gnomon.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: gnomon.hpp,v $
- * PRODUCTION Revision 1000.1 2004/04/12 17:47:53 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.2
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef ALGO_GNOMON___GNOMON__HPP
- #define ALGO_GNOMON___GNOMON__HPP
- /* $Id: gnomon.hpp,v 1000.1 2004/04/12 17:47:53 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 <corelib/ncbiobj.hpp>
- #include <objmgr/seq_vector.hpp>
- #include <objects/seq/Seq_annot.hpp>
- #include <util/range.hpp>
- BEGIN_NCBI_SCOPE
- class CClusterSet;
- class CFrameShiftInfo;
- typedef vector<CFrameShiftInfo> TFrameShifts;
- class NCBI_XALGOGNOMON_EXPORT CGnomon
- {
- public:
- CGnomon();
- ~CGnomon();
- // set our sequence, as a vector of IUPACna characters
- void SetSequence(const vector<char>& seq);
- // set our sequence, as a string of IUPACna characters
- void SetSequence(const string& seq);
- // set our sequence, as a CSeqVector. We will explicitly convert these
- // to IUPACna.
- void SetSequence(const objects::CSeqVector& vec);
- // set the name of the model data file
- void SetModelData(const string& file);
- // set the name of the a priori information file
- void SetAprioriInfo(const string& file);
- // set the name of the frame shifts file
- void SetFrameShiftInfo(const string& file);
- // set the repeats flag. By default, we do not use repeat information.
- void SetRepeats(bool val);
- // set the range to scan. By default, we scan the whole sequence.
- void SetScanRange(const CRange<TSeqPos>& range);
- // set the scan starting position
- void SetScanFrom(TSeqPos from);
- // set the scan stopping position
- void SetScanTo (TSeqPos to);
- // run the algorithm
- void Run(void);
- CRef<objects::CSeq_annot> GetAnnot(void) const;
- private:
- // our sequence
- vector<char> m_Seq;
- // our scan range
- CRange<TSeqPos> m_ScanRange;
- // the model data file
- string m_ModelFile;
- // the a priori information
- auto_ptr<CClusterSet> m_Clusters;
- // the frame shifts information
- auto_ptr<TFrameShifts> m_Fshifts;
- // flag: do we use repeat information?
- bool m_Repeats;
- // our resulting annotation
- CRef<objects::CSeq_annot> m_Annot;
- // copying is prohibited
- CGnomon(const CGnomon&);
- CGnomon& operator=(const CGnomon&);
- };
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- * $Log: gnomon.hpp,v $
- * Revision 1000.1 2004/04/12 17:47:53 gouriano
- * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.2
- *
- * Revision 1.2 2004/03/16 15:37:43 vasilche
- * Added required include
- *
- * Revision 1.1 2003/10/24 15:06:30 dicuccio
- * Initial revision
- *
- * ===========================================================================
- */
- #endif // ALGO_GNOMON___GNOMON__HPP