[FEATURE] Add layout::read_from and layout::write_to.

include/hibf/detail/layout/layout.hpp

@@ -86,6 +86,9 @@ struct layout
         }
     };
 
+    void read_from(std::istream & stream);
+    void write_to(std::ostream & stream) const;
+
     size_t top_level_max_bin_id{};
     std::vector<max_bin> max_bins{};
     std::vector<user_bin> user_bins{};

src/CMakeLists.txt

@@ -2,6 +2,7 @@ set (HIBF_SOURCE_FILES
      hierarchical_interleaved_bloom_filter.cpp
      config.cpp
      detail/layout/simple_binning.cpp
+     detail/layout/layout.cpp
      detail/layout/execute.cpp
      detail/layout/compute_fpr_correction.cpp
      detail/layout/compute_layout.cpp

src/detail/layout/layout.cpp

@@ -0,0 +1,137 @@
+// ---------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2023, 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/hibf/blob/main/LICENSE.md
+// ---------------------------------------------------------------------------------------------------
+
+#include <cassert>
+#include <charconv>
+#include <iostream>
+
+#include <hibf/config.hpp>
+#include <hibf/detail/layout/layout.hpp>
+#include <hibf/detail/prefixes.hpp>
+
+namespace hibf::layout
+{
+
+hibf::layout::layout::user_bin parse_layout_line(std::string const & current_line)
+{
+    hibf::layout::layout::user_bin result{};
+
+    size_t tmp{}; // integer buffer when reading numbers
+
+    // initialize parsing
+    std::string_view const buffer{current_line};
+    auto const buffer_end{buffer.end()};
+    auto field_end = buffer.begin();
+    assert(field_end != buffer_end);
+
+    // read user bin index
+    field_end = std::from_chars(field_end, buffer_end, tmp).ptr;
+    result.idx = tmp;
+    assert(field_end != buffer_end && *field_end == '\t');
+
+    do // read bin_indices
+    {
+        ++field_end; // skip tab or ;
+        assert(field_end != buffer_end && *field_end != '\t');
+        field_end = std::from_chars(field_end, buffer_end, tmp).ptr;
+        result.previous_TB_indices.push_back(tmp);
+    }
+    while (field_end != buffer_end && *field_end != '\t');
+
+    result.storage_TB_id = result.previous_TB_indices.back();
+    result.previous_TB_indices.pop_back();
+
+    do // read number of technical bins
+    {
+        ++field_end; // skip tab or ;
+        field_end = std::from_chars(field_end, buffer_end, tmp).ptr;
+        result.number_of_technical_bins = tmp; // only the last number really counts
+    }
+    while (field_end != buffer_end && *field_end != '\t');
+
+    return result;
+}
+
+void hibf::layout::layout::read_from(std::istream & stream)
+{
+    // parse header
+    auto parse_bin_indices = [](std::string_view const & buffer)
+    {
+        std::vector<size_t> result;
+
+        auto buffer_start = &buffer[0];
+        auto const buffer_end = buffer_start + buffer.size();
+
+        size_t tmp{};
+
+        while (buffer_start < buffer_end)
+        {
+            buffer_start = std::from_chars(buffer_start, buffer_end, tmp).ptr;
+            ++buffer_start; // skip ;
+            result.push_back(tmp);
+        }
+
+        return result;
+    };
+
+    auto parse_first_bin = [](std::string_view const & buffer)
+    {
+        size_t tmp{};
+        std::from_chars(&buffer[0], &buffer[0] + buffer.size(), tmp);
+        return tmp;
+    };
+
+    std::string line;
+
+    std::getline(stream, line); // get first line that is always the max bin index of the top level bin
+    assert(line.substr(0, hibf::prefix::first_header_line.size()) == hibf::prefix::first_header_line);
+
+    // parse High Level max bin index
+    assert(line.substr(hibf::prefix::high_level.size() + 2, 11) == "max_bin_id:");
+    std::string_view const hibf_max_bin_str{line.begin() + 27, line.end()};
+    top_level_max_bin_id = parse_first_bin(hibf_max_bin_str);
+
+    // read and parse header records, in order to sort them before adding them to the graph
+    while (std::getline(stream, line) && line != hibf::prefix::column_ids)
+    {
+        assert(line.substr(1, hibf::prefix::merged_bin.size()) == hibf::prefix::merged_bin);
+
+        // parse header line
+        std::string_view const indices_str{
+            line.begin() + 1 /*#*/ + hibf::prefix::merged_bin.size() + 1 /*_*/,
+            std::find(line.begin() + hibf::prefix::merged_bin.size() + 2, line.end(), ' ')};
+
+        assert(line.substr(hibf::prefix::merged_bin.size() + indices_str.size() + 3, 11) == "max_bin_id:");
+        std::string_view const max_id_str{line.begin() + hibf::prefix::merged_bin.size() + indices_str.size() + 14,
+                                          line.end()};
+
+        max_bins.emplace_back(parse_bin_indices(indices_str), parse_first_bin(max_id_str));
+    }
+
+    assert(line == hibf::prefix::column_ids);
+
+    // parse the rest of the file
+    while (std::getline(stream, line))
+        user_bins.emplace_back(parse_layout_line(line));
+}
+
+void hibf::layout::layout::write_to(std::ostream & stream) const
+{
+    // write layout header with max bin ids
+    stream << prefix::first_header_line << " max_bin_id:" << top_level_max_bin_id << '\n';
+    for (auto const & max_bin : max_bins)
+        stream << max_bin << '\n';
+
+    // write header line
+    stream << prefix::column_ids << '\n';
+
+    // write layout entries
+    for (auto const & user_bin : user_bins)
+        stream << user_bin << '\n';
+}
+
+} // namespace hibf::layout

