using System;

namespace Science.Biology.PopulationGenetics
{
	/// <summary>
	/// Chromosome
	/// </summary>
	public class Chromosome
	{
		private int numberOfAllele = 1,numberOfGenes = 1; 
		private int[,] configuration;
		private double[,] mutation; // mutation between chromosomes
		private double[] recombination;
			
		public int NumberOfAllele
		{
			get{return numberOfAllele;}
		}
		public int NumberOfGenes
		{
			get{return numberOfGenes;}
		}
		public int[,] Configuration  // gene configuration
		{
			get{return configuration;}
		}
		public double[,] Mutation  // property of mutation
		{
			get{return mutation;}
		}	
		public double[] Recombination  // property of Recombination
		{
			get{return recombination;}
		}

		private Gene[] genes;  
		public Chromosome()
		{
			configuration = new int[numberOfAllele,numberOfGenes];
			mutation = new double[numberOfAllele,numberOfAllele];
			configuration[0,0] = 0;
			mutation[0,0] = 1.0;
		}	
		public Chromosome(Gene inputGene1) // ordering inputGenes
		{
			genes = new Gene[1];
			genes[0] = inputGene1;
			numberOfGenes = genes.Length;
			doit();
		}
		public Chromosome(Gene inputGene1, 
			Gene inputGene2) // ordering inputGenes
		{
			genes = new Gene[2];
			genes[0] = inputGene1;
			genes[1] = inputGene2;
			numberOfGenes = genes.Length;
			doit();
		}
		public Chromosome(Gene inputGene1, Gene inputGene2,
			Gene inputGene3) // ordering inputGenes
		{
			genes = new Gene[3];
			genes[0] = inputGene1;
			genes[1] = inputGene2;
			genes[2] = inputGene3;
			numberOfGenes = genes.Length;
			doit();
		}
		public Chromosome(Gene inputGene1, Gene inputGene2, 
			Gene inputGene3, Gene inputGene4) // ordering inputGenes
		{
			genes = new Gene[4];
			genes[0] = inputGene1;
			genes[1] = inputGene2;
			genes[2] = inputGene3;
			genes[3] = inputGene4;
			numberOfGenes = genes.Length;
			doit();
		}
		public Chromosome(Gene[] inputGenes) // ordering inputGenes
		{
			genes = inputGenes;
			numberOfGenes = genes.Length;
			doit();
		}

		private void doit()
		{
    		for(int i = 0; i < numberOfGenes; i++) 
				numberOfAllele *= genes[i].NumberOfAllele;
			FindConfiguration();
			FindMutation();
			FindRecombination();
		}

		private void FindConfiguration() 
		{
			configuration = new int[numberOfAllele,numberOfGenes];
			int temp;
			for(int i = 0; i < numberOfAllele; i++)
			{
				temp = i;
				for(int j = numberOfGenes -1; j >= 0 ; j--)
				{
					configuration[i,j] = temp % genes[j].NumberOfAllele;
					temp -= configuration[i,j];
					temp /= genes[j].NumberOfAllele;
				}
			}
		}

		private void FindMutation() 
		{
			mutation = new double[numberOfAllele,numberOfAllele];
			for(int i = 0; i < numberOfAllele; i++)
			{
				for(int j = 0; j < numberOfAllele; j++)
				{
					mutation[i,j] = 1.0;
					for(int k = 0; k < numberOfGenes ; k++)
					{
						mutation[i,j] *= genes[k].Mutation
							[configuration[i,k],configuration[j,k]];
					}	
				}
			}
		}

			
		private double factor3 = 0.0000001;
		public double RecombinationFactor
		{
			set{factor3=value;}
		}
        private void FindRecombination()
		{
			recombination = new Double[numberOfGenes - 1];
			for(int i  = 0; i < numberOfGenes - 1; i++)
			{
				recombination[i] = factor3*(genes[i+1].StartBase - genes[i].EndBase);
			}
		}

		public int Allele(int[] geneConfiguration) 
		{
			int y = 0;
			for(int i = 0; i < numberOfGenes; i++)
			{
				y = genes[i].NumberOfAllele*y + geneConfiguration[i];
			}
			return y;
		}
	}	
}