seq_masker_window_ambig.cpp

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/*  $Id: seq_masker_window_ambig.cpp 46615 2010-07-26 12:40:34Z dicuccio $
 * ===========================================================================
 *
 *                            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:
 *   CSeqMaskerWindowAmbig class member and method definitions.
 *
 */
 
#include <ncbi_pch.hpp>
#include <string>
 
#include <algo/winmask/seq_masker_window_ambig.hpp>
#include <objmgr/seq_vector.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
 
//-------------------------------------------------------------------------
CSeqMaskerWindowAmbig::CSeqMaskerWindowAmbig(const CSeqVector& arg_data,
                                             Uint1 arg_unit_size,
                                             Uint1 arg_window_size,
                                             Uint4 arg_window_step,
                                             TUnit arg_ambig_unit,
                                             Uint4 window_start,
                                             Uint1 arg_unit_step )
    : CSeqMaskerWindow( arg_data, arg_unit_size, 
                        arg_window_size, arg_window_step, arg_unit_step ),
      ambig_unit( arg_ambig_unit ), ambig( false )
{
    FillWindow( window_start );
}
 
//-------------------------------------------------------------------------
void CSeqMaskerWindowAmbig::Advance( Uint4 step )
{
    if( ambig || step >= window_size || unit_step > 1 ) 
    {
        FillWindow( start + step );
        return;
    }
 
    Uint1 num_units = NumUnits();
    Uint1 last_unit = first_unit ? first_unit - 1 : num_units - 1;
    Uint4 unit = units[last_unit];
    Uint4 iter = 0;
    Uint4 newstart = start + step;
 
    for( ; ++end < data.size() && iter < step ; ++iter )
    {
        Uint1 letter = LOOKUP[unsigned(data[end])];
 
        if( !(letter--) )
        { 
            FillWindow( newstart );
            return;
        }
 
        unit = ((unit<<2)&unit_mask) + letter;
 
        if( ++first_unit == num_units ) first_unit = 0;
 
        if( ++last_unit == num_units ) last_unit = 0;
 
        units[last_unit] = unit;
    }
 
    --end;
    start = end - window_size + 1;
 
    if( iter != step ) state = false;
}
 
//-------------------------------------------------------------------------
void CSeqMaskerWindowAmbig::FillWindow( Uint4 winstart )
{
    first_unit = 0;
    TUnit unit = 0;
    Int4 iter = 0;
    Int4 ambig_pos = -1;
    start = end = winstart;
    ambig = false;
 
    for( ; iter < window_size && end < data.size(); 
         ++iter, ++end, --ambig_pos )
    {
        Uint1 letter = LOOKUP[unsigned(data[end])];
 
        if( !(letter--) )
        {
            ambig_pos = unit_size - 1;
            ambig = true;
        }
 
        unit = ((unit<<2)&unit_mask) + letter;
 
        if( iter >= unit_size - 1 )  {
            if( !((iter + 1 - unit_size)%unit_step) ) {
                if( ambig_pos >= 0 ) 
                    units[(iter + 1 - unit_size)/unit_step] = ambig_unit;
                else
                    units[(iter + 1- unit_size)/unit_step] = unit;
            }
        }
    }
 
    --end;
    state = (iter == window_size);
}
 
 
END_NCBI_SCOPE