transg_src.cpp

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/* $Id: transg_src.cpp 28832 2013-09-04 16:47:31Z chenj $
 * ===========================================================================
 *
 *
 *                            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:  Jie Chen 
 * File:  Set transgenic BioSource
 *  
 */
 
#include <ncbi_pch.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
 
#include "gui/packages/pkg_sequence_edit/citem_util.hpp"
 
using namespace ncbi;
using namespace objects;
 
bool CSetTransgSrcDesc :: x_HasTransgenicSubtype(const CBioSource& biosrc)
{
   if (!biosrc.CanGetSubtype()) return false;
   ITERATE (list <CRef <CSubSource> >, it, biosrc.GetSubtype()) {
      if ((*it)->GetSubtype() == CSubSource :: eSubtype_transgenic) return true;
   }
   return false;
};
 
void CSetTransgSrcDesc:: apply_to(const CSeq_entry_Handle& tse, CRef <CCmdComposite> composite)
{
   for (CBioseq_CI bit(tse); bit; ++bit) {
     CSeqdesc_CI s_ci(*bit, CSeqdesc::e_Source);
     if ( s_ci && CFeat_CI(*bit, CSeqFeatData::e_Biosrc) ) {
        if (!x_HasTransgenicSubtype(s_ci->GetSource())) {
           CRef <CBioSource> new_obj(new CBioSource);
           new_obj->Assign(s_ci->GetSource());
           CRef <CSubSource> new_subsrc(new CSubSource);
           new_subsrc->SetSubtype(CSubSource:: eSubtype_transgenic);
           new_subsrc->SetName(" "); 
           new_obj->SetSubtype().push_back(new_subsrc);
           add_to_cmd<objects::CBioSource> (
                (CObject*)(&(s_ci->GetSource())), (CObject*)(new_obj.GetPointer()), composite); 
        }
     }
   }
};