predict_coiled_coil.cpp

来自「ncbi源码」· C++ 代码 · 共 320 行

/*
 * ===========================================================================
 * PRODUCTION $Log: predict_coiled_coil.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:55:30  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: predict_coiled_coil.cpp,v 1000.5 2004/06/01 20:55:30 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:  Josh Cherry
 *
 * File Description:  gbench plugin for predicting coiled coil regions
 *
 */


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

#include <algo/sequence/coiled_coil.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/core/version.hpp>
#include <gui/dialogs/col/multi_col_dlg.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginReply.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/objutils/utils.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


CAlgoPlugin_PredictCoiledCoil::~CAlgoPlugin_PredictCoiledCoil()
{
}


// standard plugin announce bopilerplate
void CAlgoPlugin_PredictCoiledCoil::GetInfo(CPluginInfo& info)
{
    info.Reset();
    
    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_PredictCoiledCoil", "Protein analysis/Predict coiled coil regions",
                 "Predict coiled coil regions from protein sequence",
                 "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddAlgoCommand(eAlgoCommand_run);
    args.AddArgument("locs", "Locations to evaluate",
                     CSeq_loc::GetTypeInfo(),
                     CPluginArg::TData::e_Array);
    args.SetConstraint("locs",
                       (*CPluginValueConstraint::CreateSeqMol(),
                        CSeq_inst::eMol_aa));

    args.AddDefaultArgument("win_len", "Window length",
                            CPluginArg::eInteger, "28");

}


void CAlgoPlugin_PredictCoiledCoil::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    _TRACE("CAlgoPlugin_PredictCoiledCoil::RunCommand()");
    
    if ( !m_Dialog.get() ) {
        m_Dialog.reset(new CMultiColDlg());

        m_Dialog->SetWindowSize(800, 450);
        m_Dialog->SetTitle("Predicted Coiled Coil Regions");
        
        m_Dialog->SetColumn(0, "Sequence", FL_ALIGN_LEFT, 0.5f);
        m_Dialog->SetColumn(1, "Location", FL_ALIGN_LEFT, 0.5f);
        m_Dialog->SetColumn(2, "Range", FL_ALIGN_CENTER, 0.4f);
        m_Dialog->SetColumn(3, "Maximum Score", FL_ALIGN_CENTER, 0.5f);
        m_Dialog->SetColumn(4, "Coiled Coil Prob.", FL_ALIGN_CENTER, 0.5f);
    }

    // clear any previous contents
    m_Dialog->SetRows(0);

    int row = 0;
    plugin_args::TLocList locs;
    GetArgValue(args["locs"], locs);

    int win_len = args["win_len"].AsInteger();

    ITERATE (plugin_args::TLocList, iter, locs) {
        const CSeq_loc&  loc = *iter->second;
        const IDocument& doc = *iter->first;

        // find the best ID for this bioseq
        try {
            CBioseq_Handle handle = doc.GetScope().GetBioseqHandle(loc);

            // get sequence vector
            CSeqVector vec =
                handle.GetSequenceView(loc,
                                       CBioseq_Handle::eViewConstructed,
                                       CBioseq_Handle::eCoding_Iupac);


            string& id_str  = m_Dialog->SetCell(row, 0);
            string& loc_str = m_Dialog->SetCell(row, 1);

            const CSeq_id& best_id =
                sequence::GetId(handle, sequence::eGetId_Best);
            id_str.erase();
            best_id.GetLabel(&id_str);
            loc_str = CPluginUtils::GetLabel(loc, &doc.GetScope());

            // a new feature table
            CRef<CSeq_annot> annot(new CSeq_annot());

            // places to store coiled coil regions and their max scores
            vector<CRef<CSeq_loc> > regions;
            vector<double> max_scores;

            // find the regions
            double top_score = CCoiledCoil::
                PredictRegions(vec, regions, max_scores, win_len);
            _TRACE("Predicted " << regions.size() << " coiled coil regions");

            // add description to annot
            annot->AddName("Predicted coiled coil regions");
            string comment = string("Predicted coiled coil regions "
                                    "using window length = ")
                + NStr::IntToString(win_len);
            annot->AddComment(comment);

            NON_CONST_ITERATE (vector< CRef<CSeq_loc> >, region, regions) {
                // must set the ID field
                (**region).SetId(sequence::GetId(loc));
                *region = CSeqUtils::RemapChildToParent(loc, **region);

