public DnaSequence Evolve(DnaSequence dnaSequence, double time)
{
DnaSequence evolvedDnaSequence = new DnaSequence(dnaSequence.Size());
for (int i = 0; i < dnaSequence.Size(); i++)
{
evolvedDnaSequence[i] = this.evolutionModel.GenerateNextBase(dnaSequence.ElementAt(i), time);
}
return(evolvedDnaSequence);
}
// Constructor for root node
public PhyloTreeNode(DnaSequence dnaSequence)
{
this.dnaSequence = dnaSequence;
double timeToEvolve = ExponentialDistribution.randomExponential.NextDouble();
this.timeFromStart = timeToEvolve;
this.creationTime = 0;
this.childrenNodes = new List <PhyloTreeNode>();
NodeEvolutionScheduler.scheduler.ScheduleNodeEvolution(this, timeToEvolve);
}
private void Evolve()
{
DnaSequence evolvedDnaSequence1 = DnaSequenceEvolver.evolver.Evolve(this.dnaSequence, this.timeFromStart);
DnaSequence evolvedDnaSequence2 = DnaSequenceEvolver.evolver.Evolve(this.dnaSequence, this.timeFromStart);
List <PhyloTreeNode> childrenNodes = new List <PhyloTreeNode>()
{
new PhyloTreeNode(this, evolvedDnaSequence1),
new PhyloTreeNode(this, evolvedDnaSequence2)
};
this.childrenNodes = childrenNodes;
}
static void Main(string[] args)
{
string userInputSequence = string.Empty;
SetupEnviroment();
Console.WriteLine("Please input root sequence:");
userInputSequence = Console.ReadLine();
DnaSequence userSequence = new DnaSequence(userInputSequence);
NodeEvolutionScheduler.scheduler.StartScheduler();
PhyloTree tree = new PhyloTree(userSequence);
Program.tree = tree;
Program.evolutionTimer.Enabled = true;
Console.ReadLine();
}
public PhyloTree(DnaSequence rootDnaSequence)
{
this.rootNode = new PhyloTreeNode(rootDnaSequence);
}