using System;

namespace Science.Biology.PopulationGenetics
{
	/// <summary>
	/// MaleGenotype
	/// </summary>
	public class GenotypeMale
	{
		private int numberOfAllele = 1;
		private int[,] configuration;
		private int[,,] configurationdetail;
		private double[,] mutation; // mutation between genotypes
				
		public int NumberOfAllele
		{
			get{return numberOfAllele;}
		}
		public int[,] Configuration  // chromosomepair configuration
		{
			get{return configuration;}
		}
		public int[,,] ConfigurationDetail  // chromosomepairdetail configuration
		{
			get{return configurationdetail;}
		}
		public double[,] Mutation  // property of mutation
		{
			get{return mutation;}
		}	

		private int[] gtpart;	
		public GenotypeMale(ChromosomePair[] ac, Chromosome x, Chromosome y, Mitochondria mito, SocialGene[] socialgene)
		{
			gtpart = new int[ac.Length+1+1+1+socialgene.Length];
			for(int i = 0; i < ac.Length; i++) gtpart[i] = ac[i].NumberOfAllele;
			gtpart[ac.Length] = x.NumberOfAllele;
			gtpart[ac.Length+1] = y.NumberOfAllele;
			gtpart[ac.Length+2] = mito.NumberOfAllele;
			for(int i = 0; i < socialgene.Length; i++) gtpart[ac.Length+3+i] = socialgene[i].NumberOfAllele;
			for(int i = 0; i < gtpart.Length; i++) numberOfAllele *= gtpart[i];
			
			configuration = new int[numberOfAllele,gtpart.Length];
			int temp;
			for(int i = 0; i < numberOfAllele; i++)
			{
				temp = i;
				for(int j = gtpart.Length - 1; j >= 0 ; j--)
				{
					configuration[i,j] = temp % gtpart[j];
					temp -= configuration[i,j];
					temp /= gtpart[j];
				}
			}

			configurationdetail = new int[numberOfAllele,ac.Length,2];
			for(int i = 0; i < numberOfAllele; i++)
			{
				for(int j = 0; j < ac.Length; j++)
				{
					configurationdetail[i,j,0] = ac[j].Configuration[configuration[i,j],0];
					configurationdetail[i,j,1] = ac[j].Configuration[configuration[i,j],1];					
				}
			}

			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 < ac.Length; k++)
					{
						mutation[i,j] *= ac[k].Mutation
							[configuration[i,k],configuration[j,k]];
					}	
					mutation[i,j] *= x.Mutation[configuration[i,ac.Length],configuration[j,ac.Length]]
						*y.Mutation[configuration[i,ac.Length+1],configuration[j,ac.Length+1]]
						*mito.Mutation[configuration[i,ac.Length+2],configuration[j,ac.Length+2]];
					for(int k = 0; k < socialgene.Length; k++)
					{
						mutation[i,j] *= socialgene[k].Mutation[configuration[i,ac.Length+3+k],configuration[j,ac.Length+3+k]];
					}
				}
			}

            socialGene = socialgene;
		}

		public int Allele(int[] cpc)  // used inside
		{
			int y = 0;
			for(int i = 0; i < cpc.Length; i++)
			{
				y = gtpart[i]*y + cpc[i];
			}
			return y;
		}

        private SocialGene[] socialGene;
        public SocialGene[] SocialGenes
        {
            get { return socialGene; }
        }
	}
}