From 4a50eab1571b36d91d75499bfe0429871822e65a Mon Sep 17 00:00:00 2001
From: rrahn <rene.rahn@fu-berlin.de>
Date: Wed, 4 Sep 2019 00:09:49 +0200
Subject: [PATCH] [FEATURE] Adds alignment cache.

---
 .../detail/alignment_algorithm_cache.hpp      | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 include/seqan3/alignment/pairwise/detail/alignment_algorithm_cache.hpp

diff --git a/include/seqan3/alignment/pairwise/detail/alignment_algorithm_cache.hpp b/include/seqan3/alignment/pairwise/detail/alignment_algorithm_cache.hpp
new file mode 100644
index 00000000000..3bdd51bc1f0
--- /dev/null
+++ b/include/seqan3/alignment/pairwise/detail/alignment_algorithm_cache.hpp
@@ -0,0 +1,52 @@
+// -----------------------------------------------------------------------------------------------------
+// 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
+// -----------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides seqan3::detail::alignment_algorithm_cache.
+ * \author Rene Rahn <rene.rahn AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <seqan3/alignment/matrix/alignment_coordinate.hpp>
+#include <seqan3/alignment/matrix/alignment_optimum.hpp>
+
+namespace seqan3::detail
+{
+/*!\brief Local cache for the standard alignment algorithm.
+ * \tparam score_type The type of the score.
+ * \ingroup pairwise_alignment
+ *
+ * \details
+ *
+ * This cache is used internally for the standard alignment algorithm and caches the gap extension and gap open scores
+ * as well as the current alignment optimum.
+ * The alignment optimum stores the current score and the corresponding matrix coordinate in
+ * the underlying two-dimensional matrix.
+ */
+template <typename score_type>
+struct alignment_algorithm_cache
+{
+    //!\brief The cached gap open score.
+    score_type gap_open_score{};
+    //!\brief The cached gap extension score.
+    score_type gap_extension_score{};
+    //!\brief The current alignment optimum.
+    alignment_optimum<score_type> optimum{std::numeric_limits<score_type>::lowest(),
+                                          alignment_coordinate{column_index_type{0u}, row_index_type{0u}}};
+};
+
+/*!\name Type deduction guides
+ * \relates seqan3::detail::alignment_algorithm_cache
+ * \{
+ */
+
+//!\brief Deduces the template parameter for the score type from construction with gap open and gap extension scores.
+template <typename score_type>
+alignment_algorithm_cache(score_type, score_type) -> alignment_algorithm_cache<score_type>;
+//!\}
+}  // namespace seqan3::detail