[Avida-SVN] r3536 - branches/biounit/source/main

[brysonda at myxo.css.msu.edu]

Author: brysonda
Date: 2009-11-20 11:48:55 -0500 (Fri, 20 Nov 2009)
New Revision: 3536

Modified:
   branches/biounit/source/main/cBirthChamber.cc
   branches/biounit/source/main/cBirthChamber.h
   branches/biounit/source/main/cBirthEntry.h
Log:
Fix passing bio groups through the birth chamber.

Modified: branches/biounit/source/main/cBirthChamber.cc
===================================================================
--- branches/biounit/source/main/cBirthChamber.cc	2009-11-19 06:29:22 UTC (rev 3535)
+++ branches/biounit/source/main/cBirthChamber.cc	2009-11-20 16:48:55 UTC (rev 3536)
@@ -26,6 +26,7 @@
 #include "cBirthChamber.h"
 
 #include "cAvidaContext.h"
+#include "cBioGroup.h"
 #include "cBirthDemeHandler.h"
 #include "cBirthGenomeSizeHandler.h"
 #include "cBirthGlobalHandler.h"
@@ -108,9 +109,25 @@
     entry.merit = parent->GetPhenotype().GetMerit();
   }
   entry.parent_genotype = parent_genotype;
-  entry.timestamp = m_world->GetStats().GetUpdate();  
+  entry.timestamp = m_world->GetStats().GetUpdate();
+  entry.groups = parent->GetBioGroups();
+  
+  for (int i = 0; i < entry.groups.GetSize(); i++) {
+    entry.groups[i]->AddReference();
+  }
 }
 
+
+void cBirthChamber::ClearEntry(cBirthEntry& entry)
+{
+  entry.timestamp = -1;
+
+  for (int i = 0; i < entry.groups.GetSize(); i++) {
+    entry.groups[i]->RemoveReference();
+  }
+}
+
+
 bool cBirthChamber::RegionSwap(cGenome& genome0, cGenome& genome1, int start0, int end0, int start1, int end1)
 {
    assert( start0 >= 0  &&  start0 < genome0.GetSize() );
@@ -219,8 +236,8 @@
   merit_array[1] = parent.GetPhenotype().GetMerit();
 
   // Setup the genotypes for both children...
-  SetupGenotypeInfo(child_array[0], old_entry.parent_genotype, NULL);
-  SetupGenotypeInfo(child_array[1], parent.GetGenotype(), NULL);
+  SetupGenotypeInfo(child_array[0], old_entry.parent_genotype, &old_entry.groups);
+  SetupGenotypeInfo(child_array[1], parent.GetGenotype(), &parent.GetBioGroups());
 
   // We are now also done with the parent genotype that we were saving in
   // the birth chamber, so we can un-defer that one.
@@ -382,11 +399,12 @@
 }
 
 
-void cBirthChamber::SetupGenotypeInfo(cOrganism* organism, cGenotype* parent0, cGenotype* parent1)
+void cBirthChamber::SetupGenotypeInfo(cOrganism* organism, cGenotype* parent0, const tArray<cBioGroup*>* p0grps,
+                                      cGenotype* parent1, const tArray<cBioGroup*>* p1grps)
 {
   tArray<const tArray<cBioGroup*>*> pgrps;
-  if (parent0) pgrps.Push(&parent0->GetBioGroups());
-  if (parent1) pgrps.Push(&parent1->GetBioGroups());
+  if (p0grps) pgrps.Push(p0grps);
+  if (p1grps) pgrps.Push(p1grps);
   organism->SelfClassify(pgrps);
 
   // Setup the genotypes for both children...
@@ -420,7 +438,8 @@
   if (old_entry == NULL) return false;
 
   // We have now found a waiting entry.  Mark it no longer waiting and use it.
-  old_entry->timestamp = -1;
+  // @TODO - should this really be cleared here? It removes references before we are actually done with the bio groups
+  ClearEntry(*old_entry);
 
