[Avida-SVN] r2392 - in development/source: cpu main

[dknoester at myxo.css.msu.edu]

Author: dknoester
Date: 2008-02-28 11:16:03 -0500 (Thu, 28 Feb 2008)
New Revision: 2392

Modified:
   development/source/cpu/cTestCPUInterface.h
   development/source/main/cEnvironment.cc
   development/source/main/cOrgInterface.h
   development/source/main/cPhenotype.cc
   development/source/main/cPopulationInterface.cc
   development/source/main/cPopulationInterface.h
   development/source/main/cReactionProcess.h
   development/source/main/cReactionResult.cc
   development/source/main/cReactionResult.h
Log:
Last commit to enable deme merit.  Reaction processes now apply process:demefrac to the heritable merit of each deme.

Modified: development/source/cpu/cTestCPUInterface.h
===================================================================
--- development/source/cpu/cTestCPUInterface.h	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/cpu/cTestCPUInterface.h	2008-02-28 16:16:03 UTC (rev 2392)
@@ -46,6 +46,7 @@
 
   int GetCellID() { return -1; }
   int GetDemeID() { return -1; }
+  cDeme* GetDeme() { return 0; }
   void SetCellID(int in_id) { ; }
   void SetDemeID(int in_id) { ; }
 

Modified: development/source/main/cEnvironment.cc
===================================================================
--- development/source/main/cEnvironment.cc	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cEnvironment.cc	2008-02-28 16:16:03 UTC (rev 2392)
@@ -1021,8 +1021,11 @@
     // Mark the reaction as having been performed if we get here.
     result.MarkReaction(reaction_id);
     
-    // Calculate the bonus
-    double bonus = consumed * cur_process->GetValue();
+    // How much of this bonus belongs to the deme, and how much belongs to the organism?
+    double deme_bonus = cur_process->GetDemeFraction() * consumed * cur_process->GetValue();
+    double bonus = (1.0 - cur_process->GetDemeFraction()) * consumed * cur_process->GetValue();
+
+    result.DemeBonus(deme_bonus);
     
     switch (cur_process->GetType()) {
       case nReaction::PROCTYPE_ADD:

Modified: development/source/main/cOrgInterface.h
===================================================================
--- development/source/main/cOrgInterface.h	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cOrgInterface.h	2008-02-28 16:16:03 UTC (rev 2392)
@@ -36,6 +36,7 @@
 
 class cAvidaContext;
 class cCodeLabel;
+class cDeme;
 class cGenome;
 class cOrganism;
 class cOrgMessage;
@@ -55,6 +56,7 @@
 
   virtual int GetCellID() = 0;
   virtual int GetDemeID() = 0;
+  virtual cDeme* GetDeme() = 0;
   virtual void SetCellID(int in_id) = 0;
   virtual void SetDemeID(int in_id) = 0;
 

Modified: development/source/main/cPhenotype.cc
===================================================================
--- development/source/main/cPhenotype.cc	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cPhenotype.cc	2008-02-28 16:16:03 UTC (rev 2392)
@@ -26,6 +26,7 @@
 #include "cPhenotype.h"
 
 #include "cEnvironment.h"
+#include "cDeme.h"
 #include "cHardwareManager.h"
 #include "cInstSet.h"
 #include "cReactionResult.h"
@@ -1005,6 +1006,11 @@
   cur_bonus *= result.GetMultBonus();
   cur_bonus += result.GetAddBonus();
   
+  // Update deme merit.
+  if(taskctx.GetOrganism()->GetOrgInterface().GetDeme()) {
+    taskctx.GetOrganism()->GetOrgInterface().GetDeme()->UpdateHeritableDemeMerit(result.GetDemeBonus());
+  }
+    
   // Update the energy bonus
   cur_energy_bonus += result.GetAddEnergy();
   

Modified: development/source/main/cPopulationInterface.cc
===================================================================
--- development/source/main/cPopulationInterface.cc	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cPopulationInterface.cc	2008-02-28 16:16:03 UTC (rev 2392)
@@ -41,7 +41,12 @@
 #define NULL 0
 #endif
 
+cDeme* cPopulationInterface::GetDeme()
+{
+  return &m_world->GetPopulation().GetDeme(m_deme_id);
+}
 
+
 bool cPopulationInterface::Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome)
 {
   assert(parent != NULL);

Modified: development/source/main/cPopulationInterface.h
===================================================================
--- development/source/main/cPopulationInterface.h	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cPopulationInterface.h	2008-02-28 16:16:03 UTC (rev 2392)
@@ -35,6 +35,7 @@
 #ifndef cWorldDriver_h
 #include "cWorldDriver.h"
 #endif
+#include "cDeme.h"
 
 class cPopulation;
 class cOrgMessage;
@@ -57,6 +58,7 @@
 
   int GetCellID() { return m_cell_id; }
   int GetDemeID() { return m_deme_id; }
+  cDeme* GetDeme();
   void SetCellID(int in_id) { m_cell_id = in_id; }
   void SetDemeID(int in_id) { m_deme_id = in_id; }
 

Modified: development/source/main/cReactionProcess.h
===================================================================
--- development/source/main/cReactionProcess.h	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cReactionProcess.h	2008-02-28 16:16:03 UTC (rev 2392)
@@ -122,7 +122,7 @@
   void SetDepletable(bool _in) { depletable = _in; }
   void SetLethal(int _in) { lethal = _in; }
   void SetSterile(int _in) { sterilize = _in; }
-  void SetDemeFraction(double _in) { deme_fraction = _in; }
+  void SetDemeFraction(double _in) { assert(_in>=0.0); assert(_in<=1.0); deme_fraction = _in; }
   void SetDetect(cResource* _in) { detect = _in; }
   void SetDetectionThreshold(double _in) { detection_threshold = _in; }
   void SetDetectionError(double _in) { detection_error = _in; }

Modified: development/source/main/cReactionResult.cc
===================================================================
--- development/source/main/cReactionResult.cc	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cReactionResult.cc	2008-02-28 16:16:03 UTC (rev 2392)
@@ -44,6 +44,7 @@
   , lethal(false)
   , sterilize(false)
   , active_reaction(false)
+  , deme_bonus(0.0)
 {
 }
 
@@ -135,6 +136,13 @@
   bonus_mult *= value;
 }
 
+void cReactionResult::DemeBonus(double value)
+{
+  ActivateReaction();
+  deme_bonus += value;
+}
+
+
 void cReactionResult::AddInst(int id)
 {
   insts_triggered.Push(id);

Modified: development/source/main/cReactionResult.h
===================================================================
--- development/source/main/cReactionResult.h	2008-02-28 15:32:07 UTC (rev 2391)
+++ development/source/main/cReactionResult.h	2008-02-28 16:16:03 UTC (rev 2392)
@@ -48,6 +48,8 @@
   bool sterilize;
   bool active_reaction;
 
+  double deme_bonus; //!< Bonus applied to the deme as a result of this reaction.
+  
   inline void ActivateReaction();
   
   cReactionResult(); // @not_implemented
@@ -71,6 +73,7 @@
   void AddEnergy(double value);
   void AddBonus(double value, int id);
   void MultBonus(double value);
+  void DemeBonus(double value);
   
   void AddInst(int id);
   
@@ -88,6 +91,7 @@
   double GetReactionAddBonus(const int i) { return reaction_add_bonus[i]; }
   double GetMultBonus() { return bonus_mult; }
   tArray<int>& GetInstArray() { return insts_triggered; }
+  double GetDemeBonus() { return deme_bonus; }
 };