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[MISC] Separate Bloom Filter strong types #3357

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Merged
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Apr 2, 2025
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[MISC] Separate Bloom Filter strong types #3357

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38 changes: 2 additions & 36 deletions include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
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Expand Up @@ -14,47 +14,13 @@

#include <seqan3/contrib/sdsl-lite.hpp>
#include <seqan3/core/concept/cereal.hpp>
#include <seqan3/core/detail/strong_type.hpp>
//Todo: When removing, the contents of the following header can be moved into utility/bloom_filter/bloom_filter.hpp
#include <seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp>

SEQAN3_DEPRECATED_HEADER("This header and its functionality is deprecated and will be removed in a future version of SeqAn. Please use the hibf-library (url: https://github.com/seqan/hibf) instead.");

namespace seqan3
{
//!\brief Determines if the Interleaved Bloom Filter is compressed.
//!\ingroup search_dream_index
enum data_layout : bool
{
uncompressed, //!< The Interleaved Bloom Filter is uncompressed.
compressed //!< The Interleaved Bloom Filter is compressed.
};

//!\brief A strong type that represents the number of bins for the seqan3::interleaved_bloom_filter.
//!\ingroup search_dream_index
struct bin_count : public detail::strong_type<size_t, bin_count, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, bin_count, detail::strong_type_skill::convert>::strong_type;
};

//!\brief A strong type that represents the number of bits for each bin in the seqan3::interleaved_bloom_filter.
//!\ingroup search_dream_index
struct bin_size : public detail::strong_type<size_t, bin_size, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, bin_size, detail::strong_type_skill::convert>::strong_type;
};

//!\brief A strong type that represents the number of hash functions for the seqan3::interleaved_bloom_filter.
//!\ingroup search_dream_index
struct hash_function_count : public detail::strong_type<size_t, hash_function_count, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, hash_function_count, detail::strong_type_skill::convert>::strong_type;
};

//!\brief A strong type that represents the bin index for the seqan3::interleaved_bloom_filter.
//!\ingroup search_dream_index
struct bin_index : public detail::strong_type<size_t, bin_index, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, bin_index, detail::strong_type_skill::convert>::strong_type;
};

/*!\brief The IBF binning directory. A data structure that efficiently answers set-membership queries for multiple bins.
* \ingroup search_dream_index
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6 changes: 5 additions & 1 deletion include/seqan3/utility/bloom_filter/bloom_filter.hpp
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#pragma once

#include <seqan3/search/dream_index/interleaved_bloom_filter.hpp>
#include <seqan3/contrib/sdsl-lite.hpp>
#include <seqan3/core/concept/cereal.hpp>
//Todo: When removing search/dream_index/interleaved_bloom_filter.hpp, the contents of the following header can be
// moved into this file
#include <seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp>

namespace seqan3
{
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56 changes: 56 additions & 0 deletions include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp
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@@ -0,0 +1,56 @@
// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

/*!\file
* \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
* \brief Provides strong types for the (Interleaved) Bloom Filter.
*/

#pragma once

#include <seqan3/core/detail/strong_type.hpp>

//Todo: When removing search/dream_index/interleaved_bloom_filter.hpp, the contents of this header can be moved
// into utility/bloom_filter/bloom_filter.hpp

namespace seqan3
{

//!\brief Determines if the Interleaved Bloom Filter is compressed.
//!\ingroup utility_bloom_filter
enum data_layout : bool
{
uncompressed, //!< The Interleaved Bloom Filter is uncompressed.
compressed //!< The Interleaved Bloom Filter is compressed.
};

//!\brief A strong type that represents the number of bins for the seqan3::interleaved_bloom_filter.
//!\ingroup utility_bloom_filter
struct bin_count : public detail::strong_type<size_t, bin_count, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, bin_count, detail::strong_type_skill::convert>::strong_type;
};

//!\brief A strong type that represents the number of bits for each bin in the seqan3::interleaved_bloom_filter.
//!\ingroup utility_bloom_filter
struct bin_size : public detail::strong_type<size_t, bin_size, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, bin_size, detail::strong_type_skill::convert>::strong_type;
};

//!\brief A strong type that represents the number of hash functions for the seqan3::interleaved_bloom_filter.
//!\ingroup utility_bloom_filter
struct hash_function_count : public detail::strong_type<size_t, hash_function_count, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, hash_function_count, detail::strong_type_skill::convert>::strong_type;
};

//!\brief A strong type that represents the bin index for the seqan3::interleaved_bloom_filter.
//!\ingroup utility_bloom_filter
struct bin_index : public detail::strong_type<size_t, bin_index, detail::strong_type_skill::convert>
{
using detail::strong_type<size_t, bin_index, detail::strong_type_skill::convert>::strong_type;
};

} // namespace seqan3