gnomon.cpp

来自「ncbi源码」· C++ 代码 · 共 256 行

/*
 * ===========================================================================
 * PRODUCTION $Log: gnomon.cpp,v $
 * PRODUCTION Revision 1000.4  2004/06/01 20:56:23  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: gnomon.cpp,v 1000.4 2004/06/01 20:56:23 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 "gnomon.hpp"
#include <corelib/ncbiapp.hpp>
#include <algo/gnomon/gnomon.hpp>
#include <gui/core/version.hpp>
#include <gui/core/idocument.hpp>
#include <gui/utils/system_path.hpp>
#include <gui/utils/message_box.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginArg.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>

#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);


static const string sc_human("Human (Homo sapiens)");
static const string sc_worm ("Worm (Caenorhabditas elegans)");
static const string sc_fly  ("Fly (Drosophila melanogaster)");

void CPluginGnomon::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CPluginGnomon",
                 "Search/Ab-Initio Predicion of Genes",
                 "Search for genes using a pure ab-initio method",
                 "");

    // command info
    CPluginCommand& cmd = info.SetCommands().AddAlgoCommand(eAlgoCommand_run);
    cmd.AddArgument("loc", "Sequence to evaluate",
                    CSeq_loc::GetTypeInfo());
    cmd.SetConstraint("loc",
                     (*CPluginValueConstraint::CreateSeqMol(),
                      CSeq_inst::eMol_na,
                      CSeq_inst::eMol_dna));

    cmd.AddDefaultArgument("model", "Model Organism Data",
                           CPluginArg::eString, sc_worm);
    cmd.SetConstraint("model",
        (*CPluginValueConstraint::CreateSet(),
         sc_human, sc_worm, sc_fly));
}


void CPluginGnomon::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& cmd = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    reply.SetStatus(eMessageStatus_failed);

    const CSeq_loc& loc = dynamic_cast<const CSeq_loc&>(cmd["loc"].AsObject());
    const IDocument* doc = cmd["loc"].GetDocument();

    // retrieve the sequence to scan
    CBioseq_Handle handle = doc->GetScope().GetBioseqHandle(loc);
    CSeqVector vec =
        handle.GetSequenceView(loc, CBioseq_Handle::eViewConstructed);

    //
    // retrieve the correct model file
    //
    string model_file;
    {{
        model_file = cmd["model"].AsString();
        if (model_file == sc_human) {
            model_file = "Human.inp";
        } else if (model_file == sc_worm) {
            model_file = "Worm.inp";
        } else if (model_file == sc_fly) {
            model_file = "Fly.inp";
        }
    }}
    {{
        CNcbiApplication* app = CNcbiApplication::Instance();
        _ASSERT(app);
        CNcbiRegistry& registry = app->GetConfig();

        // By default the rebase "NAR format" file 
        // is assumed to be <std>/etc/rebase.nar.
        // This can be overridden in gbench.ini, via the application registry
        // variable [PROSITE_SEARCH] PrositeData.
        string model_path = registry.GetString("GNOMON", "ModelDataPath", "");
        if ( !model_path.empty() ) {
            model_path += model_file + ", ";
        }
        model_path += "<home>/etc/" + model_file +
                      ", <std>/etc/" + model_file;
        model_file = CSystemPath::ResolvePathExisting(model_path);
    }}

    if ( model_file.empty() ) {
        NcbiMessageBox("Couldn't find model data.");
        return;
    }

    CRef<CSeq_annot> annot;

    //
    // run GNOMON!
    //

    try {
        CGnomon gnomon;
        gnomon.SetSequence(vec);
        gnomon.SetModelData(model_file);
        gnomon.Run();
        annot = gnomon.GetAnnot();
    }
    catch (CException& e) {
        string msg("Gene scan failed:\n");
        msg += e.GetMsg();
        NcbiMessageBox(msg);
        return;
    }

    if ( !annot  ||  !annot->GetData().IsFtable()  ||
        annot->GetData().GetFtable().size() == 0) {
        NcbiMessageBox("No genes found in the selected region");
        return;
    }

    //
    // correct our locations
    // this involves remapping the locations through our seq-loc
    // and setting our IDs correctly
    // while we're at it, fill in our dialog
    //
    if ( !m_Dialog.get() ) {
        m_Dialog.reset(new CMultiColDlg());

        m_Dialog->SetTitle("Ab-Initio Gene Scan");
        m_Dialog->SetColumn(0, "Feature",  FL_ALIGN_LEFT, 0.5f);
        m_Dialog->SetColumn(1, "Location", FL_ALIGN_LEFT, 0.5f);
    }

    string label("Ab-Initio prediction found ");
    label += NStr::IntToString(annot->GetData().GetFtable().size() / 2);
    label += " potential genes:";

    m_Dialog->SetLabel(label);
    m_Dialog->SetRows(0);

    int row = 0;
    const CSeq_id& id = sequence::GetId(loc);
    NON_CONST_ITERATE (CSeq_annot::TData::TFtable, iter,
                       annot->SetData().SetFtable()) {
        CSeq_feat& feat = **iter;
        feat.SetLocation().SetId(id);
        feat.SetLocation
            (*CSeqUtils::RemapChildToParent(loc, feat.GetLocation()));

        feature::GetLabel(feat, &m_Dialog->SetCell(row, 0), feature::eBoth);
        feat.GetLocation().GetLabel(&m_Dialog->SetCell(row, 1));

        ++row;
    }

    const_cast<IDocument*>(doc)->AttachAnnot(*annot);
    const_cast<IDocument*>(doc)->PostDocumentChanged();

    m_Dialog->SetRows(row);
    m_Dialog->Show();
    reply.SetStatus(eMessageStatus_success);
}



END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: gnomon.cpp,v $
 * Revision 1000.4  2004/06/01 20:56:23  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 *
 * Revision 1.8  2004/05/21 22:27:47  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.7  2004/05/03 13:05:42  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.6  2004/02/17 20:35:26  rsmith
 * moved core/settings.[ch]pp and core/system_path.[ch]pp to config and utils, respectively.
 *
 * Revision 1.5  2003/12/22 19:27:06  dicuccio
 * Changed to match API change in IDocument - UpdateAllViews() goes away
 *
 * Revision 1.4  2003/12/09 15:46:54  dicuccio
 * Use CException::GetMsg() instead of what()
 *
 * Revision 1.3  2003/11/24 15:45:30  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.2  2003/11/05 14:28:25  dicuccio
 * Changed calling semantics to match new plugin API
 *
 * Revision 1.1  2003/10/24 16:56:50  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */