Init version
This commit is contained in:
189
DEC_GUI/DEC-0.0/population/BisexualPopulation.cpp
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189
DEC_GUI/DEC-0.0/population/BisexualPopulation.cpp
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#include "Population.h"
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#include <algorithm>
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#include <iostream>
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#include <sstream>
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#include <cstdlib>
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#include <ctime>
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BisexualPopulation::~BisexualPopulation(){
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// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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}
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void BisexualPopulation::calculateFitnessAll(){
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// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD>
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}
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void BisexualPopulation::breedAll(){
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this->breedingStrategy->breed(this);
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}
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void BisexualPopulation::selectionAll(){
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}
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void BisexualPopulation::mutationAll(){
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// !!! <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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srand((unsigned int)time(NULL));
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float mutProb = 1 / 1e+6f; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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std::list<Individual*>::iterator it;
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for(it = this->females.begin(); it != this->females.end(); it++){
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// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2014
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Chromosome chrom = (*it)->genotype->getMotherGenome().getChromosome(0);
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std::vector<Gene> genes = chrom.getGenesAsVector();
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int wholeSeqLength = 0;
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for(unsigned int i = 0; i < genes.size(); i++){
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wholeSeqLength += genes.at(i).getSequence().size();
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}
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//std::string seq = (*it)->genotype->getRawGene(0,0,0); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2013
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int positionToMutate = rand() % (int)(1/mutProb);
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if(positionToMutate < wholeSeqLength){
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std::string seq = genes.at(0).getSequence();
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int geneNum = positionToMutate / seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2014
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positionToMutate = positionToMutate % seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2014
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//Gene geneToMutate = genes.at(geneNum);
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int nucl = rand() % 3;
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switch(seq.c_str()[positionToMutate]){
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case 'A':
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if(nucl == 0) seq.replace(positionToMutate,1,"C");
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if(nucl == 1) seq.replace(positionToMutate,1,"G");
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if(nucl == 2) seq.replace(positionToMutate,1,"T");
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break;
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case 'C':
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if(nucl == 0) seq.replace(positionToMutate,1,"A");
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if(nucl == 1) seq.replace(positionToMutate,1,"G");
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if(nucl == 2) seq.replace(positionToMutate,1,"T");
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break;
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case 'G':
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if(nucl == 0) seq.replace(positionToMutate,1,"C");
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if(nucl == 1) seq.replace(positionToMutate,1,"A");
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if(nucl == 2) seq.replace(positionToMutate,1,"T");
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break;
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case 'T':
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if(nucl == 0) seq.replace(positionToMutate,1,"C");
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if(nucl == 1) seq.replace(positionToMutate,1,"G");
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if(nucl == 2) seq.replace(positionToMutate,1,"A");
