func mutateAll(seqMap map[int][]byte, lambda float64, l int, rng *randist.RNG) {
for _, seq := range seqMap {
count := randist.PoissonRandomInt(rng, lambda)
for i := 0; i < count; i++ {
idx := randist.UniformRandomInt(rng, l)
a := NucleicAcids[randist.UniformRandomInt(rng, len(NucleicAcids))]
for a == seq[idx] {
a = NucleicAcids[randist.UniformRandomInt(rng, len(NucleicAcids))]
}
seq[idx] = a
}
}
}
// evolutionary operators: mutation and transfer
func (pop *SeqPop) manipulate() {
// calculate the number of events, which is poisson distribution
lambda := float64(pop.Size) * float64(pop.Length) * (pop.Mutation + pop.Transfer)
if pop.ExpTime {
t := randist.ExponentialRandomFloat64(pop.rng, 1.0)
lambda = t * lambda
}
k := randist.PoissonRandomInt(pop.rng, lambda)
// given k, the number of mutations or transfers are following Binormial distribution.
// therefore, we can do k times of Bernoulli test
for i := 0; i < k; i++ {
// determine whether this event is a mutation or transfer
ratio := pop.Mutation / (pop.Mutation + pop.Transfer) // the ratio of mutation
r := randist.UniformRandomFloat64(pop.rng) // randomly produce a probability
if r <= ratio { // determin whether is a mutation or transfer
pop.mutate()
} else {
pop.transfer()
}
}
}
