Fixed some issues based on eseilers review

seqan · Aug 7, 2018 · 9287193 · 9287193
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commit 9287193
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diff --git a/include/seqan3/index/all.hpp b/include/seqan3/index/all.hpp
@@ -1,4 +1,41 @@
+// ============================================================================
+//                 SeqAn - The Library for Sequence Analysis
+// ============================================================================
+//
+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin
+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik
+// All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above copyright
+//       notice, this list of conditions and the following disclaimer in the
+//       documentation and/or other materials provided with the distribution.
+//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
+//       its contributors may be used to endorse or promote products derived
+//       from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+// DAMAGE.
+//
+
+/*!\file
+ * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
+ * \brief Meta-header for the index module.
+ */
+
 #pragma once
 
 #include <seqan3/index/fm_index.hpp>
-// #include <seqan3/index/bidirectional_suffix_array.hpp>
diff --git a/include/seqan3/index/concept.hpp b/include/seqan3/index/concept.hpp
@@ -2,8 +2,8 @@
 //                 SeqAn - The Library for Sequence Analysis
 // ============================================================================
 //
-// Copyright (c) 2006-2017, Knut Reinert & Freie Universitaet Berlin
-// Copyright (c) 2016-2017, Knut Reinert & MPI Molekulare Genetik
+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin
+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -31,14 +31,17 @@
 // DAMAGE.
 //
 // ============================================================================
-// Author: Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
-// ============================================================================
+
+/*!\file
+ * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
+ * \brief Contains the concepts for the seqan3::fm_index and its traits and iterators.
+ */
 
 #pragma once
 
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 #include <seqan3/core/metafunction/range.hpp>
-#include <seqan3/range/concept.hpp>
+#include <seqan3/std/concept/range.hpp>
 
 #include <sdsl/suffix_arrays.hpp>
 

diff --git a/include/seqan3/index/detail/fm_index_iterator.hpp b/include/seqan3/index/detail/fm_index_iterator.hpp
@@ -31,8 +31,11 @@
 // DAMAGE.
 //
 // ============================================================================
-// Author: Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
-// ============================================================================
+
+/*!\file
+ * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
+  * \brief Contains the internal representation of a node of the seqan3::fm_index_iterator.
+ */
 
 #pragma once
 
@@ -42,16 +45,11 @@
 
 #include <seqan3/core/platform.hpp>
 
-
-/*!\file
- * \brief TODO
- * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
- */
-
 namespace seqan3::detail
 {
 
-template <typename index_t> // TODO: suffix_array_concept does not work here. not looked into it yet
+// NOTE: index_t requires fm_index_concept. circular dependency
+template <typename index_t>
 struct fm_index_iterator_node
 {
     using size_type = typename index_t::size_type;

diff --git a/include/seqan3/index/fm_index.hpp b/include/seqan3/index/fm_index.hpp
@@ -2,8 +2,8 @@
 //                 SeqAn - The Library for Sequence Analysis
 // ============================================================================
 //
-// Copyright (c) 2006-2017, Knut Reinert & Freie Universitaet Berlin
-// Copyright (c) 2016-2017, Knut Reinert & MPI Molekulare Genetik
+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin
+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -31,10 +31,13 @@
 // DAMAGE.
 //
 // ============================================================================
-// Author: Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
-// ============================================================================
 
-// #include <seqan3/index/concept.hpp>
+/*!\file
+ * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
+ * \brief Contains the unidirectional seqan3::fm_index.
+ */
+
+#include <seqan3/index/concept.hpp>
 #include <seqan3/index/fm_index_iterator.hpp>
 #include <seqan3/core/metafunction/range.hpp>
 
@@ -65,7 +68,8 @@ struct fm_index_default_traits
 
 // TODO: noexcept is still missing
 
-// TODO: check whether input_range_concept is the correct one! depends on open decisions in sdsl (im-construction, writing in-memory data to tmpfs and on the construction algorithms)
+// TODO: check whether input_range_concept is the correct one! depends on open decisions in sdsl
+// (im-construction, writing in-memory data to tmpfs and on the construction algorithms)
 
