html/_alg_clonalg_8h_source.html

#ifndef Clonalg_h

#define Clonalg_h


#include "Algorithm.h"

#include "floatingpoint/FloatingPoint.h"


class Clonalg : public Algorithm

{

protected:


    double ubound;

    double lbound;

    uint dimension;

    bool areGenotypesAdded_;


    uint n;

    double beta;

    double c;

    double d;

    std::string cloningVersion;

    std::string selectionScheme;


    static bool sortPopulationByFitness (IndividualP ab1,IndividualP ab2) { return ( ab1->fitness->isBetterThan(ab2->fitness)); }


    static bool sortPopulationByParentAndFitness (IndividualP ab1,IndividualP ab2)

    {

        FloatingPointP flp = boost::dynamic_pointer_cast<FloatingPoint::FloatingPoint> (ab1->getGenotype(1));

        double &parentAb1 = flp->realValue[0];

        flp = boost::dynamic_pointer_cast<FloatingPoint::FloatingPoint> (ab2->getGenotype(1));

        double &parentAb2 = flp->realValue[0];


        if (parentAb1 <parentAb2) return true;

        if (parentAb1 == parentAb2) return (ab1->fitness->isBetterThan(ab2->fitness));


        return false;

    }


public:


    Clonalg();

    void registerParameters(StateP state);

    bool initialize(StateP state);

    bool advanceGeneration(StateP state, DemeP deme);


    bool markAntibodies(DemeP deme);

    bool cloningPhase(StateP state, DemeP deme, std::vector<IndividualP> &clones);

    bool hypermutationPhase(StateP state, DemeP deme, std::vector<IndividualP> &clones);

    bool selectionPhase(StateP state, DemeP deme, std::vector<IndividualP> &clones);

    bool birthPhase(StateP state, DemeP deme, std::vector<IndividualP> &clones);

    bool replacePopulation(StateP state, DemeP deme, std::vector<IndividualP> &clones);


};

typedef boost::shared_ptr<Clonalg> ClonalgP;


#endif // Clonalg_h


Algorithm
Algorithm base class.
Definition: Algorithm.h:20

Clonalg
Clonal Selection Algorithm (see e.g. http://en.wikipedia.org/wiki/Clonal_Selection_Algorithm).
Definition: AlgClonalg.h:25

Clonalg::d
double d
fraction of population regenerated every generation
Definition: AlgClonalg.h:36

Clonalg::sortPopulationByFitness
static bool sortPopulationByFitness(IndividualP ab1, IndividualP ab2)
sort vector of antibodies in regards to their fitness
Definition: AlgClonalg.h:41

Clonalg::sortPopulationByParentAndFitness
static bool sortPopulationByParentAndFitness(IndividualP ab1, IndividualP ab2)
sort vector of antibodies first by their antibody parents and then by their fitness
Definition: AlgClonalg.h:44

Clonalg::cloningVersion
std::string cloningVersion
specifies whether to use static or proportional cloning
Definition: AlgClonalg.h:37

Clonalg::initialize
bool initialize(StateP state)
Initialize the algorithm, read parameters from the system, do a sanity check.
Definition: AlgClonalg.cpp:33

Clonalg::markAntibodies
bool markAntibodies(DemeP deme)
mark antibodies so the alg can know which clone belongs to which parent Antibody
Definition: AlgClonalg.cpp:141

Clonalg::n
uint n
number of antibodies cloned every generation
Definition: AlgClonalg.h:33

Clonalg::beta
double beta
parameter which determines the number of clones for every antibody
Definition: AlgClonalg.h:34

Clonalg::advanceGeneration
bool advanceGeneration(StateP state, DemeP deme)
Perform a single generation on a single deme.
Definition: AlgClonalg.cpp:125

Clonalg::replacePopulation
bool replacePopulation(StateP state, DemeP deme, std::vector< IndividualP > &clones)
replace population with the contents of clones vector
Definition: AlgClonalg.cpp:296

Clonalg::c
double c
mutation parameter
Definition: AlgClonalg.h:35

Clonalg::selectionScheme
std::string selectionScheme
specifies which selection scheme to use CLONALG1 or CLONALG2
Definition: AlgClonalg.h:38

Clonalg::registerParameters
void registerParameters(StateP state)
Register algorithm's parameters (if any).
Definition: AlgClonalg.cpp:16