void tAgent::setupRandomAgent(int nucleotides){
int i;
genome.resize(nucleotides);
for(i=0;i<nucleotides;i++)
genome[i]=127;//rand()&255;
ampUpStartCodons();
setupPhenotype();
}
void tAgent::loadAgent(char* filename){
FILE *f=fopen(filename,"r+t");
int i;
genome.clear();
while(!(feof(f))){
fscanf(f,"%i ",&i);
genome.push_back((unsigned char)(i&255));
}
setupPhenotype();
}
void tAgent::loadAgentWithTrailer(char* filename){
#ifdef useANN
ANN=new tANN;
ANN->load(filename);
#else
FILE *f=fopen(filename,"r+t");
int i;
genome.clear();
fscanf(f,"%i ",&i);
while(!(feof(f))){
fscanf(f,"%i ",&i);
genome.push_back((unsigned char)(i&255));
}
setupPhenotype();
#endif
}
void tAgent::inherit(tAgent *from,double mutationRate,int theTime){
int i,s,o,w;
int nucleotides;
vector<unsigned char> buffer;
born=theTime;
dormancyPeriod = from->dormancyPeriod;
if (randDouble < 0.05)
{
dormancyPeriod += (int)(randDouble * 20.0) - 10;
dormancyPeriod = max(dormancyPeriod, 0);
}
ancestor=from;
from->nrPointingAtMe++;
nucleotides=(int)from->genome.size();
genome.clear();
genome.resize(nucleotides);
for(i=0;i<nucleotides;i++)
if(randDouble<mutationRate)
genome[i]=rand()&255;
else
genome[i]=from->genome[i];
if((randDouble<0.05)&&(genome.size()<20000)){
//duplication
w=15+rand()&511;
s=rand()%((int)genome.size()-w);
o=rand()%(int)genome.size();
buffer.clear();
buffer.insert(buffer.begin(),genome.begin()+s,genome.begin()+s+w);
genome.insert(genome.begin()+o,buffer.begin(),buffer.end());
}
if((randDouble<0.02)&&(genome.size()>1000)){
//deletion
w=15+rand()&511;
s=rand()%((int)genome.size()-w);
genome.erase(genome.begin()+s,genome.begin()+s+w);
}
setupPhenotype();
fitness=0.0;
}
void tAgent::inherit(tAgent *from,double mutationRate,int theTime){
int nucleotides=from->genome.size();
int i,s,o,w;
double localMutationRate=4.0/from->genome.size();
vector<unsigned char> buffer;
born=theTime;
ancestor=from;
from->nrPointingAtMe++;
from->nrOfOffspring++;
genome.clear();
genome.resize(from->genome.size());
for(i=0;i<nucleotides;i++)
if(((double)rand()/(double)RAND_MAX)<mutationRate)
genome[i]=rand()&255;
else
genome[i]=from->genome[i];
if((((double)rand()/(double)RAND_MAX)<0.05)&&(genome.size()<20000)){
//duplication
w=15+rand()&511;
s=rand()%(genome.size()-w);
o=rand()%genome.size();
buffer.clear();
buffer.insert(buffer.begin(),genome.begin()+s,genome.begin()+s+w);
genome.insert(genome.begin()+o,buffer.begin(),buffer.end());
}
if((((double)rand()/(double)RAND_MAX)<0.02)&&(genome.size()>1000)){
//deletion
w=15+rand()&511;
s=rand()%(genome.size()-w);
genome.erase(genome.begin()+s,genome.begin()+s+w);
}
setupPhenotype();
fitness=0.0;
#ifdef useANN
ANN->inherit(ancestor->ANN,mutationRate);
#endif
}
