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* indentations + whitespace cleanup

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This commit is contained in:
Caner Candan 2011-05-05 16:54:00 +02:00
commit 56c6edab04
285 changed files with 6068 additions and 6223 deletions
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7
eo/src/ga/Readme
View file

@ -1,11 +1,11 @@
This directory contains:
- some standard EO source files, named eoXXXXX, that define objects
- some standard EO source files, named eoXXXXX, that define objects
for the eoBit<FitT> representation (bitstrings).
- some make_XXX.cpp files that are instanciations for EO bitstrings
(eoBit<double> AND eoBit<eoMinimizingFitness>) of the tempatized code
that is defined in the EO src/do dir.
(eoBit<double> AND eoBit<eoMinimizingFitness>) of the tempatized code
that is defined in the EO src/do dir.
This MK's trick allows to actually compile all these bits in a library
(eolibga.a) and to only recompile the bits you need for your own
(bitstring!) application.
@ -18,4 +18,3 @@ that constructs the EOType initializer (make_genotype.h) and the one
that buils up the operators (make_op.h).
MS, April 23, 2001CVS

8
eo/src/ga/eoBit.h
View file

@ -106,11 +106,11 @@ public:
std::string bits;
is >> bits;
if (is)
{
resize(bits.size());
std::transform(bits.begin(), bits.end(), begin(),
{
resize(bits.size());
std::transform(bits.begin(), bits.end(), begin(),
std::bind2nd(std::equal_to<char>(), '1'));
}
}
}
};

105
eo/src/ga/eoBitOp.h
View file

@ -87,10 +87,10 @@ template<class Chrom> class eoDetBitFlip: public eoMonOp<Chrom>
{
// does not check for duplicate: if someone volunteers ....
for (unsigned k=0; k<num_bit; k++)
{
unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true;
}
{
unsigned i = eo::rng.random(chrom.size());
chrom[i] = (chrom[i]) ? false : true;
}
return true;
}
private:
@ -126,9 +126,9 @@ template<class Chrom> class eoBitMutation: public eoMonOp<Chrom>
double actualRate = (normalize ? rate/chrom.size() : rate);
bool changed_something = false;
for (unsigned i = 0; i < chrom.size(); i++)
if (eo::rng.flip(actualRate))
if (eo::rng.flip(actualRate))
{
chrom[i] = !chrom[i];
chrom[i] = !chrom[i];
changed_something = true;
}
@ -137,7 +137,7 @@ template<class Chrom> class eoBitMutation: public eoMonOp<Chrom>
private:
double rate;
bool normalize; // divide rate by chromSize
bool normalize; // divide rate by chromSize
};
@ -187,16 +187,16 @@ template<class Chrom> class eoBitNext: public eoMonOp<Chrom>
bool operator()(Chrom& chrom)
{
for (int i = chrom.size() - 1; i >= 0; i--)
if (chrom[i])
{
chrom[i] = 0;
continue;
}
else
{
chrom[i] = 1;
break;
}
if (chrom[i])
{
chrom[i] = 0;
continue;
}
else
{
chrom[i] = 1;
break;
}
return true;
}
@ -221,16 +221,16 @@ template<class Chrom> class eoBitPrev: public eoMonOp<Chrom>
bool operator()(Chrom& chrom)
{
for (int i = chrom.size() - 1; i >= 0; i--)
if (chrom[i])
{
chrom[i] = 0;
break;
}
else
{
chrom[i] = 1;
continue;
}
if (chrom[i])
{
chrom[i] = 0;
break;
}
else
{
chrom[i] = 1;
continue;
}
return true;
}
@ -281,7 +281,7 @@ template<class Chrom> class eoUBitXover: public eoQuadOp<Chrom>
eoUBitXover(const float& _preference = 0.5): preference(_preference)
{
if ( (_preference <= 0.0) || (_preference >= 1.0) )
std::runtime_error("UxOver --> invalid preference");
std::runtime_error("UxOver --> invalid preference");
}
/// The class name.
virtual std::string className() const { return "eoUBitXover"; }
@ -295,18 +295,18 @@ template<class Chrom> class eoUBitXover: public eoQuadOp<Chrom>
bool operator()(Chrom& chrom1, Chrom& chrom2)
{
if ( chrom1.size() != chrom2.size())
std::runtime_error("UxOver --> chromosomes sizes don't match" );
std::runtime_error("UxOver --> chromosomes sizes don't match" );
bool changed = false;
for (unsigned int i=0; i<chrom1.size(); i++)
{
if (chrom1[i] != chrom2[i] && eo::rng.flip(preference))
{
bool tmp = chrom1[i];
chrom1[i]=chrom2[i];
chrom2[i] = tmp;
changed = true;
}
}
{
if (chrom1[i] != chrom2[i] && eo::rng.flip(preference))
{
bool tmp = chrom1[i];
chrom1[i]=chrom2[i];
chrom2[i] = tmp;
changed = true;
}
}
return changed;
}
private:
@ -390,9 +390,9 @@ template<class Chrom> class eoBitGxOver: public eoQuadOp<Chrom>
gene_size(_gene_size), num_points(_num_points)
{
if (gene_size < 1)
std::runtime_error("GxOver --> invalid gene size");
std::runtime_error("GxOver --> invalid gene size");
if (num_points < 1)
std::runtime_error("GxOver --> invalid number of points");
std::runtime_error("GxOver --> invalid number of points");
}
/// The class name
@ -412,22 +412,22 @@ template<class Chrom> class eoBitGxOver: public eoQuadOp<Chrom>
// selects genes to swap
do {
unsigned bit = eo::rng.random(max_genes);
if (points[bit])
continue;
else
{
points[bit] = true;
cut_genes--;
}
unsigned bit = eo::rng.random(max_genes);
if (points[bit])
continue;
else
{
points[bit] = true;
cut_genes--;
}
} while (cut_genes);
// swaps genes
for (unsigned i = 0; i < points.size(); i++)
if (points[i])
std::swap_ranges(chrom1.begin() + i * gene_size,
chrom1.begin() + i * gene_size + gene_size,
chrom2.begin() + i * gene_size);
if (points[i])
std::swap_ranges(chrom1.begin() + i * gene_size,
chrom1.begin() + i * gene_size + gene_size,
chrom2.begin() + i * gene_size);
return true;
}
@ -442,4 +442,3 @@ template<class Chrom> class eoBitGxOver: public eoQuadOp<Chrom>
//-----------------------------------------------------------------------------
//@}
#endif