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break;
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} // (END) switch(...)
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(*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
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} // (END) if (mutate)
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} // (END) for
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// !!! --------------------------------
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}
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std::string BisexualPopulation::getSatistics(){
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std::string ans;
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return ans;
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}
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void BisexualPopulation::putGeneticStatisticsToStream(std::ostream& out){
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out<<"Females\n=======\n";
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int i = 1;
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for(std::list<Individual*>::iterator it = females.begin(); it != females.end(); it++){
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//out<<"> Female seq mitochondrial"<<(i++)<<"\n";
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out<<(*it)->getGenotype().toSimpleFasta()<<std::endl;
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out<<std::endl;
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}
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out<<"\nMales\n=======\n";
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i = 1;
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for(std::list<Individual*>::iterator it = males.begin(); it != males.end(); it++){
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out<<"> Male seq "<<(i++)<<"\n";
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out<<(*it)->getGenotype().toSimpleFasta()<<std::endl;
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out<<std::endl;
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}
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}
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void BisexualPopulation::putGeneticSimpleStatisticsToStream(std::ostream& out){
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out<<"Population statistics:\tMales =\t"<<males.size();
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out<<"\tFemales =\t"<<females.size()<<std::endl;
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//out<<"Genome statistics (mitochondrial DNA sequence):\n\n";
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}
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void BisexualPopulation::putGeneticMaxModuleStatisticsToStream(std::ostream& out){
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}
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std::string BisexualPopulation::mutualMigration(BisexualPopulation* p1, BisexualPopulation* p2, float frac1, float frac2){
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std::stringstream ss;
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int sizeP1 = p1->males.size() + p1->females.size();
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int sizeP2 = p2->males.size() + p2->females.size();
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int indsP1toP2 = (int) (frac1*sizeP1)/2;
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int indsP2toP1 = (int) (frac2*sizeP2)/2;
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD>
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std::list<Individual*> malesTemp;
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std::list<Individual*> femalesTemp;
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// P1 -> temp
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// males
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std::list<Individual*>::iterator it1 = p1->males.begin();
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std::list<Individual*>::iterator it2 = it1;
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std::advance(it2, indsP1toP2);
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malesTemp.splice(malesTemp.begin(), p1->males, it1, it2);
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// females
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it1 = p1->females.begin();
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it2 = it1;
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std::advance(it2, indsP1toP2);
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femalesTemp.splice(femalesTemp.begin(), p1->females, it1, it2);
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/////////////////////////////////////////////////////////////
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// P2 -> P1
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// males
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it1 = p2->males.begin();
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it2 = it1;
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std::advance(it2, indsP2toP1);
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p1->males.splice(p1->males.end(), p2->males, it1, it2);
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// females
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it1 = p2->females.begin();
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it2 = it1;
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std::advance(it2, indsP2toP1);
