// -*- c++ -*-
/*****************************************************************************/
// Copyright (c) Illumina 2008
// Author: Richard Shaw
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
/*****************************************************************************/

#ifndef NON_BLANK_FILTER_H
#define NON_BLANK_FILTER_H

/*****************************************************************************/

#include <cassert>
#include <string>
#include <valarray>

/*****************************************************************************/

const char the_blank_ch('N');

/*****************************************************************************/

class Non_Blank_Filter
{
public:
    Non_Blank_Filter(std::valarray<unsigned int>& non_blank_mask,
                     std::string& blank_pattern_str,
                     unsigned int& num_blanks)
        : my_non_blank_mask(non_blank_mask), my_ele_ind(0),
          my_blank_pattern_str(blank_pattern_str),
          my_blank_pattern_ch_iter(my_blank_pattern_str.begin()),
          my_num_blanks(num_blanks) { }
    ~Non_Blank_Filter() { }

    void operator()(const char ch) {
        // assert(ch != '.');
        const bool is_blank(ch == the_blank_ch);
        my_non_blank_mask[my_ele_ind++] = (is_blank ? 0 : 1);
        *my_blank_pattern_ch_iter++ = (is_blank ? '.' : 'N');
        my_num_blanks += (is_blank ? 1 : 0);
    }

    void reset() {
        my_ele_ind = 0;
        my_blank_pattern_ch_iter = my_blank_pattern_str.begin();
        my_num_blanks = 0;
    }

private:
    std::valarray<unsigned int>& my_non_blank_mask;
    size_t my_ele_ind;
    std::string& my_blank_pattern_str;
    std::string::iterator my_blank_pattern_ch_iter;
    unsigned int& my_num_blanks;
};

/*****************************************************************************/

#endif // ! NON_BLANK_FILTER_H

/*****************************************************************************/