227
eo/src/ga/eoBitOpFactory.h
View file

@ -4,7 +4,7 @@
//-----------------------------------------------------------------------------
// eoOpFactory.h
// (c) GeNeura Team, 1998
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -39,135 +39,134 @@ that are created here
@ingroup Variators
*/
template< class EOT>
class eoBitOpFactory: public eoFactory<EOT>
class eoBitOpFactory: public eoFactory<EOT>
{
public:
/// @name ctors and dtors
//{@
/// constructor
eoBitOpFactory( ) {};
/// destructor
virtual ~eoBitOpFactory() {};
//@}
/** Another factory method: creates an object from an std::istream, reading from
it whatever is needed to create the object. Usually, the format for the std::istream will be\\
objectType parameter1 parameter2 ... parametern\\
If there are problems, an std::exception is raised; it should be caught at the
upper level, because it might be something for that level\\
At the same time, it catches std::exceptions thrown at a lower level, which will
indicate that whatever is in the stream is for this method to process
@param _is an stream from where a single line will be read
@throw runtime_std::exception if the object type is not known
*/
virtual eoOp<EOT>* make(std::istream& _is)
/// @name ctors and dtors
//{@
/// constructor
eoBitOpFactory( ) {};
/// destructor
virtual ~eoBitOpFactory() {};
//@}
/** Another factory method: creates an object from an std::istream, reading from
it whatever is needed to create the object. Usually, the format for the std::istream will be\\
objectType parameter1 parameter2 ... parametern\\
If there are problems, an std::exception is raised; it should be caught at the
upper level, because it might be something for that level\\
At the same time, it catches std::exceptions thrown at a lower level, which will
indicate that whatever is in the stream is for this method to process
@param _is an stream from where a single line will be read
@throw runtime_std::exception if the object type is not known
*/
virtual eoOp<EOT>* make(std::istream& _is)
{
eoOp<EOT> * opPtr = NULL;
try {
opPtr = eoFactory<EOT>::make( _is );
} catch ( const std::string& objectTypeStr ) {
if ( objectTypeStr == "eoBinBitFlip" ) {
opPtr = new eoOneBitFlip<EOT>( );
}
// handles old operator names as well as new ones
if ( objectTypeStr == "eoOneBitFlip" ) {
opPtr = new eoOneBitFlip<EOT>( );
}
eoOp<EOT> * opPtr = NULL;
try {
opPtr = eoFactory<EOT>::make( _is );
} catch ( const std::string& objectTypeStr ) {
if ( objectTypeStr == "eoBinBitFlip" ) {
opPtr = new eoOneBitFlip<EOT>( );
}
// handles old operator names as well as new ones
if ( objectTypeStr == "eoOneBitFlip" ) {
opPtr = new eoOneBitFlip<EOT>( );
}
// Standard BitFilp Mutation
if ( objectTypeStr == "eoBinMutation" ) {
float rate;
_is >> rate;
opPtr = new eoBitMutation<EOT>( rate );
}
if ( objectTypeStr == "eoBitMutation" ) {
float rate;
_is >> rate;
opPtr = new eoBitMutation<EOT>( rate );
}
// Standard BitFilp Mutation
if ( objectTypeStr == "eoBinMutation" ) {
float rate;
_is >> rate;
opPtr = new eoBitMutation<EOT>( rate );
}
if ( objectTypeStr == "eoBitMutation" ) {
float rate;
_is >> rate;
opPtr = new eoBitMutation<EOT>( rate );
}
// Bit inversion
