Fix base class for genome window functions

lib/genesis/population/window/base_window.hpp

@@ -33,6 +33,7 @@
 
 #include <stdexcept>
 #include <string>
+#include <unordered_map>
 
 #include "genesis/population/genome_region.hpp"
 
@@ -47,6 +48,13 @@ namespace population {
  * @brief Base class for Window and WindowView, to share common functionality.
  *
  * See Window for usage and details on the functions offered here.
+ *
+ * The class also adds a special case for when we are streaming over a whole genome.
+ * In that case, we cannot use our usual notation of first and last positions on a chromosome,
+ * as we are using the whole genome instead. As the notation is however useful in all other cases,
+ * we want to keep it. A cleaner approach from a software design perspective would be to have base
+ * classes for both cases, but that would lead to having incompatible types of WindowStream classes,
+ * which would add too much complexity for the current use case.
  */
 template<class D>
 class BaseWindow
@@ -174,6 +182,48 @@ class BaseWindow
         return last_position_ - first_position_ + 1;
     }
 
+    // -------------------------------------------------------------------------
+    //     Whole Genome
+    // -------------------------------------------------------------------------
+
+    /**
+     * @brief Return if this instance is intended to be used for a whole genome stream.
+     */
+    bool is_whole_genome() const
+    {
+        return is_whole_genome_;
+    }
+
+
+    /**
+     * @brief Set whether this instance is intended to be used for a whole genome stream.
+     */
+    void is_whole_genome( bool value )
+    {
+        is_whole_genome_ = value;
+    }
+
+    /**
+     * @brief Get the list of all chromosomes along the genome, with their length.
+     *
+     * This is based on the chromsomoes and their lengths as encountered in the input data,
+     * or on the sequence dictionary if provided to the GenomeWindowStream.
+     *
+     * Usage of this member is only valid if is_whole_genome() is set.
+     */
+    std::unordered_map<std::string, size_t> const& chromosomes() const
+    {
+        return chromosomes_;
+    }
+
+    /**
+     * @brief Get the list of all chromosomes along the genome, with their length.
+     */
+    std::unordered_map<std::string, size_t>& chromosomes()
+    {
+        return chromosomes_;
+    }
+
     // -------------------------------------------------------------------------
     //     Modifiers and Helpers
     // -------------------------------------------------------------------------
@@ -186,6 +236,8 @@ class BaseWindow
         chromosome_     = "";
         first_position_ = 0;
         last_position_  = 0;
+        is_whole_genome_ = false;
+        chromosomes_.clear();
         clear_();
     }
 
@@ -209,10 +261,15 @@ class BaseWindow
 
 private:
 
+    // Normal case of window within chromosome
     std::string chromosome_;
     size_t first_position_ = 0;
     size_t last_position_  = 0;
 
+    // Special case of window over whole genome
+    bool is_whole_genome_ = false;
+    std::unordered_map<std::string, size_t> chromosomes_;
+
 };
 
 } // namespace population

lib/genesis/population/window/window_view.hpp

@@ -39,7 +39,6 @@
 #include <stdexcept>
 #include <string>
 #include <vector>
-#include <unordered_map>
 
 namespace genesis {
 namespace population {
@@ -72,14 +71,6 @@ namespace population {
  * Because of its streaming approach, its memory footprint is smaller than that of a Window,
  * and hence allows to iterator whole chromosomes or genomes. On the flipside, its a single pass
  * iterator with no random access to the data in the window.
- *
- *
- * The class also adds a special case for when we are streaming over a whole genome.
- * In that case, we cannot use our usual notation of first and last positions on a chromosome,
- * as we are using the whole genome instead. As the notation is however useful in all other cases,
- * we want to keep it. A cleaner approach from a software design perspective would be to have base
- * classes for both cases, but that would lead to having incompatible types of WindowStream classes,
- * which would add too much complexity for the current use case.
  */
 template<class D>
 class WindowView final : public BaseWindow<D>
@@ -322,48 +313,6 @@ class WindowView final : public BaseWindow<D>
         return Iterator( nullptr );
     }
 
-    // -------------------------------------------------------------------------
-    //     Genome Window View
-    // -------------------------------------------------------------------------
-
-    /**
-     * @brief Return if this instance is intended to be used for a whole genome stream.
-     */
-    bool is_whole_genome() const
-    {
-        return is_whole_genome_;
-    }
-
-
-    /**
-     * @brief Set whether this instance is intended to be used for a whole genome stream.
-     */
-    void is_whole_genome( bool value )
-    {
-        is_whole_genome_ = value;
-    }
-
-    /**
-     * @brief Get the list of all chromosomes along the genome, with their length.
-     *
-     * This is based on the chromsomoes and their lengths as encountered in the input data,
-     * or on the sequence dictionary if provided to the GenomeWindowStream.
-     *
-     * Usage of this member is only valid if is_whole_genome() is set.
-     */
-    std::unordered_map<std::string, size_t> const& chromosomes() const
-    {
-        return chromosomes_;
-    }
-
-    /**
-     * @brief Get the list of all chromosomes along the genome, with their length.
-     */
-    std::unordered_map<std::string, size_t>& chromosomes()
-    {
-        return chromosomes_;
-    }
-
     // -------------------------------------------------------------------------
     //     Data Members
     // -------------------------------------------------------------------------
@@ -384,10 +333,6 @@ class WindowView final : public BaseWindow<D>
 
     mutable bool started_ = false;
 
-    // Genome window view
-    bool is_whole_genome_ = false;
-    std::unordered_map<std::string, size_t> chromosomes_;
-
 };
 
 } // namespace population