/// <summary>
/// Defines the parental haplotypes according to the recombination type
/// </summary>
/// <param name="recType"></param>
public void DefineParentalHaplotypes(RecombinationType recType)
{
mother = new Individ();
father = new Individ();
Random s_Random = new Random();
switch (recType)
{
case RecombinationType.Backcross:
for (int i = 0; i < mother.Haplotype0.Length; i++)
{
mother.Haplotype0[i] = 0;
}
for (int i = 0; i < father.Haplotype0.Length; i++)
{
father.Haplotype0[i] = 1;
}
break;
case RecombinationType.BackcrossWithNoise:
for (int i = 0; i < mother.Haplotype0.Length; i++)
{
int perCent = s_Random.Next(0, 100);
if (perCent < 20)
{
mother.Haplotype0[i] = 1;
}
else
{
mother.Haplotype0[i] = 0;
}
}
for (int i = 0; i < father.Haplotype0.Length; i++)
{
int perCent = s_Random.Next(0, 100);
if (perCent < 20)
{
mother.Haplotype0[i] = 0;
}
else
{
mother.Haplotype0[i] = 1;
}
}
break;
}
}
public void SimulateRecombination(int amountOfIndivids)
{
//create population of 200 children -individulas
pop = new Population();
for (int i = 0; i < amountOfIndivids; i++)
{
//the same parents
Individ offSpring = new Individ();
offSpring.Parent0 = mother;
offSpring.Parent1 = father;
pop.Individ.Add(offSpring);
}
//calculate recombination pathways
//FusionSimple()
//gameta_get()
}
private void HaplotypeInheritOrderedListOfLoci(List <Locus> OrderedListOfLoci, Individ parent, IList <Position> RecEventsParent,
out List <int> Haplotype,
out List <bool> HaplotypeOk)
{
int Phase = 0;
int NRec = RecEventsParent.Count;
int NLoci = OrderedListOfLoci.Count;
//NotBeforePosition(Position Pos)
Haplotype = new List <int>();
HaplotypeOk = new List <bool>();
if (NLoci > 0)
{
Position PosLast = new Position();
PosLast.Chromosome = OrderedListOfLoci[NLoci].Position.Chromosome;
PosLast.PositionChrGenetic = OrderedListOfLoci[NLoci].Position.PositionChrGenetic + 10;
Position PosNextRec = new Position();
if (NRec == 0)
{
PosNextRec = PosLast;
}
else
{
PosNextRec = RecEventsParent[0];
}
int IRec = 0;
int ILocus = 0;
List <int> ParentHaplotype;
List <bool> ParentHaplotypeOk;
foreach (Locus locus in OrderedListOfLoci)
{
while (!PosNextRec.NotBeforePosition(locus.Position))
{
IRec++;
if (IRec >= NRec)
{
PosNextRec = PosLast;
}
else
{
PosNextRec = RecEventsParent[IRec];
}
Phase = 1 - Phase;//0<->1
}
if (Phase == 0)
{
ParentHaplotype = this.Haplotype0;
ParentHaplotypeOk = this.Haplotype0Ok;
}
else
{
ParentHaplotype = this.Haplotype1;
ParentHaplotypeOk = this.Haplotype1Ok;
}
Haplotype.Add(ParentHaplotype[ILocus]);
HaplotypeOk.Add(ParentHaplotypeOk[ILocus]);
ILocus++;
}
}
}
//dRec=expectation of number of recombination events in the interval (1 cM=0.01 recombination event)
//Independent recombination or start from he begin of chromosome => exponential distribution of distance to the next recombination
//E{exp(lambda)}=1/lambda=100 cM => lambda=1/100
//density: p(x)=lambda e^{- lambda*x}
//comulative distribution function: P(x)=P(exp(lambda)<x)=1 - e^{- lambda*x} ~ U[0,1] => e^{- lambda*x}=1-U[0,1] => - lambda*x=ln(1-U[0,1]) => x=(-1/lambda)*ln(1-U[0,1]) = -100*ln(1-U[0,1])
/// <summary>
/// Simulates the recombination events for the production of the children from two parents
/// </summary>
/// <param name="amountOfIndivids"></param>
public void SimulateRecombination(int amountOfIndivids = 200)
{
Random rand = new Random();
double p, previousPosition, currentPosition = 0.0, l, lambda = 0.01;
//create population of 200 children -individulas
pop = new Population();
for (int i = 0; i < amountOfIndivids; i++)
{
//the same parents
Individ offSpring = new Individ();
offSpring.Parent0 = mother;
offSpring.Parent1 = father;
//define recombination events positions H0 haplotyes for children
for (int j = 0; j < go.Chromosome.Count; j++)
{
//genereate random number P = 0 to 1
p = rand.NextDouble();
if (p < 0.5)
{
//begin with grandmother (copy haplotpes H0)
//first recombination happens at coordinate 0
Position pos = new Position();
pos.Chromosome = go.Chromosome[j];
pos.PositionChrGenetic = 0.0;
offSpring.RecEventsParent0.Add(pos);
}
previousPosition = 0.0;
while (go.Chromosome[j].LenGenetcM > currentPosition)
{
// l=generate random number with exponantional distribution with lambda = 1/100
l = generateRandExponantionalDist(go.Chromosome[j].LenGenetcM, 0, lambda);
currentPosition = previousPosition + l;
Position pos = new Position();
pos.Chromosome = go.Chromosome[j];
pos.PositionChrGenetic = currentPosition;
offSpring.RecEventsParent0.Add(pos);
previousPosition = currentPosition;
}
}
//reset all the values
p = 0.0;
previousPosition = 0.0;
currentPosition = 0.0;
l = 0.0;
//define recombination events positions H1 haplotyes for children
for (int k = 0; k < go.Chromosome.Count; k++)
{
//genereate random number P = 0 to 1
p = rand.NextDouble();
if (p < 0.5)
{
//begin with grandmother (copy haplotpes H0)
//first recombination happens at coordinate 0
Position pos = new Position();
pos.Chromosome = go.Chromosome[k];
pos.PositionChrGenetic = 0.0;
offSpring.RecEventsParent1.Add(pos);
}
previousPosition = 0.0;
while (go.Chromosome[k].LenGenetcM > currentPosition)
{
// l=generate random number with exponantional distribution with lambda = 1/100
l = generateRandExponantionalDist(go.Chromosome[k].LenGenetcM, 0, lambda);
currentPosition = previousPosition + l;
Position pos = new Position();
pos.Chromosome = go.Chromosome[k];
pos.PositionChrGenetic = currentPosition;
offSpring.RecEventsParent1.Add(pos);
previousPosition = currentPosition;
}
}
pop.Individ.Add(offSpring);
}
}
