/// <summary>
/// Chromosome copying constructor.
/// </summary>
/// <param name="c"></param>
public Chromosome(Chromosome c)
{
this.Lengths_3 = new List<int>(c.Lengths_3);
this.Lengths_5 = new List<int>(c.Lengths_5);
this.Score = new ScoreTotal (c.Score);
this.Overlaps = new List<Overlap>();
foreach (Overlap o in c.Overlaps)
{
this.Overlaps.Add(new Overlap(o));
}
}
/// <summary>
/// Mutate one chromosome.
/// </summary>
/// <param name="solution">Solution to mutate.</param>
/// <param name="rand">Randomizer.</param>
/// <returns>Mutated chromosome.</returns>
private Chromosome Mutate(Chromosome solution, Random rand)
{
int index;
int value;
if (rand.NextDouble() < 0.5D)
{
//Mutate 3'
index = rand.Next(solution.Lengths_3.Count);
value = rand.Next(this.Settings.MinLen_3, this.Settings.MaxLen_3 + 1);
solution.Lengths_3[index] = value;
}
else
{
//Mutate 5'
index = rand.Next(solution.Lengths_5.Count);
value = rand.Next(this.Settings.MinLen_5, this.Settings.MaxLen_5 + 1);
solution.Lengths_5[index] = value;
}
return solution;
}
/// <summary>
/// Lamarckian evolutionary algorithm for overlap optimization.
/// </summary>
/// <param name="o"></param>
/// <param name="args"></param>
public void LeaOptimizeOverlaps(object o, DoWorkEventArgs args)
{
stop = false;
this.b = o as BackgroundWorker;
Random rand = new Random();
List<Chromosome> population;
List<Chromosome> nextPopulation = new List<Chromosome>();
int progress = 0;
b.ReportProgress(progress);
List<Chromosome> tournament;
Chromosome mom, dad, child, best;
Tuple<Chromosome, Chromosome> children;
double variance;
double maxVariance = 0.0;
int i = 0;
population = Populate(rand, this.Construct.Overlaps);
//Local Search evaluates population
EvaluatePopulation(population, this.Settings.LeaSettings.IgnoreHeterodimers);
if (!stop)
population = LocalSearch(population, rand, this.Settings.LeaSettings.IgnoreHeterodimers);
best = new Chromosome(Tournament(population));
leaBest = new Chromosome(best);
List<Chromosome> bestes = new List<Chromosome>();
leaBestAcrossGenerations.Add(best.Score.NormalizedScore);
bestes.Add(new Chromosome(best));
do
{
//Selection
do
{
//Crossover
if (rand.NextDouble() <= this.Settings.LeaSettings.CrossoverRate)
{
tournament = SelectForTournament(this.Settings.LeaSettings.TournamentSize, population, rand);
mom = Tournament(tournament);
tournament = SelectForTournament(this.Settings.LeaSettings.TournamentSize, population, rand);
dad = Tournament(tournament);
children = Crossover(mom, dad, rand);
nextPopulation.Add(children.Item1);
nextPopulation.Add(children.Item2);
}
else
{
//Add two children without crossing over
tournament = SelectForTournament(this.Settings.LeaSettings.TournamentSize, population, rand);
child = new Chromosome(Tournament(tournament));
nextPopulation.Add(child);
tournament = SelectForTournament(this.Settings.LeaSettings.TournamentSize, population, rand);
child = new Chromosome(Tournament(tournament));
nextPopulation.Add(child);
}
} while (nextPopulation.Count < population.Count);
//Mutation
nextPopulation = MutatePopulation(nextPopulation, rand);
//Local Search evaluates population
if (!stop)
EvaluatePopulation(nextPopulation, this.Settings.LeaSettings.IgnoreHeterodimers);
if (!stop)
nextPopulation = LocalSearch(nextPopulation, rand, this.Settings.LeaSettings.IgnoreHeterodimers);
if (!stop)
{
best = Tournament(nextPopulation);
bestes.Add(new Chromosome(best));
leaBestAcrossGenerations.Add(best.Score.NormalizedScore);
}
if (!stop && best.Score.NormalizedScore < leaBest.Score.NormalizedScore)
{
//copy the best solution so far
leaBest = new Chromosome(best);
}
population.Clear();
population.AddRange(nextPopulation);
nextPopulation.Clear();
// assess variance only if i > MinIterations
variance = Variance(leaBestAcrossGenerations);
if (variance > maxVariance)
{
maxVariance = variance;
}
//progress = 100 if epsilon == variance
//if variance descending
if (maxVariance > variance && i > this.Settings.LeaSettings.MinIterations)
{
//don't confuse the user
progress = Math.Max((int)(100.0 * (double)i / (double)this.Settings.LeaSettings.MaxIterations), (int)((100.0 / maxVariance) * (maxVariance + this.Settings.LeaSettings.Epsilon - variance) + 0.5));
}
else
{
progress = (int)Math.Max((100.0 * (double)i / (double)this.Settings.LeaSettings.MaxIterations), (double)progress);
}
if (progress > 100)
{
//when variance lower than epsilon
progress = 100;
}
b.ReportProgress(progress);
i++;
} while (!stop && (progress < 100) && (i < this.Settings.LeaSettings.MaxIterations));
progress = 100;
b.ReportProgress(progress);
stop = false;
if (leaBest == null || leaBest.Score.Equals(ScoreTotal.Inacceptable))
{
throw new AssemblyException();
}
else
{
this.Construct.Overlaps = leaBest.ToOverlaps(this.Templates);
this.Construct.Evaluate();
}
}
/// <summary>
/// Perform uniform crossover.
/// </summary>
/// <param name="mom">Parent 1.</param>
/// <param name="dad">Parent 2.</param>
/// <param name="rand">Randomizer.</param>
/// <returns>Tuple of children.</returns>
private Tuple<Chromosome, Chromosome> Crossover(Chromosome mom, Chromosome dad, Random rand)
{
List<int> len_3_1 = new List<int>();
List<int> len_5_1 = new List<int>();
List<int> len_3_2 = new List<int>();
List<int> len_5_2 = new List<int>();
for (int i = 0; i < mom.Lengths_3.Count; i++)
{
if (rand.NextDouble() < 0.5)
{
len_3_1.Add(mom.Lengths_3[i]);
len_5_1.Add(mom.Lengths_5[i]);
len_3_2.Add(dad.Lengths_3[i]);
len_5_2.Add(dad.Lengths_5[i]);
}
else
{
len_3_1.Add(dad.Lengths_3[i]);
len_5_1.Add(dad.Lengths_5[i]);
len_3_2.Add(mom.Lengths_3[i]);
len_5_2.Add(mom.Lengths_5[i]);
}
}
Chromosome child1 = new Chromosome(len_3_1, len_5_1, this.Settings.TargetTm);
Chromosome child2 = new Chromosome(len_3_2, len_5_2, this.Settings.TargetTm);
Tuple<Chromosome, Chromosome> children = new Tuple<Chromosome, Chromosome>(child1, child2);
return children;
}