seq_masker_window.cpp

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/*  $Id: seq_masker_window.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:
 *   CSeqMaskerWindow class member and method definitions.
 *
 */
 
#include <ncbi_pch.hpp>
#include <string>
 
#include <corelib/ncbi_limits.h>
 
#include <algo/winmask/seq_masker_window.hpp>
#include <objmgr/seq_vector.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
 
//-------------------------------------------------------------------------
Uint1 CSeqMaskerWindow::LOOKUP[kMax_UI1];
 
//-------------------------------------------------------------------------
CSeqMaskerWindow::CSeqMaskerWindow( const CSeqVector & arg_data, 
                                    Uint1 arg_unit_size, 
                                    Uint1 arg_window_size,
                                    Uint4 arg_window_step,
                                    Uint1 arg_unit_step,
                                    Uint4 winstart,
                                    Uint4 arg_winend )
    : data(arg_data), state( false ), 
      unit_size( arg_unit_size ), unit_step( arg_unit_step ),
      window_size( arg_window_size ), window_step( arg_window_step ),
      end( 0 ), first_unit( 0 ), unit_mask( 0 ), winend( arg_winend )
{
    static bool first_call = true;
 
    if( first_call )
    {
        LOOKUP[unsigned('A')] = 1;
        LOOKUP[unsigned('C')] = 2;
        LOOKUP[unsigned('G')] = 3;
        LOOKUP[unsigned('T')] = 4;
        first_call = false;
    }
 
    if( data.size() < window_size ) {
        // TODO Throw an exception.
    }
    if( unit_size > window_size ) {
        // TODO Throw an exception.
    }
 
    units.resize( NumUnits(), 0 );
    unit_mask = (unit_size == 16) ? 0xFFFFFFFF : (1ULL << (unit_size << 1)) - 1;
    
    if( winend == 0 )
        winend = data.size();
 
    FillWindow( winstart );
}
 
CSeqMaskerWindow::~CSeqMaskerWindow()
{
}
 
//-------------------------------------------------------------------------
void CSeqMaskerWindow::Advance( Uint4 step )
{
    if( 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;
 
    for( ; ++end < winend && iter < step ; ++iter, ++start )
    {
        Uint1 letter = LOOKUP[unsigned(data[end])];
 
        if( !(letter--) )
        { 
            FillWindow( end );
            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;
 
    if( iter != step ) state = false;
}
 
//-------------------------------------------------------------------------
void CSeqMaskerWindow::FillWindow( Uint4 winstart )
{
    first_unit = 0;
    TUnit unit = 0;
    Int4 iter = 0;
    end = winstart;
 
    for( ; iter < window_size && end < data.size(); ++iter, ++end )
    {
        Uint1 letter = LOOKUP[unsigned(data[end])];
 
        if( !(letter--) )
        {
            iter = -1;
            continue;
        }
 
        unit = ((unit<<2)&unit_mask) + letter;
 
        if( iter >= unit_size - 1 ) 
            if( !((iter + 1 - unit_size)%unit_step) )
                units[(iter + 1- unit_size)/unit_step] = unit;
    }
 
    start = (end--) - window_size;
    state = (iter == window_size);
}
 
 
END_NCBI_SCOPE