if ( objectTypeStr == "eoBinInversion" ) {
opPtr = new eoBitInversion<EOT>( );
}
if ( objectTypeStr == "eoBitInversion" ) {
opPtr = new eoBitInversion<EOT>( );
}
// Bit inversion
if ( objectTypeStr == "eoBinInversion" ) {
opPtr = new eoBitInversion<EOT>( );
}
if ( objectTypeStr == "eoBitInversion" ) {
opPtr = new eoBitInversion<EOT>( );
}
// Next binary value
if ( objectTypeStr == "eoBinNext" ) {
opPtr = new eoBitNext<EOT>( );
}
if ( objectTypeStr == "eoBitNext" ) {
opPtr = new eoBitNext<EOT>( );
}
// Next binary value
if ( objectTypeStr == "eoBinNext" ) {
opPtr = new eoBitNext<EOT>( );
}
if ( objectTypeStr == "eoBitNext" ) {
opPtr = new eoBitNext<EOT>( );
}
// Previous binary value
if ( objectTypeStr == "eoBinPrev" ) {
opPtr = new eoBitPrev<EOT>( );
}
if ( objectTypeStr == "eoBitPrev" ) {
opPtr = new eoBitPrev<EOT>( );
}
// Previous binary value
if ( objectTypeStr == "eoBinPrev" ) {
opPtr = new eoBitPrev<EOT>( );
}
if ( objectTypeStr == "eoBitPrev" ) {
opPtr = new eoBitPrev<EOT>( );
}
// 1 point Xover
if ( objectTypeStr == "eoBinCrossover" ) {
opPtr = new eo1PtBitXover<EOT>( );
}
if ( objectTypeStr == "eo1PtBitXover" ) {
opPtr = new eo1PtBitXover<EOT>( );
}
// 1 point Xover
if ( objectTypeStr == "eoBinCrossover" ) {
opPtr = new eo1PtBitXover<EOT>( );
}
if ( objectTypeStr == "eo1PtBitXover" ) {
opPtr = new eo1PtBitXover<EOT>( );
}
// Npts Xover
if ( objectTypeStr == "eoBinNxOver" ) {
unsigned nPoints;
_is >> nPoints;
opPtr = new eoNPtsBitXover<EOT>( nPoints );
}
if ( objectTypeStr == "eoNPtsBitXover" ) {
unsigned nPoints;
_is >> nPoints;
opPtr = new eoNPtsBitXover<EOT>( nPoints );
}
// Npts Xover
if ( objectTypeStr == "eoBinNxOver" ) {
unsigned nPoints;
_is >> nPoints;
opPtr = new eoNPtsBitXover<EOT>( nPoints );
}
if ( objectTypeStr == "eoNPtsBitXover" ) {
unsigned nPoints;
_is >> nPoints;
opPtr = new eoNPtsBitXover<EOT>( nPoints );
}
// Gene Xover (obsolete)
if ( objectTypeStr == "eoBinGxOver" ) {
unsigned geneSize, nPoints;
_is >> geneSize >> nPoints;
opPtr = new eoBitGxOver<EOT>( geneSize, nPoints );
}
if ( objectTypeStr == "eoBitGxOver" ) {
unsigned geneSize, nPoints;
_is >> geneSize >> nPoints;
opPtr = new eoBitGxOver<EOT>( geneSize, nPoints );
}
// Gene Xover (obsolete)
if ( objectTypeStr == "eoBinGxOver" ) {
unsigned geneSize, nPoints;
_is >> geneSize >> nPoints;
opPtr = new eoBitGxOver<EOT>( geneSize, nPoints );
}
if ( objectTypeStr == "eoBitGxOver" ) {
unsigned geneSize, nPoints;
_is >> geneSize >> nPoints;
opPtr = new eoBitGxOver<EOT>( geneSize, nPoints );
}
// Uniform Xover
if ( objectTypeStr == "eoBinUxOver" ) {
float rate;
_is >> rate;
opPtr = new eoUBitXover<EOT>( rate );
}
if ( objectTypeStr == "eoUBitXover" ) {
float rate;
_is >> rate;
opPtr = new eoUBitXover<EOT>( rate );
}
// Uniform Xover
if ( objectTypeStr == "eoBinUxOver" ) {
float rate;
_is >> rate;
opPtr = new eoUBitXover<EOT>( rate );
}
if ( objectTypeStr == "eoUBitXover" ) {
float rate;
_is >> rate;
opPtr = new eoUBitXover<EOT>( rate );
}
// nothing read!
if ( !opPtr ) { // to be caught by the upper level
throw objectTypeStr;
}
}
return opPtr;
};
// nothing read!
if ( !opPtr ) { // to be caught by the upper level
throw objectTypeStr;
}
}
return opPtr;
};
};
#endif