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p1->females.splice(p1->females.end(), p2->females, it1, it2);
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/////////////////////////////////////////////////////////////
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// temp -> P2
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// males
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p2->males.splice(p2->males.end(), malesTemp);
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// females
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p2->females.splice(p2->females.end(), femalesTemp);
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ss<<"Migration:\tP1->P2\t"<<indsP1toP2*2<<"\t\tP2->P1\t"<<indsP2toP1*2<<std::endl;
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return ss.str();
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}
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BisexualPopulation* BisexualPopulation::createSubpopulation(float frac){
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// <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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int malesFounders = (int) (frac*this->males.size());
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int femalesFounders = (int) (frac*this->females.size());
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD>
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std::list<Individual*> malesTemp;
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std::list<Individual*> femalesTemp;
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// P1 -> temp
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// males
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std::list<Individual*>::iterator it1 = this->males.begin();
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std::list<Individual*>::iterator it2 = it1;
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std::advance(it2, malesFounders);
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malesTemp.splice(malesTemp.begin(), this->males, it1, it2);
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// females
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it1 = this->females.begin();
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it2 = it1;
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std::advance(it2, femalesFounders);
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femalesTemp.splice(femalesTemp.begin(), this->females, it1, it2);
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/////////////////////////////////////////////////////////////
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return new BisexualPopulation(malesTemp,femalesTemp, this->breedingStrategy);
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}
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@@ -0,0 +1,99 @@
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#include "NeutralEvolutionBreedStrat.h"
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#include "../../individual/Phenotype.h"
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#include "../../processor/Settings.h"
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#include <algorithm>
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#include <iostream>
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#include <cstdlib>
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#include <ctime>
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void NeutralEvolutionBreedingStrategy::breed(Population* _pop){
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BisexualPopulation* pop = dynamic_cast<BisexualPopulation*>(_pop);
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if(pop == NULL){
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std::cerr<<"Wrong dynamic cast to BisexualPopulation\n";
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return;
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}
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int numMales = pop->males.size();
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int numFemales = pop->females.size();
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int inds = numMales + numFemales;
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srand((unsigned int)time(NULL));
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//srand(0);
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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int toDie = int (inds * deathRate);
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for(int i = 0; i < toDie; i++){
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int indToDie = rand() % (inds-i);
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if(indToDie < numMales){
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std::list<Individual*>::iterator it = pop->males.begin();
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std::advance(it,indToDie); // it += indToDie;
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delete *it;
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pop->males.erase(it);
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numMales--;
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}
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else{
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std::list<Individual*>::iterator it = pop->females.begin();
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std::advance(it,indToDie-numMales); // it += indToDie;
