Added 'Viral' operators with test. Implements the Mobile Genetic Elements Technique

eo/test/Makefile.am

@@ -13,7 +13,7 @@ LDADDS = $(top_builddir)/src/utils/libeoutils.a $(top_builddir)/src/libeo.a
 CXXFLAGS = -g -Wall 
 ###############################################################################
 
-check_PROGRAMS = t-eoParetoFitness t-eoPareto t-eofitness t-eoRandom t-eobin t-eoStateAndParser t-eoCheckpointing t-eoSSGA  \
+check_PROGRAMS = t-eoParetoFitness t-eoPareto t-eofitness t-eoRandom t-eobin t-eoVirus t-MGE t-MGE-control t-eoStateAndParser t-eoCheckpointing t-eoSSGA  \
 	t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA t-eoReal t-eoVector t-eoESAll
 TESTS=run_tests t-eoVector t-eoRandom t-eoSSGA t-eoPareto t-eoParetoFitness
 # removing temporarily t-eoESFull
@@ -39,6 +39,24 @@ t_eobin_LDADD = $(LDADDS)
 
 ###############################################################################
 
+t_eoVirus_SOURCES = t-eoVirus.cpp binary_value.h
+t_eoVirus_DEPENDENCIES = $(DEPS)
+t_eoVirus_LDADD = $(LDADDS)
+
+###############################################################################
+
+t_MGE_SOURCES = t-MGE.cpp binary_value.h
+t_MGE_DEPENDENCIES = $(DEPS)
+t_MGE_LDADD = $(LDADDS)
+
+###############################################################################
+
+t_MGE_control_SOURCES = t-MGE-control.cpp binary_value.h
+t_MGE_control_DEPENDENCIES = $(DEPS)
+t_MGE_control_LDADD = $(LDADDS)
+
+###############################################################################
+
 t_eoStateAndParser_SOURCES = t-eoStateAndParser.cpp
 t_eoStateAndParser_DEPENDENCIES = $(DEPS)
 t_eoStateAndParser_LDFLAGS = -lm

eo/test/t-MGE-control.cpp

@@ -0,0 +1,97 @@
+//-----------------------------------------------------------------------------
+// t-eoMGE.cpp
+//-----------------------------------------------------------------------------
+
+#ifndef __GNUG__
+// to avoid long name warnings
+#pragma warning(disable:4786)
+#endif // __GNUG__
+
+#include <eo>
+#include <ga/eoBitOp.h>
+
+#include "binary_value.h"
+
+// Viri
+#include <MGE/VirusOp.h>
+#include <MGE/eoVirus.h>
+#include <MGE/eoInitVirus.h>
+
+//-----------------------------------------------------------------------------
+
+typedef eoVirus<float> Chrom;
+
+//-----------------------------------------------------------------------------
+
+int main()
+{
+  const unsigned POP_SIZE = 100, CHROM_SIZE = 16;
+  unsigned i;
+  eoBooleanGenerator gen;
+
+  // the populations: 
+  eoPop<Chrom> pop; 
+
+   // Evaluation
+  eoEvalFuncPtr<Chrom> eval(  binary_value );
+  
+  eoInitVirus<float> random(CHROM_SIZE, gen); 
+  for (i = 0; i < POP_SIZE; ++i) {
+      Chrom chrom;
+      random(chrom);
+      eval(chrom);
+      pop.push_back(chrom);
+  }
+  
+  cout << "population:" << endl;
+  for (i = 0; i < pop.size(); ++i)
+    cout << "\t" << pop[i] << " " << pop[i].fitness() << endl;
+
+  
+  // selection
+  eoDetTournamentSelect<Chrom> lottery( 3) ;
+
+  // breeder
+  eoOneBitFlip<Chrom> bf;
+  eoUBitXover<Chrom> xover;
+  eoProportionalOp<Chrom> propSel;
+  eoGeneralBreeder<Chrom> breeder( lottery, propSel );
+  propSel.add(bf, 0.75);
+  propSel.add(xover, 0.25);
+  
+  // Replace a single one
+  eoPlusReplacement<Chrom> replace;
+
+  // Terminators
+  eoGenContinue<Chrom> continuator1(50);
+  eoFitContinue<Chrom> continuator2(65535.f);
+  eoCombinedContinue<Chrom> continuator(continuator1, continuator2);  
+  eoCheckPoint<Chrom> checkpoint(continuator);
+  eoStdoutMonitor monitor;
+  checkpoint.add(monitor);
+  eoSecondMomentStats<Chrom> stats;
+  monitor.add(stats);
+  checkpoint.add(stats);
+
+  // GA generation
+  eoEasyEA<Chrom> ea(checkpoint, eval,  breeder, replace );
+
+  // evolution
+  try
+    {
+      ea(pop);
+    }
+  catch (exception& e)
+    {
+	cout << "exception: " << e.what() << endl;;
+	exit(EXIT_FAILURE);
+    }
+  
+  cout << "pop" << endl;
+  for (i = 0; i < pop.size(); ++i)
+    cout << "\t" <<  pop[i] << " " << pop[i].fitness() << endl;
+  
+  return 0;
+}
+
+//-----------------------------------------------------------------------------