4
eo/src/ga/eoBoolFlip.h
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// eoBoolFlip.h
// (c) Marc Schoenauer, 2003
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -33,7 +33,7 @@
@ingroup Variators
*/
class eoBoolFlip : public eoMonOp<bool> {
public:
public:
/** simply flips the boolean argument */
bool operator()(bool & _b)
{

56
eo/src/ga/eoPBILAdditive.h
View file

@ -49,8 +49,8 @@ public:
* using the default values is equivalent to using eoPBILOrg
*/
eoPBILAdditive(double _LRBest, unsigned _nbBest = 1,
double _tolerance=0.0,
double _LRWorst = 0.0, unsigned _nbWorst = 0 ) :
double _tolerance=0.0,
double _LRWorst = 0.0, unsigned _nbWorst = 0 ) :
maxBound(1.0-_tolerance), minBound(_tolerance),
LR(0.0), nbBest(_nbBest), nbWorst(_nbWorst)
{
@ -59,18 +59,18 @@ public:
if (_nbBest)
{
lrb = _LRBest/_nbBest;
LR += _LRBest;
lrb = _LRBest/_nbBest;
LR += _LRBest;
}
else
lrb=0.0; // just in case
lrb=0.0; // just in case
if (_nbWorst)
{
lrw = _LRWorst/_nbWorst;
LR += _LRWorst;
lrw = _LRWorst/_nbWorst;
LR += _LRWorst;
}
else
lrw=0.0; // just in case
lrw=0.0; // just in case
}
/** Update the distribution from the current population */
@ -82,29 +82,29 @@ public:
unsigned i, popSize=_pop.size();
std::vector<const EOT*> result;
_pop.sort(result); // is it necessary to sort the whole population?
// but I'm soooooooo lazy !!!
_pop.sort(result); // is it necessary to sort the whole population?
// but I'm soooooooo lazy !!!
for (unsigned g=0; g<distrib.size(); g++)
{
p[g] *= (1-LR); // relaxation
if (nbBest) // update from some of the best
for (i=0; i<nbBest; i++)
{
const EOT & best = (*result[i]);
if ( best[g] ) // if 1, increase proba
p[g] += lrb;
}
if (nbWorst)
for (i=popSize-1; i>=popSize-nbWorst; i--)
{
const EOT & best = (*result[i]);
if ( !best[g] ) // if 0, increase proba
p[g] += lrw;
}
// stay in [0,1] (possibly strictly due to tolerance)
p[g] = std::min(maxBound, p[g]);
p[g] = std::max(minBound, p[g]);
p[g] *= (1-LR); // relaxation
if (nbBest) // update from some of the best
for (i=0; i<nbBest; i++)
{
const EOT & best = (*result[i]);
if ( best[g] ) // if 1, increase proba
p[g] += lrb;
}
if (nbWorst)
for (i=popSize-1; i>=popSize-nbWorst; i--)
{
const EOT & best = (*result[i]);
if ( !best[g] ) // if 0, increase proba
p[g] += lrw;
}
// stay in [0,1] (possibly strictly due to tolerance)
p[g] = std::min(maxBound, p[g]);
p[g] = std::max(minBound, p[g]);
}
}