   // If we are NOT recombining, handle that here.
   if (parent_phenotype.CrossNum() == 0 || 
@@ -475,7 +494,9 @@
   const int two_fold_cost = m_world->GetConfig().TWO_FOLD_COST_SEX.Get();
 
   cGenotype* parent0_genotype = old_entry->parent_genotype;
+  const tArray<cBioGroup*>* parent0_groups = &old_entry->groups;
   cGenotype* parent1_genotype = parent->GetGenotype();
+  const tArray<cBioGroup*>* parent1_groups = &parent->GetBioGroups();
   
   const int hw_type = offspring.GetHardwareType();
   const int inst_set_id = offspring.GetInstSetID();
@@ -497,8 +518,8 @@
     merit_array[1] = meritOrEnergy1;
     
     // Setup the genotypes for both children...
-    SetupGenotypeInfo(child_array[0], parent0_genotype, parent1_genotype);
-    SetupGenotypeInfo(child_array[1], parent1_genotype, parent0_genotype);
+    SetupGenotypeInfo(child_array[0], parent0_genotype, parent0_groups, parent1_genotype, parent1_groups);
+    SetupGenotypeInfo(child_array[1], parent1_genotype, parent1_groups, parent0_genotype, parent0_groups);
 
   }
   else { 			// Build only one organism	
@@ -514,7 +535,7 @@
       merit_array[0] = meritOrEnergy0;
 
       // Setup the genotype for the child...
-      SetupGenotypeInfo(child_array[0], parent0_genotype, parent1_genotype);
+      SetupGenotypeInfo(child_array[0], parent0_genotype, parent0_groups, parent1_genotype, parent1_groups);
     } 
     else {
       child_array[0] = new cOrganism(m_world, ctx, hw_type, inst_set_id, genome1, SRC_ORGANISM_DIVIDE);
@@ -525,7 +546,7 @@
       merit_array[0] = meritOrEnergy1;
 
       // Setup the genotype for the child...
-      SetupGenotypeInfo(child_array[0], parent1_genotype, parent0_genotype);
+      SetupGenotypeInfo(child_array[0], parent1_genotype, parent1_groups, parent0_genotype, parent0_groups);
     }
   } 
 

Modified: branches/biounit/source/main/cBirthChamber.h
===================================================================
--- branches/biounit/source/main/cBirthChamber.h	2009-11-19 06:29:22 UTC (rev 3535)
+++ branches/biounit/source/main/cBirthChamber.h	2009-11-20 16:48:55 UTC (rev 3536)
@@ -70,6 +70,7 @@
 
   bool ValidBirthEntry(const cBirthEntry& entry) const;
   void StoreAsEntry(const cMetaGenome& offspring_genome, cOrganism* parent, cBirthEntry& entry) const;
+  void ClearEntry(cBirthEntry& entry);
 
 private:
   cBirthSelectionHandler* getSelectionHandler(int hw_type);
@@ -91,7 +92,8 @@
   void DoModularShuffleRecombination(cAvidaContext& ctx, cGenome& genome0, cGenome& genome1,
                                      double& merit0, double& merit1);
   
-  void SetupGenotypeInfo(cOrganism* organism, cGenotype* parent0_genotype, cGenotype* parent1_genotype);
+  void SetupGenotypeInfo(cOrganism* organism, cGenotype* parent0_genotype, const tArray<cBioGroup*>* p0grps,
+                         cGenotype* parent1_genotype = NULL, const tArray<cBioGroup*>* p1grps = NULL);
 };
 
 

Modified: branches/biounit/source/main/cBirthEntry.h
===================================================================
--- branches/biounit/source/main/cBirthEntry.h	2009-11-19 06:29:22 UTC (rev 3535)
+++ branches/biounit/source/main/cBirthEntry.h	2009-11-20 16:48:55 UTC (rev 3536)
@@ -32,6 +32,7 @@
 #include "cMetaGenome.h"
 #endif
 
+class cBioGroup;
 class cGenotype;
 
 
@@ -43,8 +44,9 @@
   cMerit merit;
   cGenotype* parent_genotype;
   int timestamp; // -1 if empty
+  tArray<cBioGroup*> groups;
   
-  inline cBirthEntry() : parent_genotype(NULL), timestamp(-1) { ; }
+  inline cBirthEntry() : parent_genotype(NULL), timestamp(-1), groups(NULL) { ; }
 };
 
 #endif