eo/test/t-MGE.cpp

@@ -0,0 +1,101 @@
+//-----------------------------------------------------------------------------
+// t-eoMGE.cpp
+//-----------------------------------------------------------------------------
+
+#ifndef __GNUG__
+// to avoid long name warnings
+#pragma warning(disable:4786)
+#endif // __GNUG__
+
+#include <eo>
+#include <ga/eoBitOp.h>
+
+#include "binary_value.h"
+
+// Viri
+#include <MGE/VirusOp.h>
+#include <MGE/eoVirus.h>
+#include <MGE/eoInitVirus.h>
+
+//-----------------------------------------------------------------------------
+
+typedef eoVirus<float> Chrom;
+
+//-----------------------------------------------------------------------------
+
+int main()
+{
+  const unsigned POP_SIZE = 100, CHROM_SIZE = 16;
+  unsigned i;
+  eoBooleanGenerator gen;
+
+  // the populations: 
+  eoPop<Chrom> pop; 
+
+   // Evaluation
+  eoEvalFuncPtr<Chrom> eval(  binary_value );
+  
+  eoInitVirus<float> random(CHROM_SIZE, gen); 
+  for (i = 0; i < POP_SIZE; ++i) {
+      Chrom chrom;
+      random(chrom);
+      eval(chrom);
+      pop.push_back(chrom);
+  }
+  
+  cout << "population:" << endl;
+  for (i = 0; i < pop.size(); ++i)
+    cout << "\t" << pop[i] << " " << pop[i].fitness() << endl;
+
+  
+  // selection
+  eoDetTournamentSelect<Chrom> lottery( 3) ;
+
+  // breeder
+  VirusMutation<float> vm;
+  VirusTransmission<float> vt;
+  VirusBitFlip<float> vf;
+  eoUBitXover<Chrom> xover;
+  eoProportionalOp<Chrom> propSel;
+  eoGeneralBreeder<Chrom> breeder( lottery, propSel );
+  propSel.add(vm, 0.25);
+  propSel.add(vf, 0.25);
+  propSel.add(vt, 0.25);
+  propSel.add(xover, 0.25);
+  
+  // Replace a single one
+  eoPlusReplacement<Chrom> replace;
+
+  // Terminators
+  eoGenContinue<Chrom> continuator1(50);
+  eoFitContinue<Chrom> continuator2(65535.f);
+  eoCombinedContinue<Chrom> continuator(continuator1, continuator2);  
+  eoCheckPoint<Chrom> checkpoint(continuator);
+  eoStdoutMonitor monitor;
+  checkpoint.add(monitor);
+  eoSecondMomentStats<Chrom> stats;
+  monitor.add(stats);
+  checkpoint.add(stats);
+
+  // GA generation
+  eoEasyEA<Chrom> ea(checkpoint, eval,  breeder, replace );
+
+  // evolution
+  try
+    {
+      ea(pop);
+    }
+  catch (exception& e)
+    {
+	cout << "exception: " << e.what() << endl;;
+	exit(EXIT_FAILURE);
+    }
+  
+  cout << "pop" << endl;
+  for (i = 0; i < pop.size(); ++i)
+    cout << "\t" <<  pop[i] << " " << pop[i].fitness() << endl;
+  
+  return 0;
+}
+
+//-----------------------------------------------------------------------------