28
eo/src/ga/eoPBILDistrib.h
View file

@ -28,26 +28,26 @@
#include <eoDistribution.h>
/**
* Distribution Class for PBIL algorithm
* Distribution Class for PBIL algorithm
* (Population-Based Incremental Learning, Baluja and Caruana 96)
*
* It encodes a univariate distribution on the space of bitstrings,
* i.e. one probability for each bit to be one
*
* It is an eoValueParam<std::vector<double> > :
* It is an eoValueParam<std::vector<double> > :
* the std::vector<double> stores the probabilities that each bit is 1
*
* It is still pure virtual, as the update method needs to be specified
*/
template <class EOT>
class eoPBILDistrib : public eoDistribution<EOT>,
public eoValueParam<std::vector<double> >
class eoPBILDistrib : public eoDistribution<EOT>,
public eoValueParam<std::vector<double> >
{
public:
/** Ctor with size of genomes, and update parameters */
eoPBILDistrib(unsigned _genomeSize) :
eoDistribution<EOT>(),
eoDistribution<EOT>(),
eoValueParam<std::vector<double> >(std::vector<double>(_genomeSize, 0.5), "Distribution"),
genomeSize(_genomeSize)
{}
@ -55,10 +55,10 @@ public:
/** the randomizer of indis */
virtual void operator()(EOT & _eo)
{
_eo.resize(genomeSize); // just in case
_eo.resize(genomeSize); // just in case
for (unsigned i=0; i<genomeSize; i++)
_eo[i] = eo::rng.flip(value()[i]);
_eo.invalidate(); // DO NOT FORGET!!!
_eo.invalidate(); // DO NOT FORGET!!!
}
/** Accessor to the genome size */
@ -70,22 +70,22 @@ public:
os << value().size() << ' ';
for (unsigned i=0; i<value().size(); i++)
os << value()[i] << ' ';
}
}
/** reading...*/
virtual void readFrom(std::istream& is)
{
unsigned sz;
is >> sz;
value().resize(sz);
unsigned i;
for (i = 0; i < sz; ++i)
{
double atom;
is >> atom;
value()[i] = atom;
double atom;
is >> atom;
value()[i] = atom;
}
}

16
eo/src/ga/eoPBILOrg.h
View file

@ -58,15 +58,15 @@ public:
for (unsigned g=0; g<distrib.size(); g++)
{
// double & r = value()[g];
p[g] *= (1-LR);
if ( best[g] )
p[g] += LR;
// else nothing
// double & r = value()[g];
p[g] *= (1-LR);
if ( best[g] )
p[g] += LR;
// else nothing
// stay away from 0 and 1
p[g] = std::min(maxBound, p[g]);
p[g] = std::max(minBound, p[g]);
// stay away from 0 and 1
p[g] = std::min(maxBound, p[g]);
p[g] = std::max(minBound, p[g]);
}
}

14
eo/src/ga/make_PBILdistrib.h
View file

@ -26,7 +26,7 @@
#ifndef _make_PBILdistrib_h
#define _make_PBILdistrib_h
#include <ctime> // for time(0) for random seeding
#include <ctime> // for time(0) for random seeding
#include <ga/eoPBILOrg.h>
#include <utils/eoRNG.h>
#include <utils/eoParser.h>
@ -51,21 +51,21 @@ eoPBILDistrib<EOT> & do_make_PBILdistrib(eoParser & _parser, eoState& _state, E
// First the random seed
eoValueParam<uint32_t>& seedParam = _parser.createParam(uint32_t(0), "seed", "Random number seed", 'S');
if (seedParam.value() == 0)
seedParam.value() = time(0);
seedParam.value() = time(0);
// chromosome size:
unsigned theSize;
// but it might have been already read in the definition fo the performance
eoParam* ptParam = _parser.getParamWithLongName(std::string("chromSize"));
if (!ptParam) // not already defined: read it here
if (!ptParam) // not already defined: read it here
{
theSize = _parser.createParam(unsigned(10), "chromSize", "The length of the bitstrings", 'n',"Problem").value();
theSize = _parser.createParam(unsigned(10), "chromSize", "The length of the bitstrings", 'n',"Problem").value();
}
else // it was read before, get its value
else // it was read before, get its value
{
eoValueParam<unsigned>* ptChromSize = dynamic_cast<eoValueParam<unsigned>*>(ptParam);
theSize = ptChromSize->value();
eoValueParam<unsigned>* ptChromSize = dynamic_cast<eoValueParam<unsigned>*>(ptParam);
theSize = ptChromSize->value();
}
eoPBILDistrib<EOT> * ptDistrib = new eoPBILDistrib<EOT>(theSize);