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delete *it;
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pop->females.erase(it);
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numFemales--;
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}
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}
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//std::cout<<"PopulationBreedingStrategy::breed: "<<toDie<<" individs have died\n";
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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int toBorn = int (inds * birthRate);
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numMales = pop->males.size();
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numFemales = pop->females.size();
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inds = numMales + numFemales;
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for(int i = 0; i < toBorn; i++) {
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int fatherNum = rand() % numMales;
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int motherNum = rand() % numFemales;
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int gender = rand() % 2;
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std::list<Individual*>::iterator itFather = pop->males.begin();
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std::advance(itFather, fatherNum);
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std::list<Individual*>::iterator itMother = pop->females.begin();
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std::advance(itMother, motherNum);
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Genotype* genotype;
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double prob = Settings::ProbMtDNARecomb;
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if(prob > 0.0){
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int invProb = (int)(1/prob);
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int recombine = rand() % invProb;
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if(recombine == 0){
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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//std::cerr<<"Recomb\n";
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ChromosomeRearrangementStrategy* recombinator = RecombinationStrategies::getInstance("dummy");
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HaploidGenotype recombGenotype = recombinator->buildRecombinantGenotype(
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(*itFather)->getGenotype().getMotherGenome(), (*itMother)->getGenotype().getMotherGenome());
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genotype = new Genotype(recombGenotype, recombGenotype);
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}
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else{
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genotype = new Genotype(
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(*itMother)->getGenotype().getMotherGenome(), (*itMother)->getGenotype().getMotherGenome());
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}
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}
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else{
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genotype = new Genotype(
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(*itMother)->getGenotype().getMotherGenome(), (*itMother)->getGenotype().getMotherGenome());
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// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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}
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Phenotype* phenotype= new Phenotype((*itFather)->getPhenotype());
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Individual* ind = new Individual(genotype, phenotype, 0, Individual::Gender(gender));
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// <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
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if(gender == 0){
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pop->males.push_back(ind);
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}
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else{
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pop->females.push_back(ind);
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}
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}
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}
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@@ -0,0 +1,12 @@
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#pragma once
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#include "PopulationBreedingStrategy.h"
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class NeutralEvolutionBreedingStrategy : public PopulationBreedingStrategy {
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float birthRate;
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float deathRate;
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public:
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void setBirthRate(float b) {birthRate = b;}
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void setDeathRate(float d) {deathRate = d;}
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virtual void breed(Population* pop);
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};
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@@ -0,0 +1,71 @@
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#include "PopulationBreedingStrategy.h"
