orf.hpp

来自「ncbi源码」· HPP 代码 · 共 178 行

/*
 * ===========================================================================
 * PRODUCTION $Log: orf.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 17:47:59  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.16
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: orf.hpp,v 1000.1 2004/04/12 17:47:59 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 for finding and representing ORFs
 *
 */


#include <corelib/ncbistd.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/seq_vector.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <vector>


BEGIN_NCBI_SCOPE


//
// class COrf implements a simple open reading frame search.
//
// This class reports, as a series of seq-locs, all the possible open
// reading frames in a given sequence.  The sequence can be represented
// as either 
/// This class provides functions for finding all the ORFs
/// of a specified minimum length in a DNA sequence.

class NCBI_XALGOSEQ_EXPORT COrf
{
public:
    typedef CRange<TSeqPos> TRange;
    typedef vector<TRange>  TRangeVec;
    typedef vector< CRef<objects::CSeq_loc> > TLocVec;


    /// Find all ORFs in both orientations that
    /// are at least min_length_bp long.
    /// Report results as Seq-locs.
    /// seq must be in iupac.
    static void FindOrfs(const string& seq,
                         TLocVec& results,
                         unsigned int min_length_bp = 3,
                         int genetic_code = 1);

    static void FindOrfs(const vector<char>& seq,
                         TLocVec& results,
                         unsigned int min_length_bp = 3,
                         int genetic_code = 1);

    static void FindOrfs(const objects::CSeqVector& seq,
                         TLocVec& results,
                         unsigned int min_length_bp = 3,
                         int genetic_code = 1);

    /**
    /// This version returns an annot full of CDS features.
    /// Optionally takes a CSeq_id (by CRef) for use in
    /// the feature table; otherwise ids are left unset.
    template<class Seq>
    static CRef<objects::CSeq_annot>
    FindOrfs(const Seq& seq,
             unsigned int min_length_bp = 3,
             int genetic_code = 1,
             CRef<objects::CSeq_id> id = CRef<objects::CSeq_id>())
    {
        // place to store orfs
        TLocVec orfs;
        FindOrfs(seq, orfs, min_length_bp, genetic_code);
        return MakeCDSAnnot(orfs, genetic_code, id);
    }
    **/

    /// Build an annot full of CDS features from CSeq_loc's.
    /// Optionally takes a CSeq_id (by CRef) for use in
    /// the feature table; otherwise ids are left unset.
    static CRef<objects::CSeq_annot>
    MakeCDSAnnot(const TLocVec& orfs, int genetic_code = 1,
                 objects::CSeq_id* id = NULL);
};




END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: orf.hpp,v $
 * Revision 1000.1  2004/04/12 17:47:59  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.16
 *
 * Revision 1.16  2004/03/03 15:41:27  dicuccio
 * COmmented template definition of FindOrfs() - it is giving MSVC fits
 *
 * Revision 1.15  2003/10/15 20:26:28  dicuccio
 * Changed API of MakeCDSAnnot() to take a seq-id pointer rather than a CRef<>
 *
 * Revision 1.14  2003/09/04 19:27:53  jcherry
 * Made an ORF include the stop codon, and marked certain ORFs as
 * partial.  Put ability to construct a feature table into COrf.
 *
 * Revision 1.13  2003/08/21 12:13:10  dicuccio
 * Moved templated implementation into a private file.  Changed API to provide entry points for common sequence containers
 *
 * Revision 1.12  2003/08/20 14:26:43  ucko
 * Restore changes from revision 1.9, which seem to have been lost:
 * include Seq_interval.hpp
 *
 * Revision 1.11  2003/08/19 18:56:39  jcherry
 * Added a comment
 *
 * Revision 1.10  2003/08/19 18:36:23  jcherry
 * Reimplemented stop codon finding using CTrans_table finite state machine
 *
 * Revision 1.9   2003/08/19 17:40:02  rsmith
 * include Seq_interval.hpp
 *
 * Revision 1.8  2003/08/19 10:21:24  dicuccio
 * Compilation fixes - use objects:: namespace where appropriate
 *
 * Revision 1.7  2003/08/18 20:07:04  dicuccio
 * Corrected export specifiers
 *
 * Revision 1.6  2003/08/18 19:22:13  jcherry
 * Moved orf and seq_match to algo/sequence
 *
 * Revision 1.5  2003/08/18 18:01:58  jcherry
 * Changed COrf::FindOrfs to produce a vector of CRef<CSeq_loc>.
 * Added version of FindOrfs that takes a CSeqVector.
 *
 * Revision 1.4  2003/08/17 19:25:30  jcherry
 * Changed member variable names to follow convention
 *
 * Revision 1.3  2003/08/15 12:17:38  dicuccio
 * COmpilation fixes for MSVC
 *
 * Revision 1.2  2003/08/14 21:18:20  ucko
 * Don't repeat default argument specifications in definitions.
 *
 * Revision 1.1  2003/08/14 17:59:22  jcherry
 * Initial version
 *
 * ===========================================================================
 */