8
eo/src/ga/make_PBILupdate.h
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_PBILupdate.h
// (c) Marc Schoenauer, Maarten Keijzer, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -47,7 +47,7 @@
template <class EOT>
eoDistribUpdater<EOT> & do_make_PBILupdate(eoParser & _parser, eoState& _state, EOT)
{
// ast the moment, a single update rule is available
// ast the moment, a single update rule is available
// but at some point we'll have to choose among different rules
std::string UType = _parser.createParam(std::string("PBIL"), "updateRule", "Type of update rule (only PBIL additive at the moment)", 'U', "Algorithm").value();
@ -59,7 +59,7 @@ eoDistribUpdater<EOT> & do_make_PBILupdate(eoParser & _parser, eoState& _state,
double tolerance = _parser.createParam(0.0, "tolerance", "Keeping away from 0 and 1", 't', "Algorithm").value();
// a pointer to choose among several possible types
eoDistribUpdater<EOT> * ptUpdate;
eoDistribUpdater<EOT> * ptUpdate;
if (UType == std::string("PBIL"))
{
@ -72,7 +72,7 @@ eoDistribUpdater<EOT> & do_make_PBILupdate(eoParser & _parser, eoState& _state,
throw std::runtime_error("Only PBIL additive update rule available at the moment");
// done: don't forget to store the allocated pointers
_state.storeFunctor(ptUpdate);
_state.storeFunctor(ptUpdate);
return *ptUpdate;
}

9
eo/src/ga/make_algo_scalar_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_algo_scalar_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of pop. init.
* of the library for ***BISTRING*** evolution inside EO.
@ -35,11 +35,11 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in src/ga/ga.h
* while the TEMPLATIZED code is define in make_algo_scalar.h in the src/do dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations
*/
@ -61,4 +61,3 @@ eoAlgo<eoBit<eoMinimizingFitness> >& make_algo_scalar(eoParser& _parser, eoStat
{
return do_make_algo_scalar(_parser, _state, _eval, _continue, _op, _dist);
}

14
eo/src/ga/make_checkpoint_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_checkpoint_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of operators
* of the library for ***BISTRING*** evolution inside EO.
@ -35,11 +35,11 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in make_checkpoint_ga.h
* while the TEMPLATIZED code is define in make_checkpoint.h in the do dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations
*/
@ -48,7 +48,7 @@
// the instanciating EOType
#include <ga/eoBit.h>
/// The following function merely call the templatized do_* functions
/// The following function merely call the templatized do_* functions
// checkpoint
/////////////
@ -56,9 +56,7 @@ eoCheckPoint<eoBit<double> >& make_checkpoint(eoParser& _parser, eoState& _state
{
return do_make_checkpoint(_parser, _state, _eval, _continue);
}
eoCheckPoint<eoBit<eoMinimizingFitness> >& make_checkpoint(eoParser& _parser, eoState& _state, eoEvalFuncCounter<eoBit<eoMinimizingFitness> >& _eval, eoContinue<eoBit<eoMinimizingFitness> >& _continue)
eoCheckPoint<eoBit<eoMinimizingFitness> >& make_checkpoint(eoParser& _parser, eoState& _state, eoEvalFuncCounter<eoBit<eoMinimizingFitness> >& _eval, eoContinue<eoBit<eoMinimizingFitness> >& _continue)
{
return do_make_checkpoint(_parser, _state, _eval, _continue);
}

10
eo/src/ga/make_continue_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_continue_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of operators
* of the library for ***BISTRING*** evolution inside EO.
@ -35,11 +35,11 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga.h
* while the TEMPLATIZED code is define in make_contninue.h in the src/do dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations
*/
@ -60,5 +60,3 @@ eoContinue<eoBit<eoMinimizingFitness> >& make_continue(eoParser& _parser, eoStat
{
return do_make_continue(_parser, _state, _eval);
}

