Rename all odd visitor functions to proper observers

lib/genesis/population/functions/variant_input_iterator.cpp

@@ -1,6 +1,6 @@
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2023 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -134,10 +134,10 @@ std::function<void(Variant&)> make_variant_input_iterator_sample_name_filter_tra
 }
 
 // =================================================================================================
-//     Visitors
+//     Observers
 // =================================================================================================
 
-std::function<void(Variant const&)> make_variant_input_iterator_sequence_order_visitor(
+std::function<void(Variant const&)> make_variant_input_iterator_sequence_order_observer(
     std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict,
     bool check_sequence_lengths
 ) {
@@ -191,7 +191,7 @@ std::function<void(Variant const&)> make_variant_input_iterator_sequence_order_v
     };
 }
 
-std::function<void(Variant const&)> make_variant_input_iterator_sequence_length_visitor(
+std::function<void(Variant const&)> make_variant_input_iterator_sequence_length_observer(
     std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict
 ) {
     return [ sequence_dict ]( Variant const& variant ) {

lib/genesis/population/functions/variant_input_iterator.hpp

@@ -3,7 +3,7 @@
 
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2023 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -87,7 +87,7 @@ std::function<void(Variant&)> make_variant_input_iterator_sample_name_filter_tra
 );
 
 // =================================================================================================
-//     Visitors
+//     Observers
 // =================================================================================================
 
 /**
@@ -123,9 +123,9 @@ std::function<void(Variant&)> make_variant_input_iterator_sample_name_filter_tra
  *     // Create a VariantInputIterator, for example from a sync file
  *     auto variant_iterator = make_variant_input_iterator_from_sync_file( sync_file );
  *
- *     // Add the visitor that checks order, using a
- *     variant_iterator.add_visitor(
- *         make_variant_input_iterator_sequence_order_visitor(
+ *     // Add the observer that checks order, using a
+ *     variant_iterator.add_observer(
+ *         make_variant_input_iterator_sequence_order_observer(
  *             sequence_dict, true
  *         )
  *     );
@@ -135,7 +135,7 @@ std::function<void(Variant&)> make_variant_input_iterator_sample_name_filter_tra
  *         // ...
  *     }
  *
- * @see See @link ::genesis::utils::LambdaIterator::add_visitor() LambdaIterator::add_visitor()@endlink
+ * @see See @link ::genesis::utils::LambdaIterator::add_observer() LambdaIterator::add_observer()@endlink
  * for the function of the underlying iterator that accepts the returned function from here.
  *
  * @see make_variant_input_iterator_from_vector(),
@@ -147,7 +147,7 @@ std::function<void(Variant&)> make_variant_input_iterator_sample_name_filter_tra
  * make_variant_input_iterator_from_individual_vcf_file(),
  * make_variant_input_iterator_from_variant_parallel_input_iterator()
  */
-std::function<void(Variant const&)> make_variant_input_iterator_sequence_order_visitor(
+std::function<void(Variant const&)> make_variant_input_iterator_sequence_order_observer(
     std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict = {},
     bool check_sequence_lengths = true
 );
@@ -156,13 +156,13 @@ std::function<void(Variant const&)> make_variant_input_iterator_sequence_order_v
  * @brief Helper function to check that some Variant input has positions that agree with those
  * reported in a SequenceDict.
  *
- * Similar to make_variant_input_iterator_sequence_order_visitor(), but without the sequence order
+ * Similar to make_variant_input_iterator_sequence_order_observer(), but without the sequence order
  * check. Meant for situations where this order check is either not necessary, or already done in
  * some other way, for example in a VariantParallelInputIterator.
  *
- * See make_variant_input_iterator_sequence_order_visitor() for details on usage.
+ * See make_variant_input_iterator_sequence_order_observer() for details on usage.
  */
-std::function<void(Variant const&)> make_variant_input_iterator_sequence_length_visitor(
+std::function<void(Variant const&)> make_variant_input_iterator_sequence_length_observer(
     std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict
 );
 

lib/genesis/population/window/base_window_iterator.hpp

@@ -3,7 +3,7 @@
 
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2023 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -203,9 +203,9 @@ class BaseWindowIterator
         Iterator( std::unique_ptr<BaseIterator> base_iterator )
             : pimpl_( std::move( base_iterator ))
         {
-            // Visit the first element, if this is an active iterator.
+            // Observe the first element, if this is an active iterator.
             assert( pimpl_ );
-            execute_visitors_();
+            execute_observers_();
         }
 
     public:
@@ -300,10 +300,10 @@ class BaseWindowIterator
 
         self_type& operator ++()
         {
-            // Advance to the next element, and visit it.
+            // Advance to the next element, and observe it.
             assert( pimpl_ );
             pimpl_->increment_();
-            execute_visitors_();
+            execute_observers_();
             return *this;
         }
 
