using System;

namespace Science.Biology.PopulationGenetics
{
	/// <summary>
	/// SocialGene can be distinguished from ordinary genes.
	/// </summary>
	public class SocialGene
	{
		public SocialGene()
		{
		}
		private int numberOfAllele;
		private double[,] mutation;
		private double[,,] reproductionXX;
		private double[,,] reproductionXY;
		private void SetInitial()
		{
			mutation = new Double[numberOfAllele,numberOfAllele];
			reproductionXX = new Double[numberOfAllele,numberOfAllele,numberOfAllele];
			reproductionXY = new Double[numberOfAllele,numberOfAllele,numberOfAllele];
			for(int j = 0; j < NumberOfAllele; j++)	mutation[j,j] = 1.0;
            for (int j = 0; j < NumberOfAllele; j++)
                for (int jj = 0; jj < NumberOfAllele; jj++)
                    for (int jjj = 0; jjj < NumberOfAllele; jjj++)
                    {
                        reproductionXX[j, jj, jjj] = 1.0;
                        reproductionXY[j, jj, jjj] = 1.0;
                    }
	
		}		
		public int NumberOfAllele
		{
			get{return numberOfAllele;}
			set
			{
				numberOfAllele = value;
				SetInitial();
			}
		}		
		public double[,] Mutation
		{
			get{return mutation;}
		}
		public double[,,] ReproductionXX
		{
			get{return reproductionXX;}
		}
		public double[,,] ReproductionXY
		{
			get{return reproductionXY;}
		}

		private double modifiedvalue;
		public double ModifiedValue
		{
			set{modifiedvalue=value;}
		}

		private int from, to;
		public int From
		{
			set{from = value;}
		}
		public int To
		{
			set{to = 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 whichFemale, whichMale, whichFemaleBaby, whichMaleBaby;
    	public int WhichFemale
		{
			set{whichFemale = value;}
		}
		public int WhichMale
		{
			set{whichMale = value;}
		}
		public int WhichFemaleBaby
		{
			set{whichFemaleBaby = value;}
		}
		public int WhichMaleBaby
		{
			set{whichMaleBaby = value;}
		}
		public void SetReproductionXX()  // after set
		{
			reproductionXX[whichFemale,whichMale,whichFemaleBaby] = modifiedvalue;
		}
		public void SetReproductionXY()  // after set
		{
			reproductionXY[whichFemale,whichMale,whichMaleBaby] = modifiedvalue;
		}
	}
}