seq_masker_util.cpp

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/*  $Id: seq_masker_util.cpp 86312 2019-04-29 12:24:20Z morgulis $
 * ===========================================================================
 *
 *                            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:
 *   CSeqMaskerUtil class member and method definitions.
 *
 */
 
#include <ncbi_pch.hpp>
#include <algo/winmask/seq_masker_util.hpp>
 
BEGIN_NCBI_SCOPE
 
//-------------------------------------------------------------------------
Uint1 CSeqMaskerUtil::BitCount( Uint4 mask, Uint1 bit_value )
{
    if( !bit_value ) return BitCount( ~mask, 1 );
    else 
    {
        Uint1 result = 0;
 
        for( Uint1 i = 0; i < 8*sizeof( mask ); ++i )
            if( (1ULL<<i)&mask ) ++result;
 
        return result;
    }
}
 
//-------------------------------------------------------------------------
Uint4 CSeqMaskerUtil::reverse_complement( Uint4 seq, Uint1 size )
{
    Uint4 result( 0 );
 
    for( Uint1 i( 0 ); i < size; ++i )
    {
        Uint4 letter( ~(((seq>>(2*i))&0x3)|(~0x3)) );
        result = (result<<2)|letter;
    }
 
    return result;
}
 
END_NCBI_SCOPE