// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 Illumina, Inc.
//
// 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).
//
//

/// \file
///
/// \author Chris Saunders
///

#ifndef __POS_PROCESSOR_HH
#define __POS_PROCESSOR_HH

#include <blt_common/blt_shared.hh>
#include <blt_common/blt_streams.hh>
#include <blt_common/snp_pos_info.hh>
#include <blt_util/stream_stat.hh>

#include <boost/utility.hpp>

#include <iosfwd>
#include <memory>


struct diploid_genotype;
struct nploid_info;



/// \brief accumulate sequential position specific information and
/// send to a snp-calling routine after all position information is
/// found
///
/// pos_processor assumes that information related to each position
/// will be available in an approximately sequential fashion, where all
/// position values submitted after position X will be greater than
/// X-POS_BUFFER_SIZE+1. A violation of this assumption will trigger a
/// runtime error.
///
/// The implementation should be split into a generic semi-sequential
/// position-processor and an object with the application-specific
/// position code (here, snp-calling). Maybe once a second application
/// comes up...
///
struct pos_processor : private boost::noncopyable {

    pos_processor(const blt_options& client_opt,
                  const blt_deriv_options& client_dopt,
                  const char* const ref_seq,
                  const pos_t ref_size,
                  const blt_streams& client_io);

    ~pos_processor();


    void
    add_pos_snp_info(const pos_t pos,
                     const char ref,
                     const base_call& bc);

private:
    // process any remaining positions
    void
    reset();

    void
    handle_new_pos_value(const pos_t pos);

    bool
    is_pos_reportable(const pos_t pos){
        return _client_dopt.report_range_limit.is_pos_intersect(pos);
    }

    void
    process_pos(const pos_t pos);

    void
    process_pos_snp(const pos_t pos);

    void
    clear_pos(const pos_t pos){
        snp_pos_info& pi(_counts[pos_to_pindex(pos)]);
        pi.clear();
    }

    static
    unsigned
    pos_to_pindex(const pos_t pos){
        if(pos<0){
            return pos+POS_BUFFER_SIZE*(1-(pos/POS_BUFFER_SIZE));
        } else {
            return pos%POS_BUFFER_SIZE;
        }
    }

    std::ostream&
    get_report_os() const {
        return _client_io.report_os();
    }

    const diploid_genotype&
    get_empty_dgt(const char ref) const;

    enum { POS_BUFFER_SIZE = 500 };
    snp_pos_info _counts[POS_BUFFER_SIZE];
    pos_t _max_pos;
    pos_t _min_pos;
    bool _is_first_pos_set;

    const blt_options& _client_opt;
    const blt_deriv_options& _client_dopt;
    stream_stat _ss;
    stream_stat _used_ss;
    stream_stat _ssn;
    stream_stat _used_ssn;
    double* _ws;

    const char* const _ref_seq;
    const pos_t _ref_size;

    const blt_streams& _client_io;
    std::auto_ptr<nploid_info> _ninfo;

    unsigned _flank_size;
    std::auto_ptr<diploid_genotype> _empty_dgt[N_BASE];

    bool _is_dependent_eprob;
};

#endif