                //
                // add regions to dialog
                //

                m_Dialog->SetCell(row, 2)
                    = NStr::IntToString((**region).GetTotalRange().GetFrom() + 1) + "-"
                    + NStr::IntToString((**region).GetTotalRange().GetTo() + 1);
                m_Dialog->SetCell(row, 3) = 
                    NStr::DoubleToString(max_scores[region - regions.begin()],
                                         2);
                m_Dialog->SetCell(row, 4) = 
                    NStr::DoubleToString(CCoiledCoil::ScoreToProb
                                         (max_scores[region - regions.begin()]));

                ++row;
                
                //
                // add features to annot
                //

                CRef<CSeq_id> this_id
                    (const_cast<CSeq_id*>(&sequence::GetId(loc)));

                // create feature
                CRef<CSeq_feat> feat(new CSeq_feat());

                feat->SetExp_ev(CSeq_feat::eExp_ev_not_experimental);

                // set up the location
                feat->SetLocation(**region);
                feat->SetLocation().SetId(*this_id);
                
                feat->SetData().SetRegion() = 
                    string("Predicted coiled coil: max. score = ") +
                    NStr::DoubleToString(max_scores[region - regions.begin()], 
                                         2)
                    + " (probability = " +
                    NStr::DoubleToString(CCoiledCoil::ScoreToProb
                                         (max_scores[region - regions.begin()]),
                                         2)
                    + ")";

                
                // save in annot
                annot->SetData().SetFtable().push_back(feat);
            }

            // attach annot to doc
            //const_cast<IDocument&>(doc).AttachAnnot(*annot);
            reply.AddObject(doc, *annot);

            // if no regions found, report max score for the sequence
            if (regions.size() == 0) {
                m_Dialog->SetCell(row, 2) = "None";
                m_Dialog->SetCell(row, 3) = NStr::DoubleToString(top_score);
                m_Dialog->SetCell(row, 4) = 
                    NStr::DoubleToString(CCoiledCoil::ScoreToProb(top_score));

                ++row;
            }
        }
        catch (exception& e) {
            LOG_POST(Error << e.what());
            string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
            LOG_POST(Error << "Error processing location " << str);
        }
#ifndef _DEBUG
        catch (...) {
            string str = CPluginUtils::GetLabel(loc, &doc.GetScope());
            LOG_POST(Error << "Error processing location " << str);
        }
#endif
    }

    // update all views
    //CDocManager::UpdateAllViews();

    //
    // prepare our dialog box
    //
    m_Dialog->SetLabel(string("Predicted coiled coil regions"
                              " using a window length of ") 
                       + NStr::IntToString(win_len));
    m_Dialog->Show();
    reply.SetStatus(eMessageStatus_success);
    reply.AddAction(CPluginReplyAction::e_Add_to_document);
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: predict_coiled_coil.cpp,v $
 * Revision 1000.5  2004/06/01 20:55:30  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 *
 * Revision 1.15  2004/05/21 22:27:47  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.14  2004/05/03 13:05:42  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.13  2004/03/05 17:35:37  dicuccio
 * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
 *
 * Revision 1.12  2004/01/27 18:38:00  dicuccio
 * Code clean-up.  Use standard names for plugins.  Removed unnecessary #includes
 *
 * Revision 1.11  2004/01/07 15:50:38  dicuccio
 * Adjusted for API change in CPluginUtils::GetLabel().  Standardized exception
 * reporting in algorithms.
 *
 * Revision 1.10  2003/11/24 15:45:27  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.9  2003/11/18 17:48:37  dicuccio
 * Added standard processing of return values
 *
 * Revision 1.8  2003/11/06 20:12:12  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.7  2003/11/04 17:49:23  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.6  2003/10/27 17:46:49  dicuccio
 * Removed dead #includes
 *
 * Revision 1.5  2003/10/15 13:40:26  dicuccio
 * Mkae sure to set the 'id' for the seq-locs before calling RemapChildToParent()
 *
 * Revision 1.4  2003/10/14 16:24:37  dicuccio
 * Correctly remap new feature locations through the parent location to the master
 * sequence
 *
 * Revision 1.3  2003/10/07 13:47:00  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.2  2003/09/25 17:21:35  jcherry
 * Added name to annot
 *
 * Revision 1.1  2003/09/08 16:15:13  jcherry
 * Initial version
 *
 * ===========================================================================
 */