Skip to content

Commit

Permalink
const saving in visit
Browse files Browse the repository at this point in the history
  • Loading branch information
adamant-pwn committed Jun 22, 2024
1 parent 2d1c27b commit 7214d01
Show file tree
Hide file tree
Showing 7 changed files with 81 additions and 27 deletions.
17 changes: 13 additions & 4 deletions include/buckets.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -255,12 +255,14 @@ struct buckets {
8 * (offsets.bytes() + strings.bytes());
}

template <typename Visitor>
void visit(Visitor& visitor) const {
visit_impl(visitor, *this);
}

template <typename Visitor>
void visit(Visitor& visitor) {
visitor.visit(pieces);
visitor.visit(num_super_kmers_before_bucket);
visitor.visit(offsets);
visitor.visit(strings);
visit_impl(visitor, *this);
}

ef_sequence<true> pieces;
Expand All @@ -269,6 +271,13 @@ struct buckets {
pthash::bit_vector strings;

private:
template <typename Visitor, typename T>
static void visit_impl(Visitor& visitor, T&& t) {
visitor.visit(t.pieces);
visitor.visit(t.num_super_kmers_before_bucket);
visitor.visit(t.offsets);
visitor.visit(t.strings);
}
bool is_valid(lookup_result res) const {
return (res.contig_size != constants::invalid_uint64 and
res.kmer_id_in_contig < res.contig_size) and
Expand Down
28 changes: 19 additions & 9 deletions include/dictionary.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -117,20 +117,30 @@ struct dictionary {
void print_space_breakdown() const;
void compute_statistics() const;

template <typename Visitor>
void visit(Visitor& visitor) const {
visit_impl(visitor, *this);
}

template <typename Visitor>
void visit(Visitor& visitor) {
visitor.visit(m_size);
visitor.visit(m_seed);
visitor.visit(m_k);
visitor.visit(m_m);
visitor.visit(m_canonical_parsing);
visitor.visit(m_minimizers);
visitor.visit(m_buckets);
visitor.visit(m_skew_index);
visitor.visit(m_weights);
visit_impl(visitor, *this);
}

private:
template <typename Visitor, typename T>
static void visit_impl(Visitor& visitor, T&& t) {
visitor.visit(t.m_size);
visitor.visit(t.m_seed);
visitor.visit(t.m_k);
visitor.visit(t.m_m);
visitor.visit(t.m_canonical_parsing);
visitor.visit(t.m_minimizers);
visitor.visit(t.m_buckets);
visitor.visit(t.m_skew_index);
visitor.visit(t.m_weights);
}

uint64_t m_size;
uint64_t m_seed;
uint16_t m_k;
Expand Down
19 changes: 14 additions & 5 deletions include/ef_sequence.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -186,16 +186,25 @@ struct ef_sequence {
m_high_bits_d0.bytes() + m_low_bits.bytes());
}

template <typename Visitor>
void visit(Visitor& visitor) const {
visit_impl(visitor, *this);
}

template <typename Visitor>
void visit(Visitor& visitor) {
visitor.visit(m_universe);
visitor.visit(m_high_bits);
visitor.visit(m_high_bits_d1);
visitor.visit(m_high_bits_d0);
visitor.visit(m_low_bits);
visit_impl(visitor, *this);
}

private:
template <typename Visitor, typename T>
static void visit_impl(Visitor& visitor, T&& t) {
visitor.visit(t.m_universe);
visitor.visit(t.m_high_bits);
visitor.visit(t.m_high_bits_d1);
visitor.visit(t.m_high_bits_d0);
visitor.visit(t.m_low_bits);
}
uint64_t m_universe;
pthash::bit_vector m_high_bits;
pthash::darray1 m_high_bits_d1;
Expand Down
5 changes: 5 additions & 0 deletions include/minimizers.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,11 @@ struct minimizers {
uint64_t size() const { return m_mphf.num_keys(); }
uint64_t num_bits() const { return m_mphf.num_bits(); }

template <typename Visitor>
void visit(Visitor& visitor) const {
visitor.visit(m_mphf);
}

template <typename Visitor>
void visit(Visitor& visitor) {
visitor.visit(m_mphf);
Expand Down
21 changes: 16 additions & 5 deletions include/skew_index.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -44,20 +44,31 @@ struct skew_index {
return n;
}

template <typename Visitor>
void visit(Visitor& visitor) const {
visit_impl(visitor, *this);
}

template <typename Visitor>
void visit(Visitor& visitor) {
visitor.visit(min_log2);
visitor.visit(max_log2);
visitor.visit(log2_max_num_super_kmers_in_bucket);
visitor.visit(mphfs);
visitor.visit(positions);
visit_impl(visitor, *this);
}

uint16_t min_log2;
uint16_t max_log2;
uint32_t log2_max_num_super_kmers_in_bucket;
std::vector<kmers_pthash_type> mphfs;
std::vector<pthash::compact_vector> positions;

private:
template <typename Visitor, typename T>
static void visit_impl(Visitor& visitor, T&& t) {
visitor.visit(t.min_log2);
visitor.visit(t.max_log2);
visitor.visit(t.log2_max_num_super_kmers_in_bucket);
visitor.visit(t.mphfs);
visitor.visit(t.positions);
}
};

} // namespace sshash
16 changes: 13 additions & 3 deletions include/weights.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -168,14 +168,24 @@ struct weights {
<< " [bits/kmer]\n";
}

template <typename Visitor>
void visit(Visitor& visitor) const {
visit_impl(visitor, *this);
}

template <typename Visitor>
void visit(Visitor& visitor) {
visitor.visit(m_weight_interval_values);
visitor.visit(m_weight_interval_lengths);
visitor.visit(m_weight_dictionary);
visit_impl(visitor, *this);
}

private:
template <typename Visitor, typename T>
static void visit_impl(Visitor& visitor, T&& t) {
visitor.visit(t.m_weight_interval_values);
visitor.visit(t.m_weight_interval_lengths);
visitor.visit(t.m_weight_dictionary);
}

pthash::compact_vector m_weight_interval_values;
ef_sequence<true> m_weight_interval_lengths;
pthash::compact_vector m_weight_dictionary;
Expand Down

0 comments on commit 7214d01

Please sign in to comment.