rebase.hpp

来自「ncbi源码」· HPP 代码 · 共 103 行

/*
 * ===========================================================================
 * PRODUCTION $Log: rebase.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 19:30:13  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

#ifndef GUI_PLUGINS_ALGO_BASIC___REBASE__HPP
#define GUI_PLUGINS_ALGO_BASIC___REBASE__HPP

/*  $Id: rebase.hpp,v 1000.1 2004/04/12 19:30:13 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:  Code to deal with REBASE restriction enzyme database
 *
 */


#include <corelib/ncbistd.hpp>
#include <algo/sequence/restriction.hpp>

BEGIN_NCBI_SCOPE

///
/// This class provides utilities for dealing with
/// REBASE format restriction enzyme databases.
///

class CRebase
{
public:
    // build a CRSpec based on a string from REBASE
    static CRSpec MakeRSpec(const string& site);

    // build a CREnzyme based on two strings from REBASE
    static CREnzyme MakeREnzyme(const string& name, const string& sites);

    // whether to read all enzymes, only those commercially
    // available, or the prototype for every recognition site
    enum EEnzymesToLoad {
        eAll,
        eCommercial,
        ePrototype
    };
    // read a REBASE file in "NAR" format
    static void ReadNARFormat(istream& input,
                              vector<CREnzyme>& enzymes,
                              enum EEnzymesToLoad which);
private:
    static void x_ParseCutPair(const string& s, int& plus_cut, int& minus_cut);
};


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: rebase.hpp,v $
 * Revision 1000.1  2004/04/12 19:30:13  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.3
 *
 * Revision 1.3  2004/01/27 18:38:09  dicuccio
 * Code clean-up.  Use standard names for plugins.  Removed unnecessary #includes
 *
 * Revision 1.2  2003/08/21 19:24:16  jcherry
 * Moved restriction site finding to algo/sequence
 *
 * Revision 1.1  2003/08/12 18:52:58  jcherry
 * Initial version
 *
 * ===========================================================================
 */


#endif   // GUI_PLUGINS_ALGO_BASIC___REBASE__HPP