8
eo/src/ga/make_ga.h
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// ga.h
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -24,14 +24,14 @@
*/
//-----------------------------------------------------------------------------
/** This file contains all ***INSTANCIATED*** declarations of all components
/** This file contains all ***INSTANCIATED*** declarations of all components
* of the library for ***BISTRING*** evolution inside EO.
* It should be included in the file that calls any of the corresponding fns
*
* The corresponding ***INSTANCIATED*** definitions are contained in ga.cpp
* while the TEMPLATIZED code is define in the different makeXXX.h files
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations
*/
@ -56,7 +56,7 @@
* @{
*/
// the genotypes
// the genotypes
eoInit<eoBit<double> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<double> _eo);
eoInit<eoBit<eoMinimizingFitness> > & make_genotype(eoParser& _parser, eoState& _state, eoBit<eoMinimizingFitness> _eo);

8
eo/src/ga/make_genotype_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_genotype_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of operators
* of the library for ***BISTRING*** evolution inside EO.
@ -35,8 +35,8 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga.h in src/ga dir
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga.h in src/ga dir
* while the TEMPLATIZED code is define in make_genotype_ga.h
*/

16
eo/src/ga/make_genotype_ga.h
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_genotype.h
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -36,24 +36,24 @@
/////////////////// the bitstring ////////////////
/*
* This fuction does the initialization of what's needed for a particular
* This fuction does the initialization of what's needed for a particular
* genotype (here, bitstrings).
* It could be here tempatied only on the fitness, as it can be used to evolve
* It could be here tempatied only on the fitness, as it can be used to evolve
* bitstrings with any fitness.
* However, for consistency reasons, it was finally chosen, as in
* the rest of EO, to templatize by the full EOT, as this eventually
* However, for consistency reasons, it was finally chosen, as in
* the rest of EO, to templatize by the full EOT, as this eventually
* allows to choose the type of genotype at run time (see in es dir)
*
* It is instanciated in ga/ga.cpp - and incorporated in the ga/libga.a
*
* It returns an eoInit<eoBit<FitT> > tha can later be used to initialize
* It returns an eoInit<eoBit<FitT> > tha can later be used to initialize
* the population (see make_pop.h).
*
* It uses a parser (to get user parameters) and a state (to store the memory)
* the last argument is to disambiguate the call upon different instanciations.
*
* WARNING: that last argument will generally be the result of calling
* the default ctor of EOT, resulting in most cases in an EOT
* WARNING: that last argument will generally be the result of calling
* the default ctor of EOT, resulting in most cases in an EOT
* that is ***not properly initialized***
*
* @ingroup bitstring

