[Avida-SVN] r2179 - branches/dkdev/source/main

[dknoester at myxo.css.msu.edu]

Author: dknoester
Date: 2007-11-03 10:13:14 -0400 (Sat, 03 Nov 2007)
New Revision: 2179

Modified:
   branches/dkdev/source/main/cAvidaConfig.h
   branches/dkdev/source/main/cGermline.h
   branches/dkdev/source/main/cPopulation.cc
Log:
Added germline merit window, and removed debugging output.

Modified: branches/dkdev/source/main/cAvidaConfig.h
===================================================================
--- branches/dkdev/source/main/cAvidaConfig.h	2007-11-03 13:21:46 UTC (rev 2178)
+++ branches/dkdev/source/main/cAvidaConfig.h	2007-11-03 14:13:14 UTC (rev 2179)
@@ -167,6 +167,7 @@
   CONFIG_ADD_VAR(FILL_DEME_ON_REPLICATE, int, 0, "Whether to fill the source and target demes upon replication.");
   CONFIG_ADD_VAR(GERMLINE_REPLACES_SOURCE, int, 0, "Whether the source germline is updated on replication; 0=no.");
   CONFIG_ADD_VAR(GERMLINE_RANDOM_PLACEMENT, int, 0, "Whether the seed for a germline is placed randomly within the deme; 0=no.");
+  CONFIG_ADD_VAR(GERMLINE_MERIT_WINDOW_SIZE, int, 1, "The size of the germline merit accumulation window; >=1.");
   CONFIG_ADD_VAR(MAX_DEME_AGE, int, 500, "The maximum age of a deme (in updates) to be used for age-based replication (default=500).");
   CONFIG_ADD_VAR(TRACK_GENOTYPES, int, 0, "Whether genotypes are tracked graphically.");
   CONFIG_ADD_VAR(TWOCELLS_MIN_REGION_RATIO, double, 0.2, "Ratio of size of two-cells region to environment size.");

Modified: branches/dkdev/source/main/cGermline.h
===================================================================
--- branches/dkdev/source/main/cGermline.h	2007-11-03 13:21:46 UTC (rev 2178)
+++ branches/dkdev/source/main/cGermline.h	2007-11-03 14:13:14 UTC (rev 2179)
@@ -2,6 +2,8 @@
 #define _C_GERMLINE_H_
 
 #include <vector>
+#include <deque>
+#include <numeric>
 
 #include "cGenome.h"
 #include "cMerit.h"
@@ -12,11 +14,22 @@
 	void Add(const cGenome& genome) { _germline.push_back(genome); }
 	unsigned int Size() const { return _germline.size(); }
   
-  const cMerit& GetMerit() { return _merit; }
-  void UpdateMerit(double v) { _merit = v; }
+  const cMerit& GetMerit() {
+    _merit = std::accumulate(_merit_window.begin(), _merit_window.end(), 0.0);
+    return _merit; 
+  }
+  void UpdateMerit(double v) { UpdateWindowedMerit(v, 1); }
+  void UpdateWindowedMerit(double v, int window_size) { 
+    assert(window_size >= 1);
+    if(_merit_window.size() > window_size) {
+      _merit_window.pop_front();
+    }
+    _merit_window.push_back(v);
+  }
 
 protected:
 	std::vector<cGenome> _germline;
+  std::deque<double> _merit_window;
   cMerit _merit;
 };
 

Modified: branches/dkdev/source/main/cPopulation.cc
===================================================================
--- branches/dkdev/source/main/cPopulation.cc	2007-11-03 13:21:46 UTC (rev 2178)
+++ branches/dkdev/source/main/cPopulation.cc	2007-11-03 14:13:14 UTC (rev 2179)
@@ -107,18 +107,18 @@
     std::pair<int,int> cell1_xy = _deme.GetCellPosition(cells.first);    
     std::pair<int,int> self_xy = _deme.GetCellPosition(organism->GetCellID());
     
-    std::cout << "Organism " << organism->GetCellID() << " @ (" << self_xy.first << "," << self_xy.second << ") declares "
-     << organism->GetRegion() << " for cell1 @ (" << cell1_xy.first << "," << cell1_xy.second << ");";
+//    std::cout << "Organism " << organism->GetCellID() << " @ (" << self_xy.first << "," << self_xy.second << ") declares "
+//     << organism->GetRegion() << " for cell1 @ (" << cell1_xy.first << "," << cell1_xy.second << ");";
     
     // Has the organism declared correctly or not?  If so, increment result.
     if((self_xy.second >= (cell1_xy.second)) && (organism->GetRegionCount() > 0)) {
       result += 1.0;
-      std::cout << " up.";
+//      std::cout << " up.";
     } else if((self_xy.second <= (cell1_xy.second)) && (organism->GetRegionCount() < 0)) {
       result += 1.0;
-      std::cout << " down.";
+//      std::cout << " down.";
     }
-    std::cout << endl;
+//    std::cout << endl;
     
     // All done.
     return result;
@@ -1255,7 +1255,7 @@
     
     // Check to see if we should update the source deme's germline merit.
     if(m_world->GetConfig().DEMES_USE_GERMLINE.Get() && m_world->GetConfig().DEMES_HAVE_MERIT.Get()) {
-      source_deme.GetGermline().UpdateMerit(source_germline_merit);
+      source_deme.GetGermline().UpdateWindowedMerit(source_germline_merit, m_world->GetConfig().GERMLINE_MERIT_WINDOW_SIZE.Get());
     }
     m_world->GetStats().DemeReplication(source_deme);
 		cRandom& random = m_world->GetRandom();