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#include "VerhulstBreedingStrategy.h"
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#include "NeutralEvolutionBreedStrat.h"
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#include "../../individual/genome/strategies/InOutBreeding/InOutBreedingPopulationBreedingStrategy.h"
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#include "../../individual/genome/strategies/KolchShindyal/KolchShindyalBreedingStrategy.h"
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#include "../../processor/Settings.h"
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//#include <vector>
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#include <algorithm>
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#include <iostream>
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#include <cstdlib>
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#include <ctime>
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void PopulationBreedingStrategy::breed(Population* _pop){
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float deathRate = Settings::NaturalDeathRate;//0.01f; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
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// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>
|
||||
AsexualPopulation* pop = dynamic_cast<AsexualPopulation*>(_pop);
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if(pop == NULL){
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std::cerr<<"Wrong dynamic cast to AsexualPopulation\n";
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return;
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}
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std::sort(pop->individs.begin(), pop->individs.end(), compareOnFitness);
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int inds = pop->individs.size();
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// <20><> <20><><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> SelectionAll
|
||||
// <20> <20><><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>-<2D><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
int toDie = int (inds * deathRate);
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||||
std::vector<Individual*>::iterator start = pop->individs.begin();
|
||||
std::vector<Individual*>::iterator end = pop->individs.begin()+toDie;
|
||||
//advance(end,toDie);
|
||||
for(std::vector<Individual*>::iterator it = start; it != end; it++){
|
||||
delete *it;
|
||||
}
|
||||
pop->individs.erase(start, end);
|
||||
|
||||
std::cout<<"PopulationBreedingStrategy::breed: "<<toDie<<" individs have died\n";
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
float birthRate = Settings::BirthRate;//0.02f;
|
||||
int toBorn = int (inds * birthRate);
|
||||
inds = pop->individs.size();
|
||||
srand((unsigned int)time(NULL));
|
||||
for(int i = 0; i < toBorn; i++) {
|
||||
int male = rand() % inds;
|
||||
int female = rand() % inds;
|
||||
female = (female != male ? female : (female + 1) % inds);
|
||||
|
||||
Individual* ind = new Individual(*(pop->individs.at(male)), *(pop->individs.at(female)));
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
|
||||
pop->individs.push_back(ind);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
PopulationBreedingStrategy* PopulationBreedingStrategy::getInstance(std::string name){
|
||||
if(name.compare("Verhulst") == 0){
|
||||
return new VerhulstBreedingStrategy();
|
||||
}
|
||||
if(name.compare("inoutbreeding") == 0){
|
||||
return new InOutBreedingPopulationBreedingStrategy();
|
||||
}
|
||||
if(name.compare("kolchan_shindyal_breeding") == 0){
|
||||
return new KolchShindyalBreedingStrategy();
|
||||
}
|
||||
if(name.compare("neutral") == 0){
|
||||
return new NeutralEvolutionBreedingStrategy();
|
||||
}
|
||||
return new PopulationBreedingStrategy();
|
||||
}
|
||||
@@ -0,0 +1,10 @@
|
||||
#pragma once
|
||||
#include "../Population.h"
|
||||
|
||||
class Population;
|
||||
|
||||
class PopulationBreedingStrategy {
|
||||
public:
|
||||
virtual void breed(Population* pop);
|
||||
static PopulationBreedingStrategy* getInstance(std::string name);
|
||||
};
|
||||
@@ -0,0 +1,52 @@
|
||||
#include "VerhulstBreedingStrategy.h"
|
||||
#include "../../processor/Settings.h"
|
||||
#include <algorithm>
|
||||
#include <iostream>
|
||||
#include <cstdlib>
|
||||
#include <ctime>
|
||||
|
||||
void VerhulstBreedingStrategy::breed(Population *_pop) {
|
||||
// <09><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
// rX * (1 - X/K) = rX - (r/K)X^2
|
||||
|
||||
double birthRate = Settings::BirthRate;// 0.03;
|
||||
double r = 1 + birthRate;
|
||||
double K = _pop->region->getCapacity();
|
||||
|
||||
AsexualPopulation* pop = dynamic_cast<AsexualPopulation*>(_pop);
|
||||
if(pop == NULL){
|
||||
std::cerr<<"Wrong dynamic cast to AsexualPopulation\n";
|
||||
return;
|
||||
}
|
||||
|
||||
long int inds = pop->individs.size();
|
||||
long int toDie = (long int) inds*inds * r/K + 0.5; // 0.5 - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>-<2D><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
long int toBorn = (long int) inds*birthRate + 0.5; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>
|
||||
std::sort(pop->individs.begin(), pop->individs.end(), compareOnFitness);
|
||||
std::vector<Individual*>::iterator start = pop->individs.begin();
|
||||
std::vector<Individual*>::iterator end = pop->individs.begin()+toDie;
|
||||
for(std::vector<Individual*>::iterator it = start; it != end; it++){
