From 756c028b9aacf985e79e94461d0144054fe40cc4 Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Wed, 2 Apr 2025 15:01:59 +0200
Subject: [PATCH] [MISC] Separate Bloom Filter strong types

Such that including the bloom_filter does not trigger deprecation warnings
---
 .../dream_index/interleaved_bloom_filter.hpp  | 38 +------------
 .../utility/bloom_filter/bloom_filter.hpp     |  6 +-
 .../bloom_filter_strong_types.hpp             | 56 +++++++++++++++++++
 3 files changed, 63 insertions(+), 37 deletions(-)
 create mode 100644 include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp

diff --git a/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp b/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
index b024bbb413..16437da94d 100644
--- a/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
+++ b/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp
@@ -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
diff --git a/include/seqan3/utility/bloom_filter/bloom_filter.hpp b/include/seqan3/utility/bloom_filter/bloom_filter.hpp
index 4c095c3922..988accd1d8 100644
--- a/include/seqan3/utility/bloom_filter/bloom_filter.hpp
+++ b/include/seqan3/utility/bloom_filter/bloom_filter.hpp
@@ -9,7 +9,11 @@
 
 #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
 {
diff --git a/include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp b/include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp
new file mode 100644
index 0000000000..d77d153eb4
--- /dev/null
+++ b/include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp
@@ -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