test/unit/hibf/detail/layout/layout_test.cpp

@@ -7,6 +7,7 @@
 #include <vector>      // for vector
 
 #include <hibf/detail/layout/layout.hpp> // for layout, operator<<
+#include <hibf/test/expect_range_eq.hpp> // for expect_range_eq, EXPECT_RANGE_EQ
 
 TEST(layout_test, printing_max_bins)
 {
@@ -49,3 +50,56 @@ TEST(layout_test, printing_user_bins)
 
     EXPECT_EQ(ss.str(), expected);
 }
+
+TEST(layout_test, write_to)
+{
+    std::stringstream ss{};
+
+    hibf::layout::layout layout;
+
+    layout.top_level_max_bin_id = 111;
+    layout.max_bins.emplace_back(std::vector<size_t>{0}, 0);
+    layout.max_bins.emplace_back(std::vector<size_t>{2}, 2);
+    layout.max_bins.emplace_back(std::vector<size_t>{1, 2, 3, 4}, 22);
+    layout.user_bins.emplace_back(7, std::vector<size_t>{}, 1, 0);
+    layout.user_bins.emplace_back(4, std::vector<size_t>{1}, 22, 0);
+    layout.user_bins.emplace_back(5, std::vector<size_t>{1, 2, 3, 4}, 21, 22);
+
+    layout.write_to(ss);
+
+    std::string expected = R"layout_file(#HIGH_LEVEL_IBF max_bin_id:111
+#MERGED_BIN_0 max_bin_id:0
+#MERGED_BIN_2 max_bin_id:2
+#MERGED_BIN_1;2;3;4 max_bin_id:22
+#USER_BIN_IDX	TECHNICAL_BIN_INDICES	NUMBER_OF_TECHNICAL_BINS
+7	0	1
+4	1;0	1;22
+5	1;2;3;4;22	1;1;1;1;21
+)layout_file";
+
+    EXPECT_EQ(ss.str(), expected);
+}
+
+TEST(layout_test, read_from)
+{
+    std::stringstream ss{R"layout_file(#HIGH_LEVEL_IBF max_bin_id:111
+#MERGED_BIN_0 max_bin_id:0
+#MERGED_BIN_2 max_bin_id:2
+#MERGED_BIN_1;2;3;4 max_bin_id:22
+#USER_BIN_IDX	TECHNICAL_BIN_INDICES	NUMBER_OF_TECHNICAL_BINS
+7	0	1
+4	1;0	1;22
+5	1;2;3;4;22	1;1;1;1;21
+)layout_file"};
+
+    hibf::layout::layout layout;
+    layout.read_from(ss);
+
+    EXPECT_EQ(layout.top_level_max_bin_id, 111);
+    EXPECT_EQ(layout.max_bins[0], (hibf::layout::layout::max_bin{{0}, 0}));
+    EXPECT_EQ(layout.max_bins[1], (hibf::layout::layout::max_bin{{2}, 2}));
+    EXPECT_EQ(layout.max_bins[2], (hibf::layout::layout::max_bin{{1, 2, 3, 4}, 22}));
+    EXPECT_EQ(layout.user_bins[0], (hibf::layout::layout::user_bin{7, std::vector<size_t>{}, 1, 0}));
+    EXPECT_EQ(layout.user_bins[1], (hibf::layout::layout::user_bin{4, std::vector<size_t>{1}, 22, 0}));
+    EXPECT_EQ(layout.user_bins[2], (hibf::layout::layout::user_bin{5, std::vector<size_t>{1, 2, 3, 4}, 21, 22}));
+}