow copy of original object.
*
* Revision 1.2  2004/03/16 21:01:32  vasilche
* Added methods to move Bioseq withing Seq-entry
*
* Revision 1.1  2004/03/16 15:47:27  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.3  2004/02/09 22:09:14  grichenk
* Use CConstRef for id
*
* Revision 1.2  2004/02/09 19:18:54  grichenk
* Renamed CDesc_CI to CSeq_descr_CI. Redesigned CSeq_descr_CI
* and CSeqdesc_CI to avoid using data directly.
*
* Revision 1.1  2003/11/28 15:12:31  grichenk
* Initial revision
*
*
* ===========================================================================
*/