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;
}
}
void GeneManager::initBasicRules()
{
// <GS><GT><MD><DT><MET><DS><MS><I_E><I_U><E_E><E_U><MUT>
// growth seg
newGene(1 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 50 , 20 , 1 , 0 , 0 , 0 , 0 , 0 , 0); //0
newGene(2 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 25 , 25 , 40 , 1 , 0 , 0 , 0 , 0 , 0 , 0);
newGene(3 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 1 , 0 , 0 , 0 , 0 , 0 , 0);
newGene(4 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 1 , 0 , 0 , 0 , 0 , 0 , 0);
newGene(-1 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 40 , 20 , -1 , 0 , 0 , 0 , 0 , 0 , 0);
newGene(-2 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 20 , 20 , 40 , -1 , 0 , 0 , 0 , 0 , 0 , 0);
newGene(-3 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , -1 , 0 , 0 , 0 , 0 , 0 , 0);
newGene(-4 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , -1 , 0 , 0 , 0 , 0 , 0 , 0); //7
// growth turns
newGene(0 , 1 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 50 , 20 , 0 , 1 , 0 , 0 , 0 , 0 , 0); //8
newGene(0 , 2 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 25 , 25 , 40 , 0 , 1 , 0 , 0 , 0 , 0 , 0);
newGene(0 , 3 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 1 , 0 , 0 , 0 , 0 , 0);
newGene(0 , 4 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 1 , 0 , 0 , 0 , 0 , 0);
newGene(0 , -1 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 40 , 20 , 0 , -1 , 0 , 0 , 0 , 0 , 0);
newGene(0 , -2 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 20 , 20 , 40 , 0 , -1 , 0 , 0 , 0 , 0 , 0);
newGene(0 , -3 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , -1 , 0 , 0 , 0 , 0 , 0);
newGene(0 , -4 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , -1 , 0 , 0 , 0 , 0 , 0); //15
// maturedDuration
newGene(0 , 0 , 1 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 50 , 20 , 0 , 0 , 1 , 0 , 0 , 0 , 0); //16
newGene(0 , 0 , 2 , 0 , 0 , 0 , 0 , 100 , 10 , 25 , 25 , 40 , 0 , 0 , 1 , 0 , 0 , 0 , 0);
newGene(0 , 0 , 3 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 1 , 0 , 0 , 0 , 0);
newGene(0 , 0 , 4 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 1 , 0 , 0 , 0 , 0);
newGene(0 , 0 , -1 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 40 , 20 , 0 , 0 , -1 , 0 , 0 , 0 , 0);
newGene(0 , 0 , -2 , 0 , 0 , 0 , 0 , 100 , 10 , 20 , 20 , 40 , 0 , 0 , -1 , 0 , 0 , 0 , 0);
newGene(0 , 0 , -3 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , -1 , 0 , 0 , 0 , 0);
newGene(0 , 0 , -4 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , -1 , 0 , 0 , 0 , 0); //23
//decayTurns
newGene(0 , 0 , 0 , 1 , 0 , 0 , 0 , 100 , 10 , 50 , 50 , 20 , 0 , 0 , 0 , 1 , 0 , 0 , 0); //24
newGene(0 , 0 , 0 , 2 , 0 , 0 , 0 , 100 , 10 , 25 , 25 , 40 , 0 , 0 , 0 , 1 , 0 , 0 , 0);
newGene(0 , 0 , 0 , 3 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 0 , 1 , 0 , 0 , 0);
newGene(0 , 0 , 0 , 4 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 0 , 1 , 0 , 0 , 0);
newGene(0 , 0 , 0 , -1 , 0 , 0 , 0 , 100 , 10 , 50 , 40 , 20 , 0 , 0 , 0 , -1 , 0 , 0 , 0);
newGene(0 , 0 , 0 , -2 , 0 , 0 , 0 , 100 , 10 , 20 , 20 , 40 , 0 , 0 , 0 , -1 , 0 , 0 , 0);
