rebase.hpp
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- /*
- * ===========================================================================
- * 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