featid_table.cpp

来自「ncbi源码」· C++ 代码 · 共 241 行

/*
 * ===========================================================================
 * PRODUCTION $Log: featid_table.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 21:00:37  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: featid_table.cpp,v 1000.1 2004/06/01 21:00:37 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:
 *
 */

#include <ncbi_pch.hpp>
#include "featid_table.hpp"

#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objmgr/util/sequence.hpp>

#include <set>
#include <serial/iterator.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


CFeatIdTable::CFeatIdTable(int x, int y, int w, int h, const char* label)
    : CTablePanel< CConstRef<CSeq_loc> >(x, y, w, h, label)
{
    SetColumn(0, "Source",     eString, FL_ALIGN_LEFT, 0.5f);
    SetColumn(1, "Database",   eString, FL_ALIGN_LEFT, 0.5f);
    SetColumn(2, "Identifier", eString, FL_ALIGN_LEFT, 1.0f);
}


void CFeatIdTable::Update(const CSeq_feat& feat)
{
    size_t row = 0;

    // IDs from main location
    {{
        SetCell(row, 0) = "Sequence";

        // use the whole spanned location, not the original location
        const CSeq_id& id = sequence::GetId(feat.GetLocation());
        CRef<CSeq_loc> loc(new CSeq_loc());
        loc->SetInt().SetFrom(feat.GetLocation().GetTotalRange().GetFrom());
        loc->SetInt().SetTo(feat.GetLocation().GetTotalRange().GetTo());
        loc->SetInt().SetStrand(sequence::GetStrand(feat.GetLocation()));
        loc->SetId(id);

        SetData(row, loc);

        SetCell(row, 1, x_GetSource(id));
        SetCell(row, 2, id.AsFastaString());
        ++row;
    }}

    // IDs from the product location, if it exists
    if (feat.IsSetProduct()) {
        SetCell(row, 0, "Product");

        SetData(row, CConstRef<CSeq_loc>(&feat.GetProduct()));

        const CSeq_id& id = sequence::GetId(feat.GetProduct());
        SetCell(row, 1, x_GetSource(id));
        SetCell(row, 2, id.AsFastaString());

        ++row;
    }

    // IDs from DB xrefs
    if (feat.IsSetDbxref()) {
        SetCell(row, 0, "External DB");

        ITERATE (CSeq_feat::TDbxref, iter, feat.GetDbxref()) {
            const CDbtag& tag = **iter;

            CRef<CSeq_loc> loc(new CSeq_loc());
            loc->SetWhole(*x_GetSeqId(tag));
            SetData(row, loc);

            SetCell(row, 1, tag.GetDb());
            if (tag.GetTag().IsStr()) {
                SetCell(row, 2, tag.GetTag().GetStr());
            } else {
                SetCell(row, 2, NStr::UIntToString(tag.GetTag().GetId()));
            }

            ++row;
        }
    }
}


// get a string describing the source of a given seq-id
string CFeatIdTable::x_GetSource(const CSeq_id& id) const
{
    switch (id.Which()) {
    case CSeq_id::e_Local:
        return "Local";

    case CSeq_id::e_Gibbsq:
    case CSeq_id::e_Gibbmt:
        return "Geninfo Backbone";

    case CSeq_id::e_Giim:
        return "Geninfo Import";

    case CSeq_id::e_Genbank:
        return "Genbank";

    case CSeq_id::e_Embl:
        return "EMBL";

    case CSeq_id::e_Pir:
        return "PIR";

    case CSeq_id::e_Swissprot:
        return "Swiss-PROT";

    case CSeq_id::e_Patent:
        return "Patent";

    case CSeq_id::e_Other:
        return "Other";

    case CSeq_id::e_General:
        return "General";

    case CSeq_id::e_Gi:
        return "Genbank ID";

    case CSeq_id::e_Ddbj:
        return "DDBJ";

    case CSeq_id::e_Prf:
        return "Prf Sequence";

    case CSeq_id::e_Pdb:
        return "PDB";

    case CSeq_id::e_Tpg:
        return "Third-Party";

    case CSeq_id::e_Tpe:
        return "Third-Party/EMBL";

    case CSeq_id::e_Tpd:
        return "Third-Party/DDBJ";

    default:
        return "Unknown";
        break;
    }
}


// get a seq-id for a given Dbtag
CSeq_id* CFeatIdTable::x_GetSeqId(const CDbtag& dbtag) const
{
    static map<string, string> s_IdDictionary;
    if (s_IdDictionary.size() == 0) {
        s_IdDictionary["ENSEMBL"] = "lcl|";
        s_IdDictionary["GenBank"] = "gb|";
        s_IdDictionary["RefSeq" ] = "ref|";
        s_IdDictionary["EMBL"   ] = "gb|";
        s_IdDictionary["DDBJ"   ] = "gb|";
    }

    string str(dbtag.GetDb() + "|");
    map<string, string>::const_iterator iter =
        s_IdDictionary.find(dbtag.GetDb());
    if (iter != s_IdDictionary.end()) {
        str = iter->second;
    }

    if (dbtag.GetTag().IsStr()) {
        str += dbtag.GetTag().GetStr();
    } else {
        str += NStr::UIntToString(dbtag.GetTag().GetId());
    }

    CRef<CSeq_id> id(new CSeq_id(str));
    if (id->Which() == CSeq_id::e_not_set) {
        id.Reset(new CSeq_id("lcl|" + str));
    }
    return id.Release();
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: featid_table.cpp,v $
 * Revision 1000.1  2004/06/01 21:00:37  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
 *
 * Revision 1.3  2004/05/21 22:27:49  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.2  2004/01/20 18:17:53  dicuccio
 * Changed to match new API in CTablePanel
 *
 * Revision 1.1  2004/01/13 20:38:46  dicuccio
 * Added new view: feature IDs
 *
 * ===========================================================================
 */