@@ -344,15 +344,15 @@ class BaseWindowIterator
 
     private:
 
-        void execute_visitors_()
+        void execute_observers_()
         {
             // If there is still a parent, we are active,
-            // and execute all visitors for the element.
+            // and execute all observers for the element.
             assert( pimpl_ );
             if( pimpl_->get_parent_() ) {
                 auto& element = pimpl_->get_current_window_();
-                for( auto const& visitor : pimpl_->get_parent_()->visitors_ ) {
-                    visitor( element );
+                for( auto const& observer : pimpl_->get_parent_()->observers_ ) {
+                    observer( element );
                 }
             }
         }
@@ -538,11 +538,11 @@ class BaseWindowIterator
     friend Iterator;
 
     // -------------------------------------------------------------------------
-    //     Visitors
+    //     Observers
     // -------------------------------------------------------------------------
 
     /**
-     * @brief Add a visitor function that is executed once for each window during the iteration.
+     * @brief Add a observer function that is executed once for each window during the iteration.
      *
      * These functions are executed when starting and incrementing the iterator, once for each
      * window, in the order in which they are added here. They take the window (typically of type
@@ -553,18 +553,18 @@ class BaseWindowIterator
      * in the beginning of the loop body of the user code. Still, offering this here can reduce
      * redundant code, such as logging Windows during the iteration.
      */
-    self_type& add_visitor( std::function<void(WindowType const&)> const& visitor )
+    self_type& add_observer( std::function<void(WindowType const&)> const& observer )
     {
-        visitors_.push_back( visitor );
+        observers_.push_back( observer );
         return *this;
     }
 
     /**
      * @brief Clear all functions that are executed on incrementing to the next element.
      */
-    self_type& clear_visitors()
+    self_type& clear_observers()
     {
-        visitors_.clear();
+        observers_.clear();
         return *this;
     }
 
@@ -604,8 +604,8 @@ class BaseWindowIterator
     InputIterator begin_;
     InputIterator end_;
 
-    // Keep the visitors for each window view.
-    std::vector<std::function<void(WindowType const&)>> visitors_;
+    // Keep the observers for each window view.
+    std::vector<std::function<void(WindowType const&)>> observers_;
 
 };
 

lib/genesis/utils/containers/lambda_iterator.hpp

@@ -3,7 +3,7 @@
 
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2023 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -918,7 +918,7 @@ class LambdaIterator
     }
 
     // -------------------------------------------------------------------------
-    //     Visitors and Callbacks
+    //     Observers and Callbacks
     // -------------------------------------------------------------------------
 
     /**
@@ -1081,7 +1081,7 @@ class LambdaIterator
 
     // We have two different types of functions that we accept to operate on the data:
     // the transforms and filters are executed when filling the buffers,
-    // while the visits are executed once the iteration reaches the respective element.
+    // while the observers are executed once the iteration reaches the respective element.
     std::vector<std::function<bool(T&)>> transforms_and_filters_;
     std::vector<std::function<void(T const&)>> observers_;
 

test/src/population/region_window_iterator.cpp

@@ -1,6 +1,6 @@
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2023 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -186,11 +186,11 @@ void run_region_window_test_(
         variants.begin(), variants.end(), region_list
     );
 
-    // Also test that the visitor functions get executed once per window.
-    size_t visit_cnt = 0;
-    win_it.add_visitor( [&visit_cnt]( Window<Variant> const& ){
-        // LOG_DBG << "at " << visit_cnt;
-        ++visit_cnt;
+    // Also test that the observer functions get executed once per window.
+    size_t observe_cnt = 0;
+    win_it.add_observer( [&observe_cnt]( Window<Variant> const& ){
+        // LOG_DBG << "at " << observe_cnt;
+        ++observe_cnt;
     });
 