|
||||
delete *it;
|
||||
}
|
||||
pop->individs.erase(start, end);
|
||||
std::cout<<"VerhulstBreedingStrategy::breed: "<<toDie<<" individs have died\n";
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
inds = pop->individs.size();
|
||||
srand((unsigned int)time(NULL));
|
||||
for(long int i = 0; i < toBorn; i++) {
|
||||
int male = rand() % inds;
|
||||
int female = rand() % inds;
|
||||
female = (female != male ? female : (female + 1) % inds);
|
||||
|
||||
Individual* ind = new Individual(*(pop->individs.at(male)), *(pop->individs.at(female)));
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
|
||||
pop->individs.push_back(ind);
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,7 @@
|
||||
#pragma once
|
||||
#include "PopulationBreedingStrategy.h"
|
||||
|
||||
class VerhulstBreedingStrategy : public PopulationBreedingStrategy {
|
||||
public:
|
||||
virtual void breed(Population* pop);
|
||||
};
|
||||
162
DEC_GUI/DEC-0.0/population/Population.cpp
Normal file
162
DEC_GUI/DEC-0.0/population/Population.cpp
Normal file
@@ -0,0 +1,162 @@
|
||||
#include "Population.h"
|
||||
#include "../individual/Phenotype.h"
|
||||
#include "DEC-0.0/processor/Processor.h"
|
||||
#include <cstdlib>
|
||||
#include <sstream>
|
||||
#include <algorithm>
|
||||
|
||||
AsexualPopulation::~AsexualPopulation(){
|
||||
// TODO : <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD>
|
||||
}
|
||||
AsexualPopulation::AsexualPopulation(int size, PopulationBreedingStrategy* _strategy) :
|
||||
Population(_strategy), individs(size/*, 0*/)
|
||||
{
|
||||
|
||||
srand(0);
|
||||
int RANGE = 1000;
|
||||
float gValue;
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
for(int i = 0; i < size; i++){
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD>
|
||||
std::vector<Chromosome> fGenome;
|
||||
std::vector<Chromosome> mGenome;
|
||||
|
||||
// <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
gValue = (rand()%RANGE + 1) / (float) RANGE;
|
||||
Gene geneF1(Gene::Continious, "X", gValue);
|
||||
gValue = (rand()%RANGE + 1) / (float) RANGE;
|
||||
Gene geneF2(Gene::Continious, "Y", gValue);
|
||||
gValue = (rand()%RANGE + 1) / (float) RANGE;
|
||||
Gene geneF3(Gene::Continious, "Z", gValue);
|
||||
|
||||
Chromosome chromF("Chrom 1"); // <20><><EFBFBD><EFBFBD>
|
||||
chromF.insertGeneToEnd(geneF1);
|
||||
chromF.insertGeneToEnd(geneF2);
|
||||
chromF.insertGeneToEnd(geneF3);
|
||||
|
||||
|
||||
gValue = (rand()%RANGE + 1) / (float) RANGE;
|
||||
Gene geneM1(Gene::Continious, "X", gValue);
|
||||
gValue = (rand()%RANGE + 1) / (float) RANGE;
|
||||
Gene geneM2(Gene::Continious, "Y", gValue);
|
||||
gValue = (rand()%RANGE + 1) / (float) RANGE;
|
||||
Gene geneM3(Gene::Continious, "Z", gValue);
|
||||
|
||||
Chromosome chromM("Chrom 1"); // <20><><EFBFBD><EFBFBD>
|
||||
chromM.insertGeneToEnd(geneM1);
|
||||
chromM.insertGeneToEnd(geneM2);
|
||||
chromM.insertGeneToEnd(geneM3);
|
||||
|
||||
fGenome.push_back(chromF);
|
||||
mGenome.push_back(chromM);
|
||||
Genotype* genotype = new Genotype(fGenome, mGenome);
|
||||
// (END) <20><><EFBFBD><EFBFBD><EFBFBD>
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
Trait trait1(Trait::Continious, "X", 0.0f);
|
||||
Trait trait2(Trait::Continious, "Y", 0.0f);
|
||||
Trait trait3(Trait::Continious, "Z", 0.0f);
|
||||
Phenotype* phenotype = new Phenotype(trait1);
|
||||
phenotype->addTrait(trait2);
|
||||
phenotype->addTrait(trait3);
|
||||
// (END) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
|
||||
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
InnerSubstratesPool* subPool = 0;
|
||||
// (END) <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
|
||||
this->individs.at(i) = new Individual(genotype, phenotype, subPool, Individual::hermaphrodite, 0);
|
||||
} // (END) for(int i = 0; i < size; i++)
|
||||
}
|
||||
|
||||
void AsexualPopulation::calculateFitnessAll(){
|
||||
for(unsigned int i = 0; i < this->individs.size(); i++){
|
||||
this->individs.at(i)->calculateFitness();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
void AsexualPopulation::breedAll(){
|
||||
this->breedingStrategy->breed(this);
|
||||
}
|
||||
|
||||
void AsexualPopulation::selectionAll(){
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> breedAll
|
||||
}
|
||||
|
||||
void AsexualPopulation::mutationAll(){
|
||||
|
||||
}
|
||||
|
||||
void AsexualPopulation::setRegion(Region *_region){
|
||||
this->region = _region;
|
||||
for(unsigned int i = 0; i < this->individs.size(); i++){
|
||||
this->individs.at(i)->setRegion(_region);
|
||||
}
|
||||
}
|
||||
|
||||
std::string AsexualPopulation::getSatistics(){
|
||||
std::stringstream ans;
|
||||
long int pSize = this->individs.size();
|
||||
ans<<"Population size\t"<<pSize<<"\t";
|
||||
|
||||
//////////////////////////
|
||||
double totalFitness = 0.0;
|
||||
double best = 0.0;
|
||||
double worst= 1000.0;
|
||||
for(int i = 0; i < pSize; i++){
|
||||
double fitness = this->individs.at(i)->getFitness();
|
||||
best = fitness > best ? fitness : best;
|
||||
worst= fitness < worst? fitness : worst;
|
||||
totalFitness += fitness;
|
||||
}
|
||||
ans<<"Average fitness\t"<<(totalFitness/pSize);
|
||||
ans<<"\tBest\t"<<(best);
|
||||
ans<<"\tWorst\t"<<(worst);
|
||||
return ans.str();
|
||||
}
|
||||
|
||||
void AsexualPopulation::putGeneticStatisticsToStream(std::ostream &out){
|
||||
|
||||
out<<"Population size:\t"<<this->individs.size()<<std::endl;
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
//sort(this->individs.begin(),this->individs.end());
|
