seqid_doc.cpp

来自「ncbi源码」· C++ 代码 · 共 143 行

/*
 * ===========================================================================
 * PRODUCTION $Log: seqid_doc.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 20:44:40  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.12
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: seqid_doc.cpp,v 1000.3 2004/06/01 20:44:40 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.
 *
 * ===========================================================================
 *
 * Authors:  Mike DiCuccio
 *
 * File Description:
 *    CSeqIdDocument -- document specific for sequence data
 */


#include <ncbi_pch.hpp>
#include "seqid_doc.hpp"
#include <gui/plugin/PluginValue.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/util/sequence.hpp>

#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <serial/serial.hpp>
#include <serial/objostr.hpp>


BEGIN_NCBI_SCOPE


CSeqIdDocument::CSeqIdDocument(CScope& scope, const CSeq_id& id)
{
    m_Scope.Reset(&scope);
    m_Id.Reset(const_cast<CSeq_id*> (&id));

    CBioseq_Handle handle = m_Scope->GetBioseqHandle(*m_Id);
    const CSeq_id& best_id = sequence::GetId(handle, sequence::eGetId_Best);
    best_id.GetLabel(&m_ShortTitle);
    m_Title = m_ShortTitle + ": " + sequence::GetTitle(handle);
}

CSeqIdDocument::~CSeqIdDocument()
{
}

// serialization: write our contents to a stream
void CSeqIdDocument::Write(CObjectOStream& os) const
{
    if ( !m_Scope  ||  !m_Id ) {
        return;
    }

    CBioseq_Handle handle = m_Scope->GetBioseqHandle(*m_Id);
    os << handle.GetTopLevelSeqEntry();
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: seqid_doc.cpp,v $
 * Revision 1000.3  2004/06/01 20:44:40  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.12
 *
 * Revision 1.12  2004/05/21 22:27:40  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.11  2004/03/05 17:29:59  dicuccio
 * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
 *
 * Revision 1.10  2003/11/04 17:20:18  dicuccio
 * Removed unnecessary #includes
 *
 * Revision 1.9  2003/11/04 12:44:09  friedman
 * Explicit destructor added
 *
 * Revision 1.8  2003/10/07 13:36:09  dicuccio
 * Renamed CPluginURL* to CPluginValue*.  Moved validation code into CPluginUtils
 *
 * Revision 1.7  2003/07/19 00:41:38  dicuccio
 * Removed dead includes.  Changed encoding for long title to include accession
 *
 * Revision 1.6  2003/06/25 17:02:54  dicuccio
 * Split CPluginHandle into a handle (pointer-to-implementation) and
 * implementation file.  Lots of #include file clean-ups.
 *
 * Revision 1.5  2003/06/02 16:06:18  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 1.4  2003/05/19 13:35:59  dicuccio
 * Moved gui/core/plugin/ -> gui/plugin/.  Merged gui/core/algo, gui/core/doc/,
 * and gui/core/view/ into one library (gui/core/)
 *
 * Revision 1.3  2003/04/29 14:46:09  dicuccio
 * Removed last vestiges of old typing system
 *
 * Revision 1.2  2003/04/24 19:40:57  ucko
 * Fix capitalization of seqid_doc.hpp.
 *
 * Revision 1.1  2003/04/24 16:25:00  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */