void Host :: MutateGenes(int mutationType, KIRGene& kir_hap2, Map& kirMap, GenePool& mhcPool, int gene_type)
{
if(mutationType == 1)//pick another molecules as mutation
{
KIRGene newGene(RandomNumber(2,16));
/*if(!kirMap.IsGeneInMap(newGene))
{
kirMap.FillMap(mhcPool, newGene);
if(gene_type !=2)////force to have only one type of receptors, if the user wants it!
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
}//*/
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = newGene.BindMolecule(mhcGene);
if(L >= newGene.GetGeneSpecificity())
M_id += (1<<i);
}
newGene.SetPseudogene(M_id);
if(gene_type !=2)////force to have only one type of receptors, if the user wants it!
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
return;
}
if(mutationType == 2)//point mutation + L
{
if(RandomNumberDouble()<0.8) //pointmutation
{
kir_hap2.PointMutation();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id += (1<<i);
}
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.8) //mutate L
{
kir_hap2.MutateSpecificity();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id += (1<<i);
}
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.8)//mutate type
{
kir_hap2.MutateReceptorType();
}
return;
}
}
void Host::MutateGenesForMutualInvasion(int mutationType, KIRGene& kir_hap2, Map& kirMap, GenePool& mhcPool, double simulationTime, double time_invasion, int gene_type)
{
if(mutationType == 1)//pick another molecule as mutation
{
KIRGene newGene(RandomNumber(2,16));
/*if(!kirMap.IsGeneInMap(newGene))
{
kirMap.FillMap(mhcPool, newGene);
//cout <<simulationTime << "|" <<time_invasion <<endl;
if(simulationTime < time_invasion)//only after the invasion time, the receptor type should be allowed to mutate
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
}//*/
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = newGene.BindMolecule(mhcGene);
if(L >= newGene.GetGeneSpecificity())
M_id += (1<<i);
}
//set the Gene pseudo
newGene.SetPseudogene(M_id);
if(gene_type !=2)////force to have only one type of receptors, if the user wants it!
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
return;
}
if(mutationType == 2)//point mutation + L
{
if(RandomNumberDouble()<0.8)
{
kir_hap2.PointMutation();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id+= (1<<i);
}
//set the Gene pseudo
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.2)
{
kir_hap2.MutateSpecificity();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id+= (1<<i);
}
//set the Gene pseudo
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.2)
{
if(simulationTime >= time_invasion) //only after the invasion time, the receptor type should be allowed to mutate
kir_hap2.MutateReceptorType();
}
return;
}
}
/*FUNCTIONS OF CLASS HOST
*Constructs a host for the initialization of the population: it fills the MHC genes with a randomly picked allele from the population
* and creates KIRs that match their own MHC according to the specificity*/
Host::Host(int loci_kir, int loci_mhc, double _mutationRate, bool _tuning, int numberOfExtraKirs,Map& kirMap, MHCGenePool& mhcPool, bool hla) {
InitializeHostParameters(_mutationRate,_tuning, loci_kir, loci_mhc);
//fill the mhc Genes
for(int i = 0; i <lociMHC*TWO; i++)
{
Gene firstGene;
int mhc1 = mhcPool.RandomlyPickGene(hla);
firstGene.SetGeneID(mhc1);
mhcGenes.push_back(firstGene);
}
/*
Gene secondGene;
secondGene.SetGeneID(mhc2);
mhcGenes.push_back(secondGene);*/
//create random KIRs with random specificity for ONE haplotype
// (at the beginning of the simulation, the size of the map should equal the LOCI_NUMBER)
map< pair<int,int>, pair <int, int> > ::iterator it;
for(it = kirMap.GetMap().begin(); it != kirMap.GetMap().end(); it ++)
{
int id = it->first.first;
int geneType = it->first.second;
int L = it->second.first;
int pseudo = it->second.second;
KIRGene kir;
kir.SetGeneSpecificity(L);
kir.SetGeneID(id);
kir.SetPseudogene(pseudo);
kir.SetGeneType(geneType);
kir.SetGeneFunctionality(false);
kir.SetGeneExpression(false);
kirGenes.push_back(kir);
//cout << "printing genes in host first constructor" <<endl;
//kir.PrintGenes();
}
int size = kirGenes.size();
//make sure that the first haplotype has number lociKIR (regardless of the Map size!)
while(size < lociKIR)
{
KIRGene bla = kirGenes.at(size-1);
kirGenes.push_back(bla);
size ++;
}
//copy the first kirs into the other haplotype (all individuals are homozygous!)
for(int i=0; i<lociKIR; i++)
{
KIRGene kir = kirGenes.at(i);
kirGenes.push_back(kir);
}
if(tuning == true)
EducateKIRs();
ExpressKIRs(numberOfExtraKirs);
//CountFunctionalKIRs();
age = RandomNumber(1,70); //population initialized with a random age between 1 and 70
//cout <<inhibitoryKIRs << "|" <<activatingKIRs <<"|"<<CountExpressedKIRs() <<endl;
}