// -*- 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 READ_PATTERNS_H
#define READ_PATTERNS_H

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

#include <string>
#include <map>

#include "statistics/Pattern_Info.h"

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

class Read_Patterns {
    friend std::ostream& operator<<(std::ostream&, const Read_Patterns&);

 public:
    Read_Patterns(size_t max_patterns_to_store);
    ~Read_Patterns();

    void record_pattern(const std::string& pattern_str);
    bool find_most_frequent();
    unsigned int num_will_list() const;

 private:
     void multi_record_pattern(const std::string& pattern_str,
                               unsigned int pattern_freq);

    typedef std::map<std::string, unsigned int> Pattern_Freq_Map;
    typedef Pattern_Freq_Map::iterator Pattern_Freq_Map_Iter;
    typedef Pattern_Freq_Map::const_iterator Pattern_Freq_Map_CIter;
    Pattern_Freq_Map my_pattern_freq_map;

    typedef std::map<unsigned int, Pattern_Info> Freq_Pattern_Info_Map;
    typedef Freq_Pattern_Info_Map::iterator Freq_Pattern_Info_Map_Iter;
    typedef Freq_Pattern_Info_Map::const_iterator Freq_Pattern_Info_Map_CIter;
    typedef Freq_Pattern_Info_Map::reverse_iterator
    Freq_Pattern_Info_Map_RIter;
    typedef Freq_Pattern_Info_Map::const_reverse_iterator
    Freq_Pattern_Info_Map_CRIter;
    Freq_Pattern_Info_Map my_freq_pattern_info_map;

    enum { MAX_NUM_RANKS_TO_LIST = 30};

    const size_t my_max_patterns_to_store;
    bool my_storage_limit_reached;
};

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

std::ostream& operator<<(std::ostream& ostrm,
                         const Read_Patterns& read_patterns);

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

#endif // ! READ_PATTERNS_H

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