||||
//std::cout << "lol" << std::endl;
|
||||
for(unsigned int i = 0; i < this->individs.size(); i++){
|
||||
// out<<(i+1)<<"\t";
|
||||
// out<<"Fitness:\t"<<(this->individs.at(i)->getFitness());
|
||||
// out<<"\t";
|
||||
// out<<"Genotype:\t"<<(this->individs.at(i)->getGenotype());
|
||||
// out<<"\t";
|
||||
// out<<"Phenotype:\t"<<(this->individs.at(i)->getPhenotype());
|
||||
// out<<std::endl;
|
||||
std::cout << "lol" << std::endl;
|
||||
Processor::fillVectors(this->individs.at(i)->getGenotype());
|
||||
}
|
||||
}
|
||||
|
||||
void AsexualPopulation::putGeneticSimpleStatisticsToStream(std::ostream &out){
|
||||
for(unsigned int i = 0; i < this->individs.size(); i++){
|
||||
out<<(i+1)<<"\t"<<(this->individs.at(i)->getFitness());
|
||||
out<<"\t"<<(this->individs.at(i)->getGenotype().toSimpleString());
|
||||
//out<<"\t";
|
||||
out<<(this->individs.at(i)->getPhenotype().toSimpleString());
|
||||
out<<std::endl;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
void AsexualPopulation::putGeneticMaxModuleStatisticsToStream(std::ostream &out){
|
||||
for(unsigned int i = 0; i < this->individs.size(); i++){
|
||||
out<<(i+1)<<"\t"<<(this->individs.at(i)->getFitness());
|
||||
out<<"\t"<<(this->individs.at(i)->getGenotype().toMaxModuleAB());
|
||||
//out<<"\t";
|
||||
//out<<(this->individs.at(i)->getPhenotype().toSimpleString());
|
||||
out<<std::endl;
|
||||
}
|
||||
|
||||
}
|
||||
90
DEC_GUI/DEC-0.0/population/Population.h
Normal file
90
DEC_GUI/DEC-0.0/population/Population.h
Normal file
@@ -0,0 +1,90 @@
|
||||
#pragma once
|
||||
#include <list>
|
||||
#include <vector>
|
||||
#include "../individual/AbstractIndividual.h"
|
||||
#include "BreedingStrategies/PopulationBreedingStrategy.h"
|
||||
#include "../environment/AbstractEnvironment.h"
|
||||
|
||||
|
||||
class PopulationBreedingStrategy;
|
||||
|
||||
class Population {
|
||||
friend class PopulationBreedingStrategy;
|
||||
friend class VerhulstBreedingStrategy;
|
||||
protected:
|
||||
PopulationBreedingStrategy* breedingStrategy;
|
||||
Region* region;
|
||||
public:
|
||||
Population(PopulationBreedingStrategy* _strategy) : breedingStrategy(_strategy){}
|
||||
virtual ~Population() {};
|
||||
virtual void setBreedingStrategy(PopulationBreedingStrategy* _strategy) { breedingStrategy = _strategy;}
|
||||
virtual void setRegion(Region* _region) { region = _region;}
|
||||
virtual void calculateFitnessAll() = 0;
|
||||
virtual void breedAll() = 0;
|
||||
virtual void selectionAll() = 0;
|
||||
virtual void mutationAll() = 0;
|
||||
virtual std::string getSatistics() = 0;
|
||||
virtual void putGeneticStatisticsToStream(std::ostream& out) = 0;
|
||||
virtual void putGeneticSimpleStatisticsToStream(std::ostream& out) = 0;
|
||||
virtual void putGeneticMaxModuleStatisticsToStream(std::ostream& out) = 0;
|
||||
};
|
||||
|
||||
class AsexualPopulation : public Population {
|
||||
friend class PopulationBreedingStrategy;
|
||||
friend class VerhulstBreedingStrategy;
|
||||
friend class InOutBreedingPopulationBreedingStrategy;
|
||||
friend class KolchShindyalBreedingStrategy;
|
||||
friend class Processor;
|
||||
protected:
|
||||
std::vector<Individual*> individs;
|
||||
|
||||
public:
|
||||
AsexualPopulation(const std::vector<Individual*>& _inds, PopulationBreedingStrategy* _strategy = 0) : Population(_strategy), individs(_inds) {};
|
||||
AsexualPopulation(int size, PopulationBreedingStrategy* _strategy = 0);
|
||||
virtual ~AsexualPopulation();
|
||||
|
||||
virtual void setRegion(Region* _region);
|
||||
virtual void calculateFitnessAll();
|
||||
virtual void breedAll();
|
||||
virtual void selectionAll();
|
||||
virtual void mutationAll();
|
||||
virtual std::string getSatistics();
|
||||
virtual void putGeneticStatisticsToStream(std::ostream& out);
|
||||
virtual void putGeneticSimpleStatisticsToStream(std::ostream& out);
|
||||
virtual void putGeneticMaxModuleStatisticsToStream(std::ostream& out);
|
||||
};
|
||||
|
||||
//////////////////////////////////////////////
|
||||
//////////////////////////////////////////////
|
||||
//////////////////////////////////////////////
|
||||
class BisexualPopulation : public Population {
|
||||
friend class NeutralEvolutionBreedingStrategy;
|
||||
friend class DerevyankoReport2014;
|
||||
friend class DerevyankoReport;
|
||||
friend class Settings;
|
||||
friend class DerRep2014Window;
|
||||
friend class DerRepRFBR2013window;
|
||||
protected:
|
||||
std::list<Individual*> males;
|
||||
std::list<Individual*> females;
|
||||
public:
|
||||
BisexualPopulation(const std::list<Individual*>& _males,
|
||||
const std::list<Individual*>& _females, PopulationBreedingStrategy* _strategy = 0) :
|
||||
Population(_strategy), males(_males), females(_females) {}
|
||||
|
||||
virtual ~BisexualPopulation();
|
||||
|
||||
//virtual void setRegion(Region* _region);
|
||||
virtual void calculateFitnessAll();
|
||||
virtual void breedAll();
|
||||
virtual void selectionAll();
|
||||
virtual void mutationAll();
|
||||
virtual std::string getSatistics();
|
||||
virtual void putGeneticStatisticsToStream(std::ostream& out);
|
||||
virtual void putGeneticSimpleStatisticsToStream(std::ostream& out);
|
||||
virtual void putGeneticMaxModuleStatisticsToStream(std::ostream& out);
|
||||
|
||||
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
|
||||
static std::string mutualMigration(BisexualPopulation* p1, BisexualPopulation* p2, float frac1, float frac2 = -1.f);
|
||||
BisexualPopulation* createSubpopulation(float frac);
|
||||
};
|
||||
Reference in New Issue
Block a user