36
eo/src/ga/make_op.h
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_op.h
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -57,9 +57,9 @@
* This is why the template is the complete EOT even though only the fitness
* is actually templatized here: the following only applies to bitstrings
*
* Note : the last parameter is an eoInit: if some operator needs some info
* Note : the last parameter is an eoInit: if some operator needs some info
* about the gneotypes, the init has it all (e.g. bounds, ...)
* Simply do
* Simply do
* EOT myEO;
* _init(myEO);
* and myEO is then an ACTUAL object
@ -78,12 +78,12 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
eoValueParam<std::string>& operatorParam = _parser.createParam(std::string("SGA"), "operator", "Description of the operator (SGA only now)", 'o', "Variation Operators");
if (operatorParam.value() != std::string("SGA"))
throw std::runtime_error("Only SGA-like operator available right now\n");
throw std::runtime_error("Only SGA-like operator available right now\n");
// now we read Pcross and Pmut,
// now we read Pcross and Pmut,
// the relative weights for all crossovers -> proportional choice
// the relative weights for all mutations -> proportional choice
// and create the eoGenOp that is exactly
// and create the eoGenOp that is exactly
// crossover with pcross + mutation with pmut
eoValueParam<double>& pCrossParam = _parser.createParam(0.6, "pCross", "Probability of Crossover", 'C', "Variation Operators" );
@ -118,10 +118,10 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
bool bCross = true;
if (onePointRateParam.value()+twoPointsRateParam.value()+uRateParam.value()==0)
{
std::cerr << "Warning: no crossover" << std::endl;
bCross = false;
std::cerr << "Warning: no crossover" << std::endl;
bCross = false;
}
// Create the CombinedQuadOp
eoPropCombinedQuadOp<EOT> *ptCombinedQuadOp = NULL;
eoQuadOp<EOT> *ptQuad = NULL;
@ -129,12 +129,12 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
ptQuad = new eo1PtBitXover<EOT>;
_state.storeFunctor(ptQuad);
ptCombinedQuadOp = new eoPropCombinedQuadOp<EOT>(*ptQuad, onePointRateParam.value());
// uniform crossover for bitstring
ptQuad = new eoUBitXover<EOT>;
_state.storeFunctor(ptQuad);
ptCombinedQuadOp->add(*ptQuad, uRateParam.value());
// 2-points xover
ptQuad = new eoNPtsBitXover<EOT>;
_state.storeFunctor(ptQuad);
@ -155,7 +155,7 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
// minimum check
if ( (bitFlipRateParam.value() < 0) )
throw std::runtime_error("Invalid bitFlipRate");
eoValueParam<double> & oneBitRateParam = _parser.createParam(0.01, "oneBitRate", "Relative rate for deterministic bit-flip mutation", 'd', "Variation Operators" );
// minimum check
if ( (oneBitRateParam.value() < 0) )
@ -165,10 +165,10 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
bool bMut = true;
if (bitFlipRateParam.value()+oneBitRateParam.value()==0)
{
std::cerr << "Warning: no mutation" << std::endl;
bMut = false;
std::cerr << "Warning: no mutation" << std::endl;
bMut = false;
}
// Create the CombinedMonOp
eoPropCombinedMonOp<EOT> *ptCombinedMonOp = NULL;
eoMonOp<EOT> *ptMon = NULL;
@ -180,7 +180,7 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
ptCombinedMonOp = new eoPropCombinedMonOp<EOT>(*ptMon, bitFlipRateParam.value());
// mutate exactly 1 bit per individual
ptMon = new eoDetBitFlip<EOT>;
ptMon = new eoDetBitFlip<EOT>;
_state.storeFunctor(ptMon);
ptCombinedMonOp->add(*ptMon, oneBitRateParam.value());
@ -190,7 +190,7 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
// to simulate SGA (crossover with proba pCross + mutation with proba pMut
// we must construct
// a sequential combination of
// with proba 1, a proportional combination of
// with proba 1, a proportional combination of
// a QuadCopy and our crossover
// with proba pMut, our mutation
@ -205,7 +205,7 @@ eoGenOp<EOT> & do_make_op(eoParser& _parser, eoState& _state, eoInit<EOT>& _init
// now the sequential
eoSequentialOp<EOT> *op = new eoSequentialOp<EOT>;
_state.storeFunctor(op);
op->add(*cross, 1.0); // always crossover (but clone with prob 1-pCross
op->add(*cross, 1.0); // always crossover (but clone with prob 1-pCross
op->add(*ptCombinedMonOp, pMutParam.value());
// that's it!

9
eo/src/ga/make_op_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_op_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of operators
* of the library for ***BISTRING*** evolution inside EO.
@ -35,11 +35,11 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in make_op_ga.h
* while the TEMPLATIZED code is define in make_op.h in the ga dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations
*/
@ -59,4 +59,3 @@ eoGenOp<eoBit<eoMinimizingFitness> >& make_op(eoParser& _parser, eoState& _stat
{
return do_make_op(_parser, _state, _init);
}

8
eo/src/ga/make_pop_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_pop_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of population init
* of the library for ***BISTRING*** evolution inside EO.
@ -35,7 +35,7 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in ga/make_ga.h
* while the TEMPLATIZED code is define in make_pop.h in the src/do dir
*
@ -59,5 +59,3 @@ eoPop<eoBit<eoMinimizingFitness> >& make_pop(eoParser& _parser, eoState& _state
{
return do_make_pop(_parser, _state, _init);
}

9
eo/src/ga/make_run_ga.cpp
View file

@ -3,7 +3,7 @@
//-----------------------------------------------------------------------------
// make_run_ga.cpp
// (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2001
/*
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
@ -27,7 +27,7 @@
#ifdef _MSC_VER
// to avoid long name warnings
#pragma warning(disable:4786)
#endif
#endif
/** This file contains all ***INSTANCIATED DEFINITIONS*** of operators
* of the library for ***BISTRING*** evolution inside EO.
@ -35,11 +35,11 @@
* Compiling this file allows one to generate part of the library (i.e. object
* files that you just need to link with your own main and fitness code).
*
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* The corresponding ***INSTANCIATED DECLARATIONS*** are contained
* in make_run_ga.h
* while the TEMPLATIZED code is define in make_run.h in the do dir
*
* Unlike most EO .h files, it does not (and should not) contain any code,
* Unlike most EO .h files, it does not (and should not) contain any code,
* just declarations
*/
@ -63,4 +63,3 @@ void run_ea(eoAlgo<eoBit<eoMinimizingFitness> >& _ga, eoPop<eoBit<eoMinimizingFi
{
do_run(_ga, _pop);
}