[Avida-SVN] r2342 - development/source/main

[barrick at myxo.css.msu.edu]

Author: barrick
Date: 2008-02-18 18:51:26 -0500 (Mon, 18 Feb 2008)
New Revision: 2342

Modified:
   development/source/main/cPopulation.cc
   development/source/main/cPopulation.h
   development/source/main/cPopulationInterface.cc
Log:
Fix for spatial deme resources -- they weren't being consumed, but could be produced. Fix for deme germ-line mutation config options.


Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc	2008-02-18 22:01:49 UTC (rev 2341)
+++ development/source/main/cPopulation.cc	2008-02-18 23:51:26 UTC (rev 2342)
@@ -1177,13 +1177,13 @@
     }
     
     if((m_world->GetConfig().GERMLINE_INS_MUT.Get() > 0.0)
-       && m_world->GetRandom().P(m_world->GetConfig().DIVIDE_INS_PROB.Get())) {
+       && m_world->GetRandom().P(m_world->GetConfig().GERMLINE_INS_MUT.Get())) {
       const unsigned int mut_line = ctx.GetRandom().GetUInt(next_germ.GetSize() + 1);
       next_germ.Insert(mut_line, instset.GetRandomInst(ctx));
     }
     
     if((m_world->GetConfig().GERMLINE_DEL_MUT.Get() > 0.0)
-       && m_world->GetRandom().P(m_world->GetConfig().DIVIDE_DEL_PROB.Get())) {
+       && m_world->GetRandom().P(m_world->GetConfig().GERMLINE_DEL_MUT.Get())) {
       const unsigned int mut_line = ctx.GetRandom().GetUInt(next_germ.GetSize());
       next_germ.Remove(mut_line);
     }
@@ -3460,13 +3460,12 @@
       cPopulationCell& cell = GetCell(i);
       
       // Correct gestation time for speculative execution
-      cPhenotype & p =  GetCell(i).GetOrganism()->GetPhenotype();
-      p.SetTrialTimeUsed(p.GetTrialTimeUsed() - GetCell(i).GetSpeculativeState());
-      p.SetTimeUsed(p.GetTimeUsed() - GetCell(i).GetSpeculativeState());
+      cPhenotype & p =  cell.GetOrganism()->GetPhenotype();
+      p.SetTrialTimeUsed(p.GetTrialTimeUsed() - cell.GetSpeculativeState());
+      p.SetTimeUsed(p.GetTimeUsed() - cell.GetSpeculativeState());
 
-
-      GetCell(i).GetOrganism()->NewTrial();
-      GetCell(i).GetOrganism()->GetHardware().Reset();
+      cell.GetOrganism()->NewTrial();
+      cell.GetOrganism()->GetHardware().Reset();
     }
   }
   

Modified: development/source/main/cPopulation.h
===================================================================
--- development/source/main/cPopulation.h	2008-02-18 22:01:49 UTC (rev 2341)
+++ development/source/main/cPopulation.h	2008-02-18 23:51:26 UTC (rev 2342)
@@ -254,6 +254,8 @@
   const tArray<double>& GetResources() const { return resource_count.GetResources(); }
   const tArray<double>& GetCellResources(int cell_id) const { return resource_count.GetCellResources(cell_id); }
   const tArray<double>& GetDemeResources(int deme_id) { return GetDeme(deme_id).GetDemeResourceCount().GetResources(); }
+  const tArray<double>& GetDemeCellResources(int deme_id, int cell_id) { return GetDeme(deme_id).GetDemeResourceCount().GetCellResources( GetDeme(deme_id).GetRelativeCellID(cell_id) ); }
+
   cBirthChamber& GetBirthChamber(int id) { (void) id; return birth_chamber; }
 
   void UpdateResources(const tArray<double>& res_change);

Modified: development/source/main/cPopulationInterface.cc
===================================================================
--- development/source/main/cPopulationInterface.cc	2008-02-18 22:01:49 UTC (rev 2341)
+++ development/source/main/cPopulationInterface.cc	2008-02-18 23:51:26 UTC (rev 2342)
@@ -112,7 +112,7 @@
 
 const tArray<double> & cPopulationInterface::GetDemeResources(int deme_id)
 {
-  return m_world->GetPopulation().GetDemeResources(deme_id);
+  return m_world->GetPopulation().GetDemeCellResources(deme_id, m_cell_id);
 }
 
 void cPopulationInterface::UpdateResources(const tArray<double> & res_change)