mrna_to_neighbors.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: mrna_to_neighbors.hpp,v $
 * PRODUCTION Revision 1000.5  2004/04/12 19:27:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.14
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_PLUGINS_ALGO_ALIGN___MRNA_TO_NEIGHBORS__HPP
#define GUI_PLUGINS_ALGO_ALIGN___MRNA_TO_NEIGHBORS__HPP

/*  $Id: mrna_to_neighbors.hpp,v 1000.5 2004/04/12 19:27:46 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 <gui/core/algo_thread.hpp>
#include <gui/core/version.hpp>
#include "align_to_neighbors.hpp"
#include "blast_util.hpp"

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


class CAlgoPlugin_AlignMrnaToNeighbors
    : public CAlignToNeighbors,
      public CAlgorithm<CAlgoPlugin_AlignMrnaToNeighbors>
{
public:

    void RunCommand(CPluginMessage& msg);

    // standard info boilerplate
    static void GetInfo(CPluginInfo& info);
};

inline void
CAlgoPlugin_AlignMrnaToNeighbors::RunCommand(CPluginMessage& msg)
{
    CAlignToNeighbors::Run(msg);
}


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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_AlignMrnaToNeighbors",
                 "Alignments/Align mRNA sequence to Entrez neighbors",
                 "Create an alignment of an mRNA sequence "
                 "to its related sequences and to its genomic context",
                 "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddAlgoCommand(eAlgoCommand_run);

    args.AddArgument("mrna_feat", "mRNA sequence",
                     CSeq_feat::GetTypeInfo());
    args.SetConstraint("mrna_feat",
                       (*CPluginValueConstraint::CreateFeatSubtype(),
                        CSeqFeatData::eSubtype_mRNA));
    args.AddConstraint("mrna_feat",
                       *CPluginValueConstraint::CreateFeatProduct());

    CBlastUtils::AddBlastArgs(args, blast::eBlastn);

    args.AddArgument("genomic", "Align to the genomic sequence",
                     CPluginArg::eBoolean);

    args.AddDefaultArgument("neighbor_filter",
                            "Which entrez neighbors",
                            CPluginArg::eString, "all");

    args.SetConstraint("neighbor_filter",
                       (*CPluginValueConstraint::CreateSet(),
                        "all", "mRNA only", "genomic only",
                        "arbitrary query string (below)"));

    args.AddOptionalArgument("query_string",
                             "Entrez query for filtering",
                             CPluginArg::eString);
}




END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: mrna_to_neighbors.hpp,v $
 * Revision 1000.5  2004/04/12 19:27:46  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.14
 *
 * Revision 1.14  2004/04/07 12:53:55  dicuccio
 * Formatting changes
 *
 * Revision 1.13  2004/03/05 17:33:44  dicuccio
 * Changed plugin to run single-threaded until thread issues can be sorted out.
 * Use sequence::GetId() instead of CSeq_id::GetStringDescr()
 *
 * Revision 1.12  2004/02/17 15:17:30  jcherry
 * Removed help url in favor of new help system
 *
 * Revision 1.11  2004/01/27 18:40:12  dicuccio
 * Code clean-up.  Renamed plugin classes to follow standard pattern
 *
 * Revision 1.10  2004/01/13 20:37:40  dicuccio
 * Use CBlastUtils for standard blast argument processing
 *
 * Revision 1.9  2003/11/26 17:12:30  dicuccio
 * Switched to use CThreadedAlgorithm<>
 *
 * Revision 1.8  2003/11/24 15:45:21  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.7  2003/11/21 20:15:25  jcherry
 * Corrected help url
 *
 * Revision 1.6  2003/11/14 00:20:30  jcherry
 * Added url for help
 *
 * Revision 1.5  2003/11/06 20:12:12  dicuccio
 * Cleaned up handling of USING_SCOPE - removed from all headers
 *
 * Revision 1.4  2003/11/04 17:49:22  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.3  2003/10/17 17:45:40  jcherry
 * Default E-values -> 0.05
 *
 * Revision 1.2  2003/10/16 21:52:07  jcherry
 * Added filtering of neighbors
 *
 * Revision 1.1  2003/10/15 18:17:07  dicuccio
 * Split algo into two front-ends (one for mRNA, one for proteins)
 *
 * ===========================================================================
 */

#endif  // GUI_PLUGINS_ALGO_ALIGN___MRNA_TO_NEIGHBORS__HPP