NCBI C++ Toolkit Cross Reference


/* $Id: mask_writer_fasta.hpp 44777 2010-02-12 18:29:18Z camacho $ * =========================================================================== * * 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: Aleksandr Morgulis * * File Description: * Header file for CMaskWriterFasta class. * */ #ifndef CMASK_WRITER_FASTA_H #define CMASK_WRITER_FASTA_H #include <objtools/seqmasks_io/mask_writer.hpp> BEGIN_NCBI_SCOPE /** **\brief Output filter to write masked data in fasta format. ** ** In the output the sequence ids are preserved. The masked ** portions of sequences are printed in lower case letters. ** **/ class NCBI_XOBJREAD_EXPORT CMaskWriterFasta : public CMaskWriter { public: /** **\brief Object constructor. ** **\param arg_os the output stream used to initialize the ** base class instance. ** **/ CMaskWriterFasta( CNcbiOstream & arg_os ) : CMaskWriter( arg_os ) {} /** **\brief Object destructor. ** **/ virtual ~CMaskWriterFasta() {} /** **\brief Output masked sequence data. ** **\param bsh the bioseq handle **\param mask the resulting list of masked intervals **\param parsed_id bioseq id was parsed by CMaskReader. ** **/ virtual void Print( objects::CBioseq_Handle& bsh, const TMaskList & mask, bool parsed_id = false ); }; END_NCBI_SCOPE #endif

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