header.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

#pragma once

#include <deque>
#include <unordered_map>
#include <vector>

#include <seqan3/core/type_traits/pre.hpp>
#include <seqan3/io/alignment_file/detail.hpp>
#include <seqan3/std/ranges>

namespace seqan3
{

template <std::ranges::ForwardRange ref_ids_type = std::deque<std::string>>
class alignment_file_header
{
public:
    alignment_file_header() = default;
    alignment_file_header(alignment_file_header const &) = default;
    alignment_file_header & operator=(alignment_file_header const &) = default;
    alignment_file_header(alignment_file_header &&) = default;
    alignment_file_header & operator=(alignment_file_header &&) = default;
    ~alignment_file_header() = default;

    alignment_file_header(ref_ids_type & ref_ids) :
        ref_ids_ptr{&ref_ids, ref_ids_deleter_noop}
    {}

    alignment_file_header(ref_ids_type && ref_ids) :
        ref_ids_ptr{new ref_ids_type{std::move(ref_ids)}, ref_ids_deleter_default}
    {}

    struct program_info_t
    {
        std::string id;                
        std::string name;              
        std::string command_line_call; 
        std::string previous;          
        std::string description;       
        std::string version;           
    };

    std::string format_version; 
    std::string sorting;        
    std::string subsorting;     
    std::string grouping;       

    std::vector<program_info_t> program_infos; 

    std::vector<std::string> comments;         

private:
    using ref_ids_ptr_t = std::unique_ptr<ref_ids_type, std::function<void(ref_ids_type*)>>;
    static void ref_ids_deleter_noop(ref_ids_type *) {}
    static void ref_ids_deleter_default(ref_ids_type * ptr) { delete ptr; }
    using key_type = std::ranges::all_view<reference_t<ref_ids_type>>;
    ref_ids_ptr_t ref_ids_ptr{new ref_ids_type{}, ref_ids_deleter_default};

public:
    ref_ids_type & ref_ids()
    {
        return *ref_ids_ptr;
    }

    std::vector<std::tuple<int32_t, std::string>> ref_id_info{};

    std::unordered_map<key_type, int32_t, std::hash<key_type>, detail::view_equality_fn> ref_dict{};

    std::vector<std::pair<std::string, std::string>> read_groups;
};

} // namespace seqan3