seqid_hook.cpp

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/*
 * ===========================================================================
 *
 *                            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:  Alexey Dobronadezhdin
 *
 * File Description:
 *
 * ===========================================================================
 */
#include <ncbi_pch.hpp>
 
#include <objects/seqloc/Seq_id.hpp>
 
#include "base_report.hpp"
#include "seqid_hook.hpp"
 
USING_NCBI_SCOPE;
USING_SCOPE(objects);
 
namespace pub_report
{
 
static CConstRef<CSeq_id> GetBestId(const CBioseq::TId& ids)
{
    CConstRef<CSeq_id> best_seq_id;
 
    int best_score = INT_MAX;
    for (const CRef<CSeq_id>& it : ids) {
        if (CSeq_id::e_Genbank == it->Which()) {
            return it;
        }
 
        int score = it->BaseBestRankScore();
        if (best_score > score) {
            best_seq_id = it;
            best_score  = score;
        }
    }
 
    return best_seq_id;
}
 
CSkipSeqIdHook::CSkipSeqIdHook(CBaseReport& report) :
    m_report(report) {}
 
void CSkipSeqIdHook::SkipClassMember(CObjectIStream& in, const CObjectTypeInfoMI& member)
{
    CBioseq::TId ids;
    CObjectInfo  info(&ids, (*member).GetTypeInfo());
    in.ReadObject(info);
 
    CConstRef<CSeq_id> best_seq_id = GetBestId(ids);
 
    if (best_seq_id.NotEmpty()) {
        string label;
        best_seq_id->GetLabel(&label, CSeq_id::eContent);
        m_report.SetCurrentSeqId(label);
    }
 
    member.ResetLocalSkipHook(in);
}
 
}