blastx.hpp

来自「ncbi源码」· HPP 代码 · 共 168 行

/*
 * ===========================================================================
 * PRODUCTION $Log: blastx.hpp,v $
 * PRODUCTION Revision 1000.4  2004/04/12 19:27:24  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_PLUGINS_ALGO_BLAST___BLASTX__HPP
#define GUI_PLUGINS_ALGO_BLAST___BLASTX__HPP

/*  $Id: blastx.hpp,v 1000.4 2004/04/12 19:27:24 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.hpp>
#include <gui/core/version.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include "blast_base.hpp"
#include "blast_util.hpp"


BEGIN_NCBI_SCOPE
USING_SCOPE(ncbi::objects);


class CAlgoPlugin_BLASTx : public CAlgorithm<CAlgoPlugin_BLASTx>
                          , public CAlgoBlast_Base
{
public:

    // run our plugin
    void RunCommand(objects::CPluginMessage& msg);

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


//
// RunCommand() forwards to our base class
inline
void CAlgoPlugin_BLASTx::RunCommand(objects::CPluginMessage& msg)
{
    CAlgoBlast_Base::RunCommand(msg);
}


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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_BLASTx",
                 "Alignments/Local BLAST/Translated Nucleotide BLAST (BLASTx)",
                 "Create an alignment of nucleotide sequences "
                 "using BLAST locally",
                 "");

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

    args.AddArgument("query", "Query sequence",
                     CSeq_loc::GetTypeInfo());
    args.SetConstraint("query",
                       (*CPluginValueConstraint::CreateSeqMol(),
                        CSeq_inst::eMol_na,
                        CSeq_inst::eMol_dna,
                        CSeq_inst::eMol_rna));

    args.AddArgument("targets", "Target sequences",
                     CSeq_loc::GetTypeInfo(),
                     CPluginArg::TData::e_Array);
    args.SetConstraint("targets",
                       (*CPluginValueConstraint::CreateSeqMol(),
                        CSeq_inst::eMol_aa));

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

    // pass to the base class standard arg function
    x_AddStandardArgs(args);
}


END_NCBI_SCOPE




/*
 * ===========================================================================
 * $Log: blastx.hpp,v $
 * Revision 1000.4  2004/04/12 19:27:24  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.6
 *
 * Revision 1.6  2004/01/27 18:40:09  dicuccio
 * Code clean-up.  Renamed plugin classes to follow standard pattern
 *
 * Revision 1.5  2004/01/13 20:36:56  dicuccio
 * Use CBlastUtils for standard blast argument processing
 *
 * Revision 1.4  2003/11/24 15:45:20  dicuccio
 * Renamed CVersion to CPluginVersion
 *
 * Revision 1.3  2003/11/18 17:46:51  dicuccio
 * Standardized menu entries
 *
 * Revision 1.2  2003/11/04 17:49:22  dicuccio
 * Changed calling parameters for plugins - pass CPluginMessage instead of paired
 * CPluginCommand/CPluginReply
 *
 * Revision 1.1  2003/10/23 16:23:04  dicuccio
 * Moved code from algo/blast to algo/align
 *
 * Revision 1.5  2003/10/15 18:29:40  dicuccio
 * Made inline functions inline
 *
 * Revision 1.4  2003/10/07 13:47:01  dicuccio
 * Renamed CPluginURL* to CPluginValue*
 *
 * Revision 1.3  2003/09/29 20:01:12  dicuccio
 * Corrected arg name - use 'gencode' not 'genetic_code'
 *
 * Revision 1.2  2003/09/29 19:28:01  dicuccio
 * Implemented variants of BLAST
 *
 * Revision 1.1  2003/09/29 15:36:52  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */

#endif  // GUI_PLUGINS_ALGO_BLAST___BLASTX__HPP