concept.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 <type_traits>

#include <sdsl/suffix_arrays.hpp>

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/type_traits/range.hpp>
#include <seqan3/range/concept.hpp>
#include <seqan3/range/container/concept.hpp>

namespace seqan3::detail
{

 // ============================================================================
 //  SdslIndex
 // ============================================================================

template <typename t>
SEQAN3_CONCEPT SdslIndex = requires (t sdsl_index)
{
    typename t::size_type;

    { sdsl_index.size() } -> typename t::size_type;
    { sdsl_index[0] }; // suffix array access
    { sdsl_index.comp2char[0] } -> uint8_t;
    { sdsl_index.char2comp[0] } -> uint8_t;
    { sdsl_index.sigma };
    { sdsl_index.C[0] };

    requires requires (t sdsl_index, typename t::char_type const c, typename t::size_type const lb,
                                     typename t::size_type const rb, sdsl::int_vector<8> const text)
    {
        { sdsl_index.bwt.rank(lb, c) };
        { sdsl_index.wavelet_tree.lex_count(lb, rb, c) };
        { sdsl::construct_im(sdsl_index, text, 0) };
    };
};


} // namespace seqan3::detail

namespace seqan3
{

// ============================================================================
//  FmIndex
// ============================================================================

template <typename t>
SEQAN3_CONCEPT FmIndex = std::Semiregular<t> && requires (t index)
{
    typename t::size_type;
    // typename t::cursor_type;

    // NOTE: circular dependency
    // requires FmIndexCursor<typename t::cursor_type>;
    requires requires (t index, std::conditional_t<t::is_collection_,
                                                   std::vector<std::vector<dna4>>,
                                                   std::vector<dna4>> const text)
    {
        { t(text) };
        { index.construct(text) } -> void;
    };

    { index.begin() } -> typename t::cursor_type;

    { index.size()  } -> typename t::size_type;
    { index.empty() } -> bool;
};

// ============================================================================
//  FmIndexCursor
// ============================================================================

template <typename t>
SEQAN3_CONCEPT FmIndexCursor = std::Semiregular<t> && requires (t cur)
{
    typename t::index_type;
    typename t::size_type;

    requires FmIndex<typename t::index_type>;

    requires requires (typename t::index_type const index) { { t(index) } };

    requires requires (t cur, dna4 const c, std::vector<dna4> const seq,
                       std::conditional_t<t::index_type::is_collection_,
                                          std::vector<std::vector<dna4>>,
                                          std::vector<dna4>> const text)
    {
        { cur.extend_right()    } -> bool;
        { cur.extend_right(c)   } -> bool;
        { cur.extend_right(seq) } -> bool;
        { cur.cycle_back()      } -> bool;
        { cur.path_label(text)  } -> auto;
    };

    { cur.last_rank()    } -> typename t::size_type;
    { cur.query_length() } -> typename t::size_type;
    { cur.count()        } -> typename t::size_type;
    { cur.locate()       } -> std::conditional_t<t::index_type::is_collection_,
                                                std::vector<std::pair<typename t::size_type, typename t::size_type>>,
                                                std::vector<typename t::size_type>>;
    { cur.lazy_locate()  } -> auto;
};

// ============================================================================
//  BiFmIndex
// ============================================================================

template <typename t>
SEQAN3_CONCEPT BiFmIndex = FmIndex<t> && requires (t index)
{
    typename t::cursor_type; // already required by FmIndex but has a different documentation
    typename t::fwd_cursor_type;
    typename t::rev_cursor_type;

    // NOTE: circular dependency
    // requires BiFmIndexCursor<typename t::cursor_type>;

    { index.fwd_begin() } -> typename t::fwd_cursor_type;
    { index.rev_begin() } -> typename t::rev_cursor_type;
};

// ============================================================================
//  BiFmIndexCursor
// ============================================================================

template <typename t>
SEQAN3_CONCEPT BiFmIndexCursor = FmIndexCursor<t> && requires (t cur)
{
    requires BiFmIndex<typename t::index_type>;

    requires requires (typename t::index_type const index) { { t(index) } };

    requires requires (t cur, dna4 const c, std::vector<dna4> const seq)
    {
        { cur.extend_left()    } -> bool;
        { cur.extend_left(c)   } -> bool;
        { cur.extend_left(seq) } -> bool;
        { cur.cycle_front()    } -> bool;
    };

};


} // namespace seqan3