How to eliminate duplicates; Genetic Algorithm

this algorithm is a implementation of "Traveling Salesman problem" and genes are citys and each Chromosome is a potential solution.

the algorithm goes something like this

• random creates first population
• then it calculates the fitness (for each chromosome; it represents the length of the tour)
• it selects 2 parents and 2 EliminationChromosome (the parents recombinate and create 2 childs, these childs take the position of EliminationChromosome)
• the population mutates than (random selects some cromosomes and changes theyr 2 genes postion, just not to the best chromosome)
• calculates the fitness again
• checks if the number of iteration has reached maximum (breaking criterium, if maximum then it writes the cyti order to be visited of the best Chromosome

i changed your Method a little bit:

    public override bool Equals(object obj)
        {
            if (object.ReferenceEquals(obj, null)) return false;
            Chromosome chromosome = obj as Chromosome;
            if (object.ReferenceEquals(chromosome, null)) return false;
            for (int index = 0; index < chromosome.genes.Length; index++)
            {
               
                if (this.genes[index].ToInteger() != chromosome.genes[index].ToInteger()) return false;
            }
            return true; // all coresponding genes equal
        }

i also added my final solution as attachement

it is not an expected behavior for chromosomes to become null, dont know why that is happening and when.

Well, I've tried running the program with the initial default values, and also with iterations of 100000 and population size of 10 but I wasn't able to reproduce the problem.

On both occasions it gave me a list of 18 towns - one for each gene I imagine.

I tried some other combinations and sometimes the programming stopped responding without actually throw an exception.

It's difficult for me to figure this out without knowing much about the subject matter.

Is it in fact 'expected behavior' for all the chromosomes to sometimes become null before the iterations have completed?  If it is, then you'll need to put in a 'null test' to stop the program from hanging though doing so will, of course, slow things down.

@Vulpes thanks you helped me to get closer to the final solution
i added your code to the chromosome class (just copied it there) but i removed the while statemant from permutationRecombination and changed in Population class the Elimincija method


        public void Eliminacija(Population oldPopulation)
        {
            Chromosome parent1, parent2, eliminationChromosome1, eliminationChromosome2;
            {
              
                    parent1 = oldPopulation.rouletteWheel();
                    do
                    {
                        parent2 = oldPopulation.rouletteWheel();
                    } while (parent1 == parent2);

                    do
                    {
                        eliminationChromosome1 = oldPopulation.eliminacijaJedinke();
                    } while (eliminationChromosome1 == parent1 || eliminationChromosome1 == parent2);
                    do
                    {
                        eliminationChromosome2 = oldPopulation.eliminacijaJedinke();

                    } while (eliminationChromosome2 == parent1 || eliminationChromosome2 == parent2 || eliminationChromosome2 == eliminationChromosome1);

                    //recombination
                    recombination(parent1, parent2, eliminationChromosome1, eliminationChromosome2);

                 
        //i added this; if the eliminationChromosome equals to any other chromosome in population
                  foreach (Chromosome c in population)
                    {
                        if (eliminationChromosome1.Equals(c)&&eliminationChromosome1.fitness!=c.fitness)
                        {
                            Gene tmpGene;
                            int gene1, gene2;
                            gene1 = ga.rng.Next(chromosomeSize);

                            do
                            {
                                gene2 = ga.rng.Next(chromosomeSize);
                            } while (gene1 == gene2);


                            tmpGene = eliminationChromosome1.genes[gene1];
                            eliminationChromosome1.genes[gene1] = eliminationChromosome1.genes[gene2];
                            eliminationChromosome1.genes[gene2] = tmpGene;

                        }
                        if (eliminationChromosome2.Equals(c)&&eliminationChromosome2.fitness!=c.fitness)
                        {
                            Gene tmpGene;
                            int gene1, gene2;
                            gene1 = ga.rng.Next(chromosomeSize);

                            do
                            {
                                gene2 = ga.rng.Next(chromosomeSize);
                            } while (gene1 == gene2);


                            tmpGene = eliminationChromosome2.genes[gene1];
                            eliminationChromosome2.genes[gene1] = eliminationChromosome2.genes[gene2];
                            eliminationChromosome2.genes[gene2] = tmpGene;
                        }
                    }

                //mutation
                oldPopulation.mutation();


                //Calculate Fitness
                oldPopulation.fitness();
                oldPopulation.kumulativnaKazna();

            }

but after some iterations al my Chromosomes get the value null ( for example when i set iterations to 100000 and "Velicina populacije(this is croatian-->that means population size) to 10 the algorithm stops because all chromosomes are null

can you please help me to figure out why that is happening?!

but my problem is that i dont know how to compare the right objects

i.e. this picture shows the structure of my classes... and the genes are value int so if these values are the same for two chromosomes; it should generate again new childs:
i meen if child.genes = { 123456789} and parent parent.genes={12345678}---> they have the same order of numbers so i need to avoid this

http://img843.imageshack.us/i/capturezo.png/[^]