GEPChromosome.h

#ifndef GEPCHROMOSOME_H
#define GEPCHROMOSOME_H
 
#include "../ECF.h"
#include "../Tree/Tree.h"
#include "GEPChromosomeCrsOnePoint.h"
#include "GEPChromosomeCrsTwoPoint.h"
#include "GEPChromosomeCrsGene.h"
#include "GEPChromosomeMutOp.h"
#include "GEPChromosomeMutGauss.h"
#include <vector>
#define GEP_GENE_PREFIX "GENE_"
namespace GEPChromosome{
 
    class GEPChromosome : public std::vector<Tree::NodeP>, public Genotype
    {
    protected:
        StateP state_;
        std::vector<Tree::PrimitiveP> userFunctions_;   // programatically added functions
        std::vector<Tree::PrimitiveP> userTerminals_;   // programatically added terminals
    public:
        uint headLength; 
        uint tailLength; 
        uint dcLength;  
        uint geneLength; 
        uint linkHeadLength; 
        uint linkTailLength; 
        uint genes; 
        Tree::PrimitiveSetP primitiveSet_; // contains all functions, terminals and the ERC placeholder (if needed)
        Tree::PrimitiveSetP linkFunctionSet_; // contains all linking functions and genic terminals (integers)
        Tree::PrimitiveSetP ercSet_; // contains only the ERC ranges
        bool usesERC; 
        bool staticLink; 
        Tree::Tree *cellTree;
        std::vector<Tree::Tree*> subtrees;
 
        GEPChromosome();
        GEPChromosome* copy();
        std::vector<CrossoverOpP> getCrossoverOp();
        std::vector<MutationOpP> getMutationOp();
        void registerParameters(StateP state);
        bool initialize(StateP state);
        void initializeFirst(GEPChromosome* home);
        void write(XMLNode &xGEPChromosome);
        void read(XMLNode& xGEPChromosomeInd);
        void execute(void*);
        Tree::Tree* toTree(uint gene); 
        Tree::Tree* makeCellTree();
        void assemble();
        void generateChromosome();
        void setTerminalValue(std::string name, void* value);
    };
}
typedef boost::shared_ptr<GEPChromosome::GEPChromosome> GEPChromosomeP;
#endif // GEPChromosome_h