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[FEATURE] Make search work with dynamic mode configuration.
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Enables the dynamic mode configuration within the search algorithm by transforming it
into a static configuration.
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@rrahn
rrahn committed Dec 20, 2019
1 parent 5c23335 commit c467ff9
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Showing 3 changed files with 99 additions and 7 deletions.
42 changes: 37 additions & 5 deletions include/seqan3/search/algorithm/detail/search.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,10 @@

#pragma once

#include <variant>

#include <seqan3/core/type_traits/pre.hpp>
#include <seqan3/core/type_traits/function.hpp>
#include <seqan3/search/algorithm/detail/search_scheme_algorithm.hpp>
#include <seqan3/search/algorithm/detail/search_trivial.hpp>
#include <seqan3/search/configuration/all.hpp>
Expand Down Expand Up @@ -79,7 +82,7 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
};

// choose mode
if constexpr (cfg_t::template exists<search_cfg::mode<detail::search_mode_best>>())
if constexpr (cfg_t::template exists<internal_search_mode<search_mode_best>>())
{
detail::search_param max_error2{max_error};
max_error2.total = 0;
Expand All @@ -89,7 +92,7 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
max_error2.total++;
}
}
else if constexpr (cfg_t::template exists<search_cfg::mode<detail::search_mode_all_best>>())
else if constexpr (cfg_t::template exists<internal_search_mode<search_mode_all_best>>())
{
detail::search_param max_error2{max_error};
max_error2.total = 0;
Expand All @@ -99,7 +102,7 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
max_error2.total++;
}
}
else if constexpr (cfg_t::template exists<search_cfg::mode<search_cfg::strata>>())
else if constexpr (cfg_t::template exists<internal_search_mode<search_cfg::strata>>())
{
detail::search_param max_error2{max_error};
max_error2.total = 0;
Expand All @@ -111,7 +114,7 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
if (!internal_hits.empty())
{
internal_hits.clear(); // TODO: don't clear when using Optimum Search Schemes with lower error bounds
uint8_t const s = get<search_cfg::mode>(cfg).value;
uint8_t const s = get<internal_search_mode>(cfg).value;
max_error2.total += s - 1;
detail::search_algo<false>(index, query, max_error2, internal_delegate);
}
Expand All @@ -135,7 +138,7 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
typename index_t::size_type>;
std::vector<hit_t> hits;

if constexpr (cfg_t::template exists<search_cfg::mode<detail::search_mode_best>>())
if constexpr (cfg_t::template exists<internal_search_mode<search_mode_best>>())
{
// only one cursor is reported but it might contain more than one text position
if (!internal_hits.empty())
Expand Down Expand Up @@ -177,6 +180,9 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
* specified in `cfg` also has a strong exception guarantee; basic exception guarantee otherwise.
*/
template <typename index_t, typename queries_t, typename configuration_t>
//!\cond
requires configuration_t::template exists<internal_search_mode>()
//!\endcond
inline auto search_all(index_t const & index, queries_t & queries, configuration_t const & cfg)
{
using cfg_t = remove_cvref_t<configuration_t>;
Expand Down Expand Up @@ -209,6 +215,32 @@ inline auto search_all(index_t const & index, queries_t & queries, configuration
}
}

//!\overload
template <typename index_t, typename queries_t, typename configuration_t>
//!\cond
requires !configuration_t::template exists<internal_search_mode>()
//!\endcond
inline auto search_all(index_t const & index, queries_t & queries, configuration_t const & cfg)
{
using seqan3::get;
auto mode_config = get<search_cfg::mode>(cfg);

if constexpr (decltype(mode_config)::has_dynamic_state)
{
return std::visit(multi_invocable
{
[&] (search_mode_all_best) { return search_all(index, queries, cfg | internal_search_mode{search_cfg::all_best}); },
[&] (search_mode_best) { return search_all(index, queries, cfg | internal_search_mode{search_cfg::best}); },
[&] (search_cfg::strata const & strata) { return search_all(index, queries, cfg | internal_search_mode{strata}); },
[&] (auto) { return search_all(index, queries, cfg | internal_search_mode{search_cfg::all}); }
}, mode_config.search_modes());
}
else
{
return search_all(index, queries, cfg | internal_search_mode{mode_config.value});
}
}

//!\}

} // namespace seqan3::detail
28 changes: 26 additions & 2 deletions test/unit/search/search_configuration_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

#include <type_traits>

#include <seqan3/search/algorithm/all.hpp>
#include <seqan3/search/configuration/all.hpp>

