NCBI C++ Toolkit Cross Reference


#ifndef SEQ_ALIGN_UTIL__HPP #define SEQ_ALIGN_UTIL__HPP /* $Id: seq_align_util.hpp 33815 2007-05-04 17:18:18Z kazimird $ * =========================================================================== * * 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. * * =========================================================================== * * Author: Aleksey Grichenko * * File Description: * Seq-align utilities */ #include <corelib/ncbistd.hpp> #include <corelib/ncbiobj.hpp> #include <objects/seqalign/Seq_align.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) // Forward declarations class CSeq_loc; class CScope; BEGIN_SCOPE(sequence) /** @addtogroup ObjUtilSeqAlign * * @{ */ /** @name Seq-align mapping * Seq-align mapping * @{ */ /// Remap seq-align row to the seq-loc. /// Treats the given row as being relative to the location, maps it /// to the sequence(s) referenced by this location. /// @param align /// The seq-align object to be mapped (the object will be modified!). /// @param row /// Row to be mapped. /// @param loc /// Seq-loc to which the row should be mapped. /// @param scope /// Optional scope may be required by CSeq_loc_Mapper to process /// some locations (e.g. whole locations). /// @result /// Reference to the new seq-align with the mapped row. NCBI_XOBJUTIL_EXPORT CRef<CSeq_align> RemapAlignToLoc(const CSeq_align& align, CSeq_align::TDim row, const CSeq_loc& loc, CScope* scope = NULL); /* @} */ END_SCOPE(sequence) END_SCOPE(objects) END_NCBI_SCOPE #endif /* SEQ_ALIGN_UTIL__HPP */

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