     // ...and go through it.
@@ -382,7 +382,7 @@ void run_region_window_test_(
     EXPECT_EQ( exp_var_total_cnt_2, var_total_cnt );
     EXPECT_EQ( regions_with_vars, window_var_cnt );
     EXPECT_EQ( window_cnt_target, window_tot_cnt );
-    EXPECT_EQ( window_cnt_target, visit_cnt );
+    EXPECT_EQ( window_cnt_target, observe_cnt );
     if( ! skip_empty_regions ) {
         EXPECT_EQ( region_list->total_region_count(), window_tot_cnt );
     }

test/src/population/sliding_entries_window_iterator.cpp

@@ -1,6 +1,6 @@
 /*
     Genesis - A toolkit for working with phylogenetic data.
-    Copyright (C) 2014-2023 Lucas Czech
+    Copyright (C) 2014-2024 Lucas Czech
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -50,12 +50,12 @@ void test_sliding_entries_iterator_( WindowIterator& win_it, size_t count )
     bool found_first_win = false;
     bool found_last_win = false;
 
-    // Also test that the visitor functions get executed once per window.
-    size_t visit_cnt = 0;
+    // Also test that the observer functions get executed once per window.
+    size_t observe_cnt = 0;
     using ValueType = typename WindowIterator::InputIteratorType::value_type;
-    win_it.add_visitor( [&visit_cnt]( Window<ValueType> const& ){
-        // LOG_DBG << "at " << visit_cnt;
-        ++visit_cnt;
+    win_it.add_observer( [&observe_cnt]( Window<ValueType> const& ){
+        // LOG_DBG << "at " << observe_cnt;
+        ++observe_cnt;
     });
 
     // DBG  2R : 7790001 7790001-7800000 # 1
@@ -133,7 +133,7 @@ void test_sliding_entries_iterator_( WindowIterator& win_it, size_t count )
         ++window_cnt;
     }
     EXPECT_EQ( window_sizes.size(), window_cnt );
-    EXPECT_EQ( window_sizes.size(), visit_cnt );
+    EXPECT_EQ( window_sizes.size(), observe_cnt );
 
     EXPECT_TRUE( found_first_win );
     EXPECT_TRUE( found_last_win );
@@ -249,16 +249,16 @@ TEST( WindowIterator, SlidingEntriesWindowView )
         pileup_begin, pileup_end, 9000
     );
 
-    // Also test that the visitor functions get executed once per window.
-    size_t visit_cnt = 0;
-    win_it.add_visitor( [&visit_cnt]( WindowView<Variant> const& ){
-        // LOG_DBG << "at " << visit_cnt;
-        ++visit_cnt;
+    // Also test that the observer functions get executed once per window.
+    size_t observe_cnt = 0;
+    win_it.add_observer( [&observe_cnt]( WindowView<Variant> const& ){
+        // LOG_DBG << "at " << observe_cnt;
+        ++observe_cnt;
     });
 
     // We use a test function that takes our abstract type, to see if we set this up correctly.
     run_sliding_entries_window_view_variant_test_( win_it );
-    EXPECT_EQ( 6, visit_cnt );
+    EXPECT_EQ( 6, observe_cnt );
 
     // size_t window_cnt = 0;
     // for( auto it = win_it.begin(); it != win_it.end(); ++it ) {
@@ -283,11 +283,11 @@ TEST( WindowIterator, SlidingEntriesEmpty )
         pileup_begin, pileup_end, 10000
     );
 
-    // Also test that the visitor functions get executed once per window.
-    size_t visit_cnt = 0;
-    win_it.add_visitor( [&visit_cnt]( Window<Variant> const& ){
-        // LOG_DBG << "at " << visit_cnt;
-        ++visit_cnt;
+    // Also test that the observer functions get executed once per window.
+    size_t observe_cnt = 0;
+    win_it.add_observer( [&observe_cnt]( Window<Variant> const& ){
+        // LOG_DBG << "at " << observe_cnt;
+        ++observe_cnt;
     });
 
     size_t window_cnt = 0;
@@ -304,5 +304,5 @@ TEST( WindowIterator, SlidingEntriesEmpty )
         ++window_cnt;
     }
     EXPECT_EQ( 0, window_cnt );
-    EXPECT_EQ( 0, visit_cnt );
+    EXPECT_EQ( 0, observe_cnt );
 }