[Avida-SVN] r3527 - branches/biounit/source/classification

[brysonda at myxo.css.msu.edu]

Author: brysonda
Date: 2009-11-11 16:56:42 -0500 (Wed, 11 Nov 2009)
New Revision: 3527

Modified:
   branches/biounit/source/classification/cBGGenotype.cc
   branches/biounit/source/classification/cBGGenotype.h
   branches/biounit/source/classification/cBGGenotypeManager.cc
   branches/biounit/source/classification/cBGGenotypeManager.h
Log:
More work on biounit.  Fleshing out cBGGenotypeManager.

Modified: branches/biounit/source/classification/cBGGenotype.cc
===================================================================
--- branches/biounit/source/classification/cBGGenotype.cc	2009-11-11 19:40:41 UTC (rev 3526)
+++ branches/biounit/source/classification/cBGGenotype.cc	2009-11-11 21:56:42 UTC (rev 3527)
@@ -28,6 +28,7 @@
 cBGGenotype::cBGGenotype(cBGGenotypeManager* mgr, int in_id, cBioUnit* founder, int update, tArray<cBioGroup*>* parents)
   : m_mgr(mgr)
   , m_src(founder->GetUnitSource())
+  , m_src_args(founder->GetUnitSourceArgs())
   , m_genome(founder->GetMetaGenome())
   , m_name("001-no_name")
   , m_threshold(false)
@@ -37,6 +38,9 @@
   , m_update_deactivated(-1)
   , m_depth(0)
   , m_active_offspring_genotypes(0)
+  , m_num_organisms(0)
+  , m_last_num_organisms(0)
+  , m_total_organisms(0)
 {
   if (parents) {
     m_parents.Resize(parents->GetSize());
@@ -52,3 +56,8 @@
 {
   for (int i = 0; i < m_parents.GetSize(); i++) m_parents[i]->RemoveReference();
 }
+
+bool cBGGenotype::Matches(cBioUnit* bu)
+{
+  // @TODO 
+}

Modified: branches/biounit/source/classification/cBGGenotype.h
===================================================================
--- branches/biounit/source/classification/cBGGenotype.h	2009-11-11 19:40:41 UTC (rev 3526)
+++ branches/biounit/source/classification/cBGGenotype.h	2009-11-11 21:56:42 UTC (rev 3527)
@@ -47,10 +47,12 @@
 
 class cBGGenotype : public cBioGroup
 {
+  friend class cBGGenotypeManager;
 private:
   cBGGenotypeManager* m_mgr;
   
   cBioUnit::eUnitSource m_src;
+  cString m_src_args;
   cMetaGenome m_genome;
   cString m_name;
     
@@ -64,6 +66,9 @@
   int m_update_deactivated;
   int m_depth;
   int m_active_offspring_genotypes;
+  int m_num_organisms;
+  int m_last_num_organisms;
+  int m_total_organisms;
   
   tArray<cBioGroup*> m_parents;
   
@@ -72,7 +77,6 @@
   cCountTracker m_breed_in;
   cCountTracker m_breed_true;
   cCountTracker m_breed_out;
-  cCountTracker m_orgs;
 
   cDoubleSum m_copied_size;
   cDoubleSum m_exe_size;
@@ -95,6 +99,12 @@
 
   
   // Genotype Specific Methods
+  bool Matches(cBioUnit* bu);
+  
+  inline const cBioUnit::eUnitSource GetSource() const { return m_src; }
+  inline const cString& GetSourceArgs() const { return m_src_args; }
+  inline const cMetaGenome& GetGenome() const { return m_genome; }
+  
   inline const cString& GetName() const { return m_name; }
   
   inline bool IsThreshold() const { return m_threshold; }
@@ -104,6 +114,8 @@
   inline int GetUpdateBorn() const { return m_update_born; }
   inline int GetUpdateDeactivated() const { return m_update_deactivated; }
   
+  inline int GetNumOrganisms() const { return m_num_organisms; }
+  
   void SetThreshold() { m_threshold = true; }
   void ClearThreshold() { m_threshold = false; }
 };

