mask_writer_int.hpp

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/*  $Id: mask_writer_int.hpp 48753 2011-02-24 17:19:39Z 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 CMaskWriterInt class.
 *
 */
 
#ifndef CMASK_WRITER_INT_H
#define CMASK_WRITER_INT_H
 
#include <objtools/seqmasks_io/mask_writer.hpp>
 
BEGIN_NCBI_SCOPE
 
/**
 **\brief Output filter to print masked sequences as sets of
 **       intervals.
 **
 ** Masking data for each new sequence in the file starts with
 ** a fasta stile id. Then each contiguous interval of
 ** masked sequence starting at position 'start' and ending
 ** at position 'end' it is printed on a separate line 
 ** [start] - [end].
 **
 **/
class NCBI_XOBJREAD_EXPORT CMaskWriterInt : public CMaskWriter
{
public:
 
    /**
     **\brief Object constructor.
     **
     **\param arg_os output stream used to initialize the
     **              base class instance
     **
     **/
    CMaskWriterInt( CNcbiOstream & arg_os ) 
        : CMaskWriter( arg_os ) {}
 
    /**
     **\brief Object destructor.
     **
     **/
    virtual ~CMaskWriterInt() {}
 
    /**
     **\brief Send the masking data to the output stream.
     **
     **\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 );
 
    /** Print masks only */
    static void PrintMasks(CNcbiOstream& os, const TMaskList& mask);
};
 
END_NCBI_SCOPE
 
#endif