using System;

namespace Science.Biology.PopulationGenetics
{
	/// <summary>
	/// Gene
	/// </summary>
	public class Gene
	{
		public Gene()
		{
		}

        private double[,] mutation;
        public double[,] Mutation
        {
            get { return mutation; }
        }

        private int numberOfAllele;
		public int NumberOfAllele
		{
			get{return numberOfAllele;}
            set { numberOfAllele = value; mutation = new Double[numberOfAllele, numberOfAllele]; }
		}

        private int from, to;
        private double modifiedvalue;
        public int From
        {
            set { from = value; }
        }
        public int To
        {
            set { to = value; }
        }
        public double ModifiedValue
        {
            set { modifiedvalue = value; }
        }
        public void SetMutation()  // after set
        {
            mutation[from, to] = modifiedvalue;
            double sum = 0.0;
            for (int j = 0; j < NumberOfAllele; j++)
                if (j != from) sum += mutation[from, j];
            mutation[from, from] = 1.0 - sum;
        }

        private int locus, start, end;
		public int ChromosomeNumber
		{
			get{return locus;}
			set{locus = value;}
		}
		public int StartBase
		{
            get { return start; }
    		set{start = value;}
		}
		public int EndBase
		{
            get { return end; }
			set{end = value;}
		}
        private double factor1 = 0.0000001, factor2 = 0.0001;
        public double TransitionFactor
        {
            set { factor1 = value; }
        }
        public double RecoveringFactor
        {
            set { factor2 = value; }
        }
        public void FindMutation()  // after set
        {
            double sum;           
            for (int i = 0; i < NumberOfAllele; i++)
                for (int j = i + 1; j < NumberOfAllele; j++)
                {
                    mutation[i, j] = factor1 * Convert.ToDouble(end - start);
                    mutation[j, i] = factor2;
                }
            for (int i = 0; i < NumberOfAllele; i++)
            {
                sum = 0.0;
                for (int j = 0; j < NumberOfAllele; j++)
                    if (j != i) sum += mutation[i, j];
                mutation[i, i] = 1.0 - sum;
            }
        }		
	}
}