Modified: branches/biounit/source/classification/cBGGenotypeManager.cc
===================================================================
--- branches/biounit/source/classification/cBGGenotypeManager.cc	2009-11-11 19:40:41 UTC (rev 3526)
+++ branches/biounit/source/classification/cBGGenotypeManager.cc	2009-11-11 21:56:42 UTC (rev 3527)
@@ -24,3 +24,61 @@
 
 #include "cBGGenotypeManager.h"
 
+#include "cBGGenotype.h"
+#include "cGenome.h"
+#include "cStats.h"
+#include "cStringUtil.h"
+#include "cWorld.h"
+
+
+//const unsigned int cBGGenotypeManager::HASH_SIZE = 3203;
+
+cBioGroup* cBGGenotypeManager::ClassifyNewBioUnit(cBioUnit* bu) { return ClassifyNewBioUnit(bu, NULL); }
+
+cBGGenotype* cBGGenotypeManager::ClassifyNewBioUnit(cBioUnit* bu, tArray<cBioGroup*>* parents)
+{
+  int list_num = hashGenome(bu->GetMetaGenome().GetGenome());
+
+  cBGGenotype* found = NULL;
+  tListIterator<cBGGenotype> list_it(m_active_hash[list_num]);
+  while (list_it.Next() != NULL) {
+    if (list_it.Get()->Matches(bu)) {
+      found = list_it.Get();
+      break;
+    }
+  }
+  
+  if (!found) {
+    found = new cBGGenotype(this, m_next_id++, bu, m_world->GetStats().GetUpdate(), parents);
+    m_active_hash[list_num].Push(found);
+    m_active_sz[found->GetNumOrganisms()].Push(found);
+    m_world->GetStats().AddGenotype();
+  }
+  
+  return found;
+}
+
+
+unsigned int cBGGenotypeManager::hashGenome(const cGenome& genome) const
+{
+  unsigned int total = 0;
+  
+  for (int i = 0; i < genome.GetSize(); i++) {
+    total += (genome[i].GetOp() + 3) * i;
+  }
+  
+  return total % nBGGenotypeManager::HASH_SIZE;
+}
+
+cString cBGGenotypeManager::nameGenotype(int size, int num) const
+{
+  char alpha[6];
+  
+  for (int i = 4; i >= 0; i--) {
+    alpha[i] = (num % 26) + 'a';
+    num /= 26;
+  }
+  alpha[5] = '\0';
+  
+  return cStringUtil::Stringf("%03d-%s", size, alpha);
+}

Modified: branches/biounit/source/classification/cBGGenotypeManager.h
===================================================================
--- branches/biounit/source/classification/cBGGenotypeManager.h	2009-11-11 19:40:41 UTC (rev 3526)
+++ branches/biounit/source/classification/cBGGenotypeManager.h	2009-11-11 21:56:42 UTC (rev 3527)
@@ -25,17 +25,39 @@
 #ifndef cBGGenotypeManager_h
 #define cBGGenotypeManager_h
 
+#ifndef defs_h
+#include "defs.h"
+#endif
 #ifndef cBioGroupManager_h
 #include "cBioGroupManager.h"
 #endif
+#ifndef tList_h
+#include "tList.h"
+#endif
+#ifndef tManagedPointerArray_h
+#include "tManagedPointerArray.h"
+#endif
 
+class cBGGenotype;
+class cGenome;
 class cWorld;
 
+namespace nBGGenotypeManager {
+  const unsigned int HASH_SIZE = 3203;
+}
 
 class cBGGenotypeManager : public cBioGroupManager
 {
 private:
   cWorld* m_world;
+
+  unsigned int m_sz_count[MAX_CREATURE_SIZE];
+  tList<cBGGenotype> m_active_hash[nBGGenotypeManager::HASH_SIZE];
+  tManagedPointerArray<tList<cBGGenotype> > m_active_sz;
+  tList<cBGGenotype> m_historic;
+  int m_next_id;
+  int m_dom_prev;
+  int m_dom_time;
   
   
 public:
@@ -47,6 +69,12 @@
   
   
   // Genotype Manager Methods
+  cBGGenotype* ClassifyNewBioUnit(cBioUnit* bu, tArray<cBioGroup*>* parents);
+  
+  
+private:
+  unsigned int hashGenome(const cGenome& genome) const;
+  cString nameGenotype(int size, int num) const;
 };
 
 #endif