#include <gtest/gtest.h>

Expand All @@ -20,7 +20,8 @@ class search_configuration_test : public ::testing::Test
using test_types = ::testing::Types<search_cfg::max_error_rate<>,
search_cfg::max_error<>,
search_cfg::mode<detail::search_mode_best>,
search_cfg::output<detail::search_output_text_position>>;
search_cfg::output<detail::search_output_text_position>
>;

TYPED_TEST_CASE(search_configuration_test, test_types);

Expand Down Expand Up @@ -53,6 +54,29 @@ TYPED_TEST(search_configuration_test, configuration_exists)
EXPECT_TRUE(decltype(cfg)::template exists<TypeParam>());
}

TYPED_TEST(search_configuration_test, configuration_exists_constexpr)
{
constexpr configuration cfg{TypeParam{}};
constexpr bool cfg_exists = decltype(cfg)::template exists<TypeParam>();
EXPECT_TRUE(cfg_exists);
}

TEST(search_configuration_mode_test, select_at_runtime)
{
{
seqan3::search_cfg::mode m{seqan3::search_cfg::all};
EXPECT_FALSE(m.has_dynamic_state);
}

{
seqan3::search_cfg::mode m{};
EXPECT_TRUE(m.has_dynamic_state);

m = seqan3::search_cfg::all_best;
EXPECT_TRUE(std::holds_alternative<seqan3::detail::search_mode_all_best>(m.search_modes()));
}
}

// TEST(search_configuration_test, illegal_runtime_configurations)
// {
// std::vector<dna4> text{"ACGT"_dna4}, query{"ACG"_dna4};
Expand Down
36 changes: 36 additions & 0 deletions test/unit/search/search_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -300,6 +300,13 @@ TYPED_TEST(search_test, search_strategy_all)
configuration const cfg = max_error{total{1}} | mode{all};
EXPECT_EQ(uniquify(search("ACGT"_dna4, this->index, cfg)), (hits_result_t{0, 1, 4, 5, 8, 9}));
}

{ // Test with dynamic mode.
mode dynamic_mode{};
dynamic_mode = all;
configuration const cfg = max_error{total{1}} | dynamic_mode;
EXPECT_EQ(uniquify(search("ACGT"_dna4, this->index, cfg)), (hits_result_t{0, 1, 4, 5, 8, 9}));
}
}

TYPED_TEST(search_test, search_strategy_best)
Expand All @@ -317,6 +324,18 @@ TYPED_TEST(search_test, search_strategy_best)
EXPECT_EQ(search("AAAA"_dna4, this->index, cfg), (hits_result_t{})); // no hit
}

{ // Test with dynamic mode.
mode dynamic_mode{};
dynamic_mode = best;
configuration const cfg = max_error{total{1}} | dynamic_mode;

hits_result_t result = search("ACGT"_dna4, this->index, cfg);
ASSERT_EQ(result.size(), 1u);
EXPECT_TRUE(std::find(possible_hits.begin(), possible_hits.end(), result[0]) != possible_hits.end());

EXPECT_EQ(search("AAAA"_dna4, this->index, cfg), (hits_result_t{})); // no hit
}

{ // Find best match with 1 insertion at the end.
configuration const cfg = max_error{total{1}, insertion{1}} | mode{best};

Expand Down Expand Up @@ -386,6 +405,16 @@ TYPED_TEST(search_test, search_strategy_all_best)

EXPECT_EQ(search("AAAA"_dna4, this->index, cfg), (hits_result_t{})); // no hit
}

{ // Test with dynamic mode.
mode dynamic_mode{};
dynamic_mode = all_best;
configuration const cfg = max_error{total{1}} | dynamic_mode;

EXPECT_EQ(uniquify(search("ACGT"_dna4, this->index, cfg)), (hits_result_t{0, 4, 8})); // 1, 5, 9 are not best hits

EXPECT_EQ(search("AAAA"_dna4, this->index, cfg), (hits_result_t{})); // no hit
}
}

TYPED_TEST(search_test, search_strategy_strata)
Expand All @@ -397,6 +426,13 @@ TYPED_TEST(search_test, search_strategy_strata)
EXPECT_EQ(uniquify(search("ACGT"_dna4, this->index, cfg)), (hits_result_t{0, 4, 8}));
}

{ // Test with dynamic mode.
mode dynamic_mode{};
dynamic_mode = strata{0};
configuration const cfg = max_error{total{1}} | dynamic_mode;
EXPECT_EQ(uniquify(search("ACGT"_dna4, this->index, cfg)), (hits_result_t{0, 4, 8}));
}

{
configuration const cfg = max_error{total{1}} | mode{strata{1}};
EXPECT_EQ(uniquify(search("ACGT"_dna4, this->index, cfg)), (hits_result_t{0, 1, 4, 5, 8, 9}));
Expand Down

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