// -*- 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 STATS_SET_H
#define STATS_SET_H

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

#include <valarray>

#include "statistics/Base_Calls.h"
#include "statistics/Cum_Errs.h"
#include "common/File_Buffer.h"
#include "statistics/Basic_Stats.h"
#include "statistics/Info_Contents.h"
#include "statistics/Read_Patterns.h"

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

class Stats_Set
{
 public:
    Stats_Set(size_t max_patterns_to_store);
    ~Stats_Set();

    /// This is intended only for initialisation.
    void set_num_cycles(const unsigned int num_cycles);
    unsigned int num_cycles() const;

    void add_basecalls_stats(const std::string &read, const std::string &qual);
    void add_align_stats(unsigned int align_score,
                         unsigned int num_insertions,
                         unsigned int num_insertion_bases,
                         unsigned int num_deletions,
                         unsigned int num_deletion_bases);
    void add_align_stats(const Stats_Set& stats_set);
    void apply_non_blank_mask(const std::valarray<unsigned int>& non_blank_mask);
    void derive_stats();
    void write(File_Buffer& file_buffer) const;

    typedef Base_Calls<unsigned int> Uint_Base_Calls;
    Uint_Base_Calls& base_calls() { return my_base_calls; }
    Cum_Errs& cum_errs() { return my_cum_errs; }

    Read_Patterns& most_common_words() { return my_most_common_words; }
    Read_Patterns& most_common_blank_patterns() {
        return my_most_common_blank_patterns;
    }

    void mark_as_all_reads() { my_all_reads_flag = true; }
    bool is_all_reads() const { return my_all_reads_flag; }

    enum { MAX_NUM_BLANKS_IN_COMMON_WORDS = 2 };

    unsigned long int clustersTotal() const {return my_num_clusters_total;}
    unsigned long int basesTotal() const {return my_num_bases_total;}
    unsigned long int q20BasesTotal() const {return my_q20_bases_total;}
    unsigned long int q30BasesTotal() const {return my_q30_bases_total;}
    unsigned long int qualityScoreSum() const {return my_quality_score_sum;}
    unsigned long int basesAligned() const {return my_num_bases_aligned;}
    unsigned long int uniqueAligns() const {return my_num_unique_aligns;}
    unsigned long int alignScoreSum() const {return my_align_score_sum;}
    unsigned long int alignMismatches() const {return my_num_errs;}

 private:
    typedef Base_Calls<int> Int_Base_Calls;
    typedef Base_Calls<float> Float_Base_Calls;

    void derive_proportions(const Uint_Base_Calls& base_calls,
                            Float_Base_Calls& pc_base_calls,
                            Uint_Base_Calls::Dimension sum_dimension,
                            bool as_percents = true,
                            bool exclude_read_blanks = false,
                            bool exclude_ref_blanks = false);
    void derive_likelihoods();
    void set_formats();

    bool my_all_reads_flag;

    unsigned long int my_q20_bases_total;
    unsigned long int my_q30_bases_total;
    unsigned long int my_quality_score_sum;
    unsigned long int my_num_clusters_total;
    unsigned long int my_num_bases_total;
    unsigned long int my_num_bases_aligned;
    unsigned long int my_num_errs;
    unsigned long int my_num_blanks;
    unsigned long int my_num_unique_aligns;
    unsigned long int my_align_score_sum;
    unsigned long int my_num_insertions;
    unsigned long int my_num_insertion_bases;
    unsigned long int my_num_deletions;
    unsigned long int my_num_deletion_bases;

    std::valarray<unsigned int> my_cycle_non_blank_freqs;

    Uint_Base_Calls my_base_calls;
    Uint_Base_Calls my_sum_over_cycles_base_calls;

    Basic_Stats my_basic_stats;

    Float_Base_Calls my_pc_reads_by_ref;
    Float_Base_Calls my_pc_reads_excl_blanks_by_ref;
    Float_Base_Calls my_pc_refs_by_read;
    Float_Base_Calls my_prop_reads_by_ref_cycle;

    Info_Contents my_info_contents;
    Read_Patterns my_most_common_words;
    Read_Patterns my_most_common_blank_patterns;
    Int_Base_Calls my_likelihoods;
    Cum_Errs my_cum_errs;
};

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

#endif // ! STATS_SET_H

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