const saving in visit

jermp · Jun 22, 2024 · 7214d01 · 7214d01
1 parent 2d1c27b
commit 7214d01
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Showing 7 changed files with 81 additions and 27 deletions.
diff --git a/external/pthash b/external/pthash
diff --git a/include/buckets.hpp b/include/buckets.hpp
@@ -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;
@@ -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

diff --git a/include/dictionary.hpp b/include/dictionary.hpp
@@ -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;

diff --git a/include/ef_sequence.hpp b/include/ef_sequence.hpp
@@ -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;

diff --git a/include/minimizers.hpp b/include/minimizers.hpp
@@ -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);

diff --git a/include/skew_index.hpp b/include/skew_index.hpp
@@ -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
diff --git a/include/weights.hpp b/include/weights.hpp
@@ -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;
+1 −1		external/essentials
+17 −7		include/builders/internal_memory_builder_single_phf.hpp
+12 −2		include/encoders/bit_vector.hpp
+13 −4		include/encoders/compact_vector.hpp
+14 −4		include/encoders/darray.hpp
+12 −3		include/encoders/ef_sequence.hpp
+45 −7		include/encoders/encoders.hpp
+28 −7		include/partitioned_phf.hpp
+16 −7		include/single_phf.hpp
+25 −6		include/utils/bucketers.hpp