 /*!\brief The SeqAn FM Index.
  * \ingroup fm_index

diff --git a/include/seqan3/index/fm_index_iterator.hpp b/include/seqan3/index/fm_index_iterator.hpp
@@ -2,8 +2,8 @@
 //                 SeqAn - The Library for Sequence Analysis
 // ============================================================================
 //
-// Copyright (c) 2006-2017, Knut Reinert & Freie Universitaet Berlin
-// Copyright (c) 2016-2017, Knut Reinert & MPI Molekulare Genetik
+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin
+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -31,16 +31,21 @@
 // DAMAGE.
 //
 // ============================================================================
-// Author: Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
-// ============================================================================
+
+/*!\file
+ * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
+ * \brief Contains the seqan3::fm_index_iterator used to search in the unidirectional seqan3::fm_index.
+ */
 
 #pragma once
 
+#include <seqan3/alphabet/all.hpp>
+
 #include <seqan3/index/detail/fm_index_iterator.hpp>
 #include <seqan3/index/concept.hpp>
 #include <seqan3/std/concept/iterator.hpp>
 #include <seqan3/core/metafunction/range.hpp>
-#include <seqan3/range/concept.hpp>
+#include <seqan3/std/concept/range.hpp>
 
 #include <sdsl/suffix_trees.hpp>
 
@@ -51,7 +56,8 @@
 namespace seqan3
 {
 
-// TODO: remove mapping by overwriting backward_search. one only has to deal with incomplete alphabets then (maybe add own alphabet type to sdsl?)
+// TODO: remove mapping by overwriting backward_search.
+// one only has to deal with incomplete alphabets then (maybe add own alphabet type to sdsl?)
 
 // TODO: to_rank() + 1 consistent with comp_char, mapping and implicit_sentinel?
 
@@ -109,7 +115,12 @@ class fm_index_iterator
     {
         typename index_type::comp_char_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
         typename index_type::size_type _lb, _rb;
-        for (; c < index->m_index.sigma && !sdsl::backward_search(index->m_index, node.lb, node.rb, index->m_index.comp2char[c], _lb, _rb); ++c) {}
+        while (c < index->m_index.sigma &&
+               !sdsl::backward_search(index->m_index, node.lb, node.rb, index->m_index.comp2char[c], _lb, _rb))
+        {
+            ++c;
+        }
+
         if (c != index->m_index.sigma)
         {
             parent_lb = node.lb;
@@ -187,8 +198,11 @@ class fm_index_iterator
         typename index_type::comp_char_type c = node.last_char + 1;
         typename index_type::size_type _lb, _rb;
 
-        while (c < index->m_index.sigma && !sdsl::backward_search(index->m_index, parent_lb, parent_rb, index->m_index.comp2char[c], _lb, _rb))
+        while (c < index->m_index.sigma &&
+               !sdsl::backward_search(index->m_index, parent_lb, parent_rb, index->m_index.comp2char[c], _lb, _rb))
+        {
             ++c;
+        }
 
         if (c != index->m_index.sigma)
         {

diff --git a/test/unit/index/fm_index_iterator_test.cpp b/test/unit/index/fm_index_iterator_test.cpp
@@ -2,8 +2,8 @@
 //                 SeqAn - The Library for Sequence Analysis
 // ============================================================================
 //
-// Copyright (c) 2006-2017, Knut Reinert & Freie Universitaet Berlin
-// Copyright (c) 2016-2017, Knut Reinert & MPI Molekulare Genetik
+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin
+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without
@@ -199,7 +199,8 @@ TYPED_TEST(fm_index_iterator_test, incomplete_alphabet)
         EXPECT_EQ(it, iterator_type(sa));
     }
 
-    // search a char that does not occur in the text (some rank that is neither the smallest nor the highest smallest occurring in text)
+    // search a char that does not occur in the text
+    // (some rank that is neither the smallest nor the highest occurring in text)
     {
         text_type text {"ATATAT"_dna4};
         index_type sa{text};

diff --git a/test/unit/index/fm_index_test.cpp b/test/unit/index/fm_index_test.cpp
@@ -2,8 +2,8 @@
 //                 SeqAn - The Library for Sequence Analysis
 // ============================================================================
 //
-// Copyright (c) 2006-2017, Knut Reinert & Freie Universitaet Berlin
-// Copyright (c) 2016-2017, Knut Reinert & MPI Molekulare Genetik
+// Copyright (c) 2006-2018, Knut Reinert & Freie Universitaet Berlin
+// Copyright (c) 2016-2018, Knut Reinert & MPI Molekulare Genetik
 // All rights reserved.
 //
 // Redistribution and use in source and binary forms, with or without