locus_link.cpp

来自「ncbi源码」· C++ 代码 · 共 219 行

/*
 * ===========================================================================
 * PRODUCTION $Log: locus_link.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:56:50  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: locus_link.cpp,v 1000.5 2004/06/01 20:56:50 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 "locus_link.hpp"
#include "utils.hpp"
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginArgSet.hpp>
#include <gui/plugin/PluginArg.hpp>
#include <gui/core/version.hpp>
#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/utils/app_popup.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbireg.hpp>

#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);



// standard info boilerplate
void CAlgoLinkOut_LocusLink::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoLinkOut_LocusLink", "Link Out/LocusLink",
                 "Open items in LocusLink", "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddAlgoCommand(eAlgoCommand_run);
    args.AddArgument("gene", "Gene to search",
                     CSeq_feat::GetTypeInfo());
    args.SetConstraint("gene",
                       (*CPluginValueConstraint::CreateFeatType(),
                        CSeqFeatData::e_Gene));

    args.AddArgument("orgn", "Limit to originating organism",
                     CPluginArg::eBoolean);
}


// run our plugin
void CAlgoLinkOut_LocusLink::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();

    plugin_args::TFeatList genes;
    GetArgValue(args["gene"], genes);

    const CSeq_feat& feat = *genes.front().second;
    const IDocument& doc  = *genes.front().first;

    bool limit_to_orgn = args["orgn"].AsBoolean();

    // retrieve the default link for LocusLink
    CNcbiApplication* app = CNcbiApplication::Instance();
    _ASSERT(app);
    const CNcbiRegistry& reg = app->GetConfig();

    string locus_link_url =
        reg.GetString("LINKOUT", "LocusLink",
                      "http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?"
                      "Q=<gene>");

    string gene_name;
    feature::GetLabel(feat, &gene_name, feature::eContent, &doc.GetScope());

    locus_link_url = NStr::Replace(locus_link_url, "<gene>", gene_name);

    //
    // check for species
    //
    if (limit_to_orgn) {
        string species_tag;
        CBioseq_Handle handle =
            doc.GetScope().GetBioseqHandle(feat.GetLocation());
        CConstRef<COrg_ref> ref = GetOrganism(handle);
        if (ref) {
            switch (ref->GetTaxId()) {
            default:
                break;

            case 9606:
                // homo sapiens
                species_tag = "Hs";
                break;

            case 7227:
                // drosophila melanogaster
                species_tag = "Dm";
                break;

            case 7955:
                // danio rerio (zebrafish
                species_tag = "Dr";
                break;

            case 10090:
                // mus musculus
                species_tag = "Mm";
                break;

            case 10116:
                // rattus norvegicus
                species_tag = "Rn";
                break;
            }

            if ( !species_tag.empty() ) {
                locus_link_url += "&ORG=" + species_tag;
            }
        }
    }

    if ( !CAppPopup::PopupURL(locus_link_url) ) {
        reply.SetStatus(eMessageStatus_failed);
    } else {
        reply.SetStatus(eMessageStatus_success);
    }
}



END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: locus_link.cpp,v $
 * Revision 1000.5  2004/06/01 20:56:50  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 *
 * Revision 1.10  2004/05/21 22:27:47  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.9  2004/01/27 18:45:26  dicuccio
 * Added missing header files
 *
 * Revision 1.8  2003/11/24 15:45:31  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.7  2003/11/06 20:12:13  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.6  2003/11/04 17:49:24  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.5  2003/10/15 18:30:01  dicuccio
 * Changed to match one-of-set constraint for feature type
 *
 * Revision 1.4  2003/10/07 13:47:04  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.3  2003/09/25 17:49:17  dicuccio
 * Cleaned up handling of org-refs - implemented private function to return the
 * apporpriate COrg_ref.  Added virtual destructors where necessary
 *
 * Revision 1.2  2003/09/24 18:24:57  dicuccio
 * Cleaned up determination of tax-id from org-ref
 *
 * Revision 1.1  2003/09/23 19:45:45  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */