{"action":"created","comment":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/comments/208557973","pull_request_review_id":144389454,"id":208557973,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwODU1Nzk3Mw==","diff_hunk":"@@ -0,0 +1,521 @@\n+// ============================================================================\n+//                 SeqAn - The Library for Sequence Analysis\n+// ============================================================================\n+//\n+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin\n+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik\n+// All rights reserved.\n+//\n+// Redistribution and use in source and binary forms, with or without\n+// modification, are permitted provided that the following conditions are met:\n+//\n+//     * Redistributions of source code must retain the above copyright\n+//       notice, this list of conditions and the following disclaimer.\n+//     * Redistributions in binary form must reproduce the above copyright\n+//       notice, this list of conditions and the following disclaimer in the\n+//       documentation and/or other materials provided with the distribution.\n+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of\n+//       its contributors may be used to endorse or promote products derived\n+//       from this software without specific prior written permission.\n+//\n+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE\n+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\n+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\n+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\n+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT\n+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY\n+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH\n+// DAMAGE.\n+//\n+// ============================================================================\n+\n+/*!\\file\n+ * \\author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>\n+ * \\brief Contains the seqan3::fm_index_iterator used to search in the unidirectional seqan3::fm_index.\n+ */\n+\n+#pragma once\n+\n+#include <array>\n+\n+#include <sdsl/suffix_trees.hpp>\n+\n+#include <range/v3/view/iota.hpp>\n+#include <range/v3/view/slice.hpp>\n+#include <range/v3/view/transform.hpp>\n+\n+#include <seqan3/alphabet/all.hpp>\n+#include <seqan3/index/detail/fm_index_iterator.hpp>\n+#include <seqan3/index/concept.hpp>\n+#include <seqan3/std/concept/range.hpp>\n+#include <seqan3/std/concept/iterator.hpp>\n+#include <seqan3/core/metafunction/range.hpp>\n+\n+namespace seqan3\n+{\n+\n+/*!\\addtogroup index\n+ * \\{\n+ */\n+\n+// TODO: unify terminology (pattern, sequence)\n+// TODO: remove mapping by overwriting backward_search.\n+// one only has to deal with incomplete alphabets then (maybe add own alphabet type to sdsl?)\n+// TODO: to_rank() + 1 consistent with comp_char, mapping and implicit_sentinel?\n+\n+/*!\\brief The undirectional FM index iterator.\n+ * \\ingroup fm_index\n+ * \\implements seqan3::fm_index_iterator_concept\n+ * \\tparam index_t The type of the underlying index; must satisfy seqan3::fm_index_concept.\n+ * \\details\n+ *\n+ * The iterator's interface and behaviour is equivalent to a suffix tree with the space and time efficiency of the\n+ * underlying pure FM index. The implicit suffix tree is not compacted, i.e. going down an edge will increase 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I was just wondering :)","created_at":"2018-08-08T12:18:13Z","updated_at":"2018-08-08T12:18:13Z","html_url":"https://github.com/seqan/seqan3/pull/292#discussion_r208557973","pull_request_url":"https://api.github.com/repos/seqan/seqan3/pulls/292","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/seqan/seqan3/pulls/comments/208557973"},"html":{"href":"https://github.com/seqan/seqan3/pull/292#discussion_r208557973"},"pull_request":{"href":"https://api.github.com/repos/seqan/seqan3/pulls/292"}},"in_reply_to_id":208468221},"pull_request":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/292","id":199714225,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk5NzE0MjI1","html_url":"https://github.com/seqan/seqan3/pull/292","diff_url":"https://github.com/seqan/seqan3/pull/292.diff","patch_url":"https://github.com/seqan/seqan3/pull/292.patch","issue_url":"https://api.github.com/repos/seqan/seqan3/issues/292","number":292,"state":"open","locked":false,"title":"First 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