net_blast_reqn.hpp

来自「ncbi源码」· HPP 代码 · 共 140 行

/*
 * ===========================================================================
 * PRODUCTION $Log: net_blast_reqn.hpp,v $
 * PRODUCTION Revision 1000.3  2004/04/12 19:28:02  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.7
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_CORE_ALGO_NET_BLAST___NET_BLAST_REQN__HPP
#define GUI_CORE_ALGO_NET_BLAST___NET_BLAST_REQN__HPP

/*  $Id: net_blast_reqn.hpp,v 1000.3 2004/04/12 19:28:02 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:  Clifford Clausen, Michael DiCuccio
 *
 * File Description:
 *    CAlgoPlugin_BlastReqn -- passes nucleotide Blast requests to blastn
 */

#include <gui/core/algo.hpp>
#include <gui/core/version.hpp>
#include <objects/seq/Bioseq.hpp>
#include "net_blast_req_base.hpp"


BEGIN_NCBI_SCOPE

class CAlgoPlugin_BlastReqn
    : public CAlgorithm<CAlgoPlugin_BlastReqn>
    , public CNetBlastReq_Base
{
public:

    // call RunCommand on base class
    void RunCommand(objects::CPluginMessage& msg);

    // FinalizeArgs() retrieves the list of valid databases and
    // adds a constraint to manage these
    void FinalizeArgs(objects::CPluginMessage& msg);

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


inline
void CAlgoPlugin_BlastReqn::FinalizeArgs(objects::CPluginMessage& msg)
{
    CNetBlastReq_Base::FinalizeArgs(msg);
}

inline
void CAlgoPlugin_BlastReqn::RunCommand(objects::CPluginMessage& msg)
{
    CNetBlastReq_Base::RunCommand(msg);
}

inline
void CAlgoPlugin_BlastReqn::GetInfo(objects::CPluginInfo& info)
{
        info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_BlastReqn", 
                 "Alignments/Net BLAST/Standard Nucleotide BLAST (BLASTn)",
                 "Find sequences similar to query sequence",
                 "");

    // command info
    CPluginCommand& cmd =
        info.SetCommands().AddAlgoCommand(eAlgoCommand_run);

    cmd.AddArgument("nucleotide", "Sequences to BLAST",
                    CSeq_loc::GetTypeInfo(),
                    CPluginArg::TData::e_Array);
    cmd.SetConstraint("nucleotide",
                     ((*CPluginValueConstraint::CreateSeqMol()),
                      CSeq_inst::eMol_dna, 
                      CSeq_inst::eMol_rna, 
                      CSeq_inst::eMol_na));

    cmd.AddDefaultArgument("subject", "Database for search",
                           CPluginArg::eString, "nr");

    cmd.AddDefaultArgument("prog", "BLAST program",
                           CPluginArg::eString, "blastn");
    cmd["prog"].SetHidden(true);

    cmd.AddDefaultArgument("word", "Word Size", 
                           CPluginArg::eInteger, "11");

    cmd.AddDefaultArgument("expect", "Expect Value", 
                           CPluginArg::eDouble, "2e4");

    cmd.AddOptionalArgument("query", "Limit by Entrez Query",
                            CPluginArg::eString);

}


END_NCBI_SCOPE



/*
 * ===========================================================================
 * $Log: 
 *
 * 
 * ===========================================================================
 */

#endif  // GUI_CORE_ALGO_NET_BLAST___NET_BLAST_REQN__HPP