mask_writer_fasta.hpp

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/*  $Id: mask_writer_fasta.hpp 94083 2021-06-23 15:52:03Z fongah2 $
 * ===========================================================================
 *
 *                            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
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 *  Please cite the author in any work or product based on this material.
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 * ===========================================================================
 *
 * 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, bool hard_masking = false)
        : CMaskWriter( arg_os ), m_HardMasking(hard_masking) {}
 
    /**
     **\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 );
private:
    bool m_HardMasking;
};
 
END_NCBI_SCOPE
 
#endif