From 5d7acc9a50d4f492017ab1b789b3d646644b61d1 Mon Sep 17 00:00:00 2001 From: "seqan-actions[bot]" Date: Fri, 12 Jul 2024 09:59:46 +0200 Subject: [PATCH] [MISC] automatic linting --- include/hibf/sketch/compute_sketches.hpp | 10 +++++----- include/hibf/sketch/minHashes.hpp | 10 +++++----- src/sketch/compute_sketches.cpp | 16 ++++++++-------- test/unit/hibf/sketch/compute_sketches_test.cpp | 3 ++- test/unit/hibf/sketch/minHashes_test.cpp | 11 +++++------ 5 files changed, 25 insertions(+), 25 deletions(-) mode change 100755 => 100644 test/unit/hibf/sketch/compute_sketches_test.cpp diff --git a/include/hibf/sketch/compute_sketches.hpp b/include/hibf/sketch/compute_sketches.hpp index 145d7e6d..a0f4d89d 100644 --- a/include/hibf/sketch/compute_sketches.hpp +++ b/include/hibf/sketch/compute_sketches.hpp @@ -25,12 +25,12 @@ void compute_sketches(config const & config, std::vector & sketches); void compute_sketches_with_minhash(config const & config, - std::vector & sketches, - std::vector & minHash_sketches); + std::vector & sketches, + std::vector & minHash_sketches); void compute_sketches_with_minhash(config const & config, - std::vector & kmer_counts, - std::vector & sketches, - std::vector & minHash_sketches); + std::vector & kmer_counts, + std::vector & sketches, + std::vector & minHash_sketches); } // namespace seqan::hibf::sketch diff --git a/include/hibf/sketch/minHashes.hpp b/include/hibf/sketch/minHashes.hpp index 11b4a0b3..07981535 100644 --- a/include/hibf/sketch/minHashes.hpp +++ b/include/hibf/sketch/minHashes.hpp @@ -53,9 +53,9 @@ struct minHashes } } - inline static uint64_t const register_id_mask{15}; /// ...00001111 - inline static size_t const num_sketches{16}; - inline static size_t const sketch_size{40}; + static inline uint64_t const register_id_mask{15}; /// ...00001111 + static inline size_t const num_sketches{16}; + static inline size_t const sketch_size{40}; //!\brief A table of sketches. For LSH we need multiple sketches, stored in a table. std::vector> table{}; @@ -90,8 +90,8 @@ struct minHashes if (k_hash < heap[0]) // 0 because it is a max heap { // we do not need a guard (hash table) to check for duplications because `kmers` is already a set - std::pop_heap(heap.begin(), heap.end()); // max elements move to end of vector - heap.back() = k_hash; // replace last elements instead of physically popping and pushing + std::pop_heap(heap.begin(), heap.end()); // max elements move to end of vector + heap.back() = k_hash; // replace last elements instead of physically popping and pushing std::push_heap(heap.begin(), heap.end()); // last elements is rearranged in the heap to be pushed } } diff --git a/src/sketch/compute_sketches.cpp b/src/sketch/compute_sketches.cpp index cd6f3b2e..6fab7179 100644 --- a/src/sketch/compute_sketches.cpp +++ b/src/sketch/compute_sketches.cpp @@ -5,8 +5,8 @@ #include // for uint64_t #include // for size_t #include // for function +#include // for vector #include // for vector -#include // for vector #include // for config, insert_iterator #include // for unordered_flat_set @@ -49,8 +49,8 @@ void compute_sketches(config const & config, // Vector L2 : number_of_max_minHash_sketches (LSH ADD+OR parameter b) // Vector L3 : minHash_sketche_size (LSH ADD+OR parameter r) void compute_sketches_with_minhash(config const & config, - std::vector & sketches, - std::vector & minHash_sketches) + std::vector & sketches, + std::vector & minHash_sketches) { //inititalise sketches.resize(config.number_of_user_bins); @@ -84,7 +84,7 @@ void compute_sketches_with_minhash(config const & config, // that already had been in the heap because they are still the smallest ones. while (!minHash_sketch.is_valid()) { - heap_size *=2; + heap_size *= 2; heap.resize(heap_size, std::numeric_limits::max()); std::make_heap(heap.begin(), heap.end()); @@ -95,7 +95,7 @@ void compute_sketches_with_minhash(config const & config, std::sort(heap.begin(), heap.end()); // sort ascending to get the smallest numbers first - std::span const heap_to_consider(heap.begin() + heap_size/2, heap.end()); + std::span const heap_to_consider(heap.begin() + heap_size / 2, heap.end()); minHash_sketch.fill_up_sketches(heap_to_consider); } @@ -105,9 +105,9 @@ void compute_sketches_with_minhash(config const & config, } void compute_sketches_with_minhash(config const & config, - std::vector & kmer_counts, - std::vector & sketches, - std::vector & minHash_sketches) + std::vector & kmer_counts, + std::vector & sketches, + std::vector & minHash_sketches) { compute_sketches_with_minhash(config, sketches, minHash_sketches); kmer_counts.resize(config.number_of_user_bins); diff --git a/test/unit/hibf/sketch/compute_sketches_test.cpp b/test/unit/hibf/sketch/compute_sketches_test.cpp old mode 100755 new mode 100644 index d5a01cf5..9d26419d --- a/test/unit/hibf/sketch/compute_sketches_test.cpp +++ b/test/unit/hibf/sketch/compute_sketches_test.cpp @@ -81,7 +81,8 @@ TEST(compute_sketches_test, with_minHash) { for (size_t hidx = 0; hidx < seqan::hibf::sketch::minHashes::sketch_size; ++hidx) { - EXPECT_EQ(minHash_sketches[ub_id].table[sidx][hidx], start[ub_id] + hidx) << "ub_id:" << ub_id << " sidx:" << sidx << " hidx:" << hidx; + EXPECT_EQ(minHash_sketches[ub_id].table[sidx][hidx], start[ub_id] + hidx) + << "ub_id:" << ub_id << " sidx:" << sidx << " hidx:" << hidx; } } } diff --git a/test/unit/hibf/sketch/minHashes_test.cpp b/test/unit/hibf/sketch/minHashes_test.cpp index be6f6310..f9673868 100644 --- a/test/unit/hibf/sketch/minHashes_test.cpp +++ b/test/unit/hibf/sketch/minHashes_test.cpp @@ -4,14 +4,13 @@ #include // for Test, Message, TestInfo, TestPartResult, TEST, EXPECT_EQ -#include // for iota_vector -#include // for minHashes - -#include // for expect_range_eq, EXPECT_RANGE_EQ +#include // for iota_vector +#include // for minHashes +#include // for expect_range_eq, EXPECT_RANGE_EQ TEST(minHashes_test, static_update_heap_with) { - std::vector heap{3,4,5,6,7,8}; + std::vector heap{3, 4, 5, 6, 7, 8}; std::make_heap(heap.begin(), heap.end()); // make into proper heap // no change because 10 is larger than all values in the heap @@ -64,7 +63,7 @@ TEST(minHashes_test, fill_up_sketches) ASSERT_FALSE(minHash_sketch.is_valid()); // recreate bigger heap - std::vector bigger_heap = seqan::hibf::iota_vector(1000); + std::vector bigger_heap = seqan::hibf::iota_vector(1000); std::span const bigger_heap_non_redundant(bigger_heap.begin() + heap.size(), bigger_heap.end()); minHash_sketch.fill_up_sketches(bigger_heap_non_redundant);