newGene(0 , 0 , 0 , -3 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 0 , -1 , 0 , 0 , 0);
newGene(0 , 0 , 0 , -4 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 0 , -1 , 0 , 0 , 0); //31
//chance to get seed when decaying
newGene(0 , 0 , 0 , 0 , 0 , 5 , 0 , 100 , 10 , 50 , 50 , 20 , 0 , 0 , 0 , 0 , 0 , 5 , 0); //32
newGene(0 , 0 , 0 , 0 , 0 , 10 , 0 , 100 , 10 , 25 , 25 , 40 , 0 , 0 , 0 , 0 , 0 , 5 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 15 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 0 , 0 , 0 , 5 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 20 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 0 , 0 , 0 , 5 , 0);
newGene(0 , 0 , 0 , 0 , 0 , -5 , 0 , 100 , 10 , 50 , 40 , 20 , 0 , 0 , 0 , 0 , 0 , -5 , 0);
newGene(0 , 0 , 0 , 0 , 0 , -10 , 0 , 100 , 10 , 20 , 20 , 40 , 0 , 0 , 0 , 0 , 0 , -5 , 0);
newGene(0 , 0 , 0 , 0 , 0 , -15 , 0 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 0 , 0 , 0 , -5 , 0);
newGene(0 , 0 , 0 , 0 , 0 , -20 , 0 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 0 , 0 , 0 , -5 , 0); //39
//chance to get seed when matured
newGene(0 , 0 , 0 , 0 , 0 , 0 , 5 , 100 , 10 , 50 , 50 , 20 , 0 , 0 , 0 , 0 , 0 , 0 , 5); //40
newGene(0 , 0 , 0 , 0 , 0 , 0 , 10 , 100 , 10 , 25 , 25 , 40 , 0 , 0 , 0 , 0 , 0 , 0 , 5);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 15 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 0 , 0 , 0 , 0 , 5);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 20 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 0 , 0 , 0 , 0 , 5);
newGene(0 , 0 , 0 , 0 , 0 , 0 , -5 , 100 , 10 , 50 , 40 , 20 , 0 , 0 , 0 , 0 , 0 , 0 , -5);
newGene(0 , 0 , 0 , 0 , 0 , 0 , -10 , 100 , 10 , 20 , 20 , 40 , 0 , 0 , 0 , 0 , 0 , 0 , -5);
newGene(0 , 0 , 0 , 0 , 0 , 0 , -15 , 100 , 10 , 10 , 10 , 60 , 0 , 0 , 0 , 0 , 0 , 0 , -5);
newGene(0 , 0 , 0 , 0 , 0 , 0 , -20 , 100 , 10 , 5 , 5 , 80 , 0 , 0 , 0 , 0 , 0 , 0 , -5); //47
//special seed denying gene for stem seed.
//48
newGene(0 , 0 , 0 , 0 , 0 , -20 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0); // seed chance when decay - 20%
//49
newGene(0 , 0 , 0 , 0 , 0 , 0 , -20 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0); // seed chance when matured - 20%
// only provide mutation benefits
//maxExpressedTraits - Does not add benefits , but provide mutation benefits
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 50 , 10 , 0 , 0 , 0 , 0 , 1 , 0 , 0); //50
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 25 , 25 , 20 , 0 , 0 , 0 , 0 , 1 , 0 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 30 , 0 , 0 , 0 , 0 , 1 , 0 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 40 , 0 , 0 , 0 , 0 , 1 , 0 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 50 , 40 , 10 , 0 , 0 , 0 , 0 , -1 , 0 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 20 , 20 , 20 , 0 , 0 , 0 , 0 , -1 , 0 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 10 , 10 , 30 , 0 , 0 , 0 , 0 , -1 , 0 , 0);
newGene(0 , 0 , 0 , 0 , 0 , 0 , 0 , 100 , 10 , 5 , 5 , 40 , 0 , 0 , 0 , 0 , -1 , 0 , 0); //57
}
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;
}
}
