using System;
using L=Science.Biology.PopulationGenetics;

namespace ScienceTest.BiologyTest.PopulationGeneticsTest
{
	/// <summary>
	/// Two genes are located in chromosome1 and chromosome2, 
	/// respectively.
	/// </summary>
	public class EyeColor
	{
		private string result;
		public string Result
		{
			get{return result;}
		}

		public EyeColor()
		{
		}

		public void Compute() 
		{
			L.Chromosome[] Ac = new L.Chromosome[22];
		
			L.Gene g0 = new L.Gene(); 	// give gene Brown-blue
			g0.NumberOfAllele = 2;
			g0.ChromosomeNumber = 1;
			g0.StartBase = 1200;
			g0.EndBase = 1530;
			g0.FindMutation();
			g0.From = 1;
			g0.To = 0;
			g0.ModifiedValue = 0.0004;
			g0.SetMutation();
			
			Ac[0] = new L.Chromosome(g0);

			L.Gene g1 = new L.Gene();   // give gene Green-blue
			g1.NumberOfAllele = 2;
			g1.ChromosomeNumber = 2;
			g1.StartBase = 111530;
			g1.EndBase = 111860;
			g1.FindMutation();
			g1.From = 1;
			g1.To = 0;
			g1.ModifiedValue = 0.0004;
			g1.SetMutation();
			
			Ac[1] = new L.Chromosome(g1);
      
			Ac[2] = new L.Chromosome();
			Ac[3] = new L.Chromosome();
			Ac[4] = new L.Chromosome();
			Ac[5] = new L.Chromosome();
			Ac[6] = new L.Chromosome();
			Ac[7] = new L.Chromosome();
			Ac[8] = new L.Chromosome();
			Ac[9] = new L.Chromosome();
			Ac[10] = new L.Chromosome();
			Ac[11] = new L.Chromosome();
			Ac[12] = new L.Chromosome();
			Ac[13] = new L.Chromosome();
			Ac[14] = new L.Chromosome();
			Ac[15] = new L.Chromosome();
			Ac[16] = new L.Chromosome();
			Ac[17] = new L.Chromosome();
			Ac[18] = new L.Chromosome();
			Ac[19] = new L.Chromosome();
			Ac[20] = new L.Chromosome();
			Ac[21] = new L.Chromosome();  

            L.Chromosome X = new L.Chromosome();
			L.Chromosome Y = new L.Chromosome();
			L.Mitochondria mito = new L.Mitochondria();
			L.SocialGene[] sg = new L.SocialGene[1];
			sg[0] = new L.SocialGene();
			sg[0].NumberOfAllele = 1;

			L.ChromosomePair[] Cp = new L.ChromosomePair[22];
			for(int i = 0; i < 22; i++)
				Cp[i] = new L.ChromosomePair(Ac[i]);
			L.ChromosomePair XX = new L.ChromosomePair(X);

			L.GenotypeFemale fg = new L.GenotypeFemale(Cp,XX,mito,sg);
			L.GenotypeMale mg = new L.GenotypeMale(Cp,X,Y,mito,sg);

			L.PhenotypeFemale fph = new L.PhenotypeFemale(fg);
			L.PhenotypeMale mph = new L.PhenotypeMale(mg);

			fph.MapFrom = 0;
			fph.MapTo = 0;
			fph.SetMap();

			fph.MapFrom = 1;
			fph.MapTo = 0;
			fph.SetMap();

			fph.MapFrom = 2;
			fph.MapTo = 0;
			fph.SetMap();

			fph.MapFrom = 3;
			fph.MapTo = 0;
			fph.SetMap();

			fph.MapFrom = 4;
			fph.MapTo = 0;
			fph.SetMap();

			fph.MapFrom = 5;
			fph.MapTo = 0;
			fph.SetMap();

			fph.MapFrom = 6;
			fph.MapTo = 1;
			fph.SetMap();

			fph.MapFrom = 7;
			fph.MapTo = 1;
			fph.SetMap();

			fph.MapFrom = 8;
			fph.MapTo = 2;
			fph.SetMap();

			mph.MapFrom = 0;
			mph.MapTo = 0;
			mph.SetMap();

			mph.MapFrom = 1;
			mph.MapTo = 0;
			mph.SetMap();

			mph.MapFrom = 2;
			mph.MapTo = 0;
			mph.SetMap();

			mph.MapFrom = 3;
			mph.MapTo = 0;
			mph.SetMap();

			mph.MapFrom = 4;
			mph.MapTo = 0;
			mph.SetMap();

			mph.MapFrom = 5;
			mph.MapTo = 0;
			mph.SetMap();

			mph.MapFrom = 6;
			mph.MapTo = 1;
			mph.SetMap();

			mph.MapFrom = 7;
			mph.MapTo = 1;
			mph.SetMap();

			mph.MapFrom = 8;
			mph.MapTo = 2;
			mph.SetMap();

			L.Mating mating = new L.Mating();
            mating.ObjectiveMating(fph,mph); 
	
			mating.ModifiedValue = -1.0; 
			mating.WhichFemale = 0;
			mating.WhichMale = 0;
			mating.SetBreedParameter();  

			mating.ModifiedValue = -1.0; 
			mating.WhichFemale = 1;
			mating.WhichMale = 1;
			mating.SetBreedParameter();  

			mating.ModifiedValue = -1.0; 
			mating.WhichFemale = 2;
			mating.WhichMale = 2;
			mating.SetBreedParameter();   // non-random mating

			L.Mutation mut = new L.Mutation(fg,mg); 

			L.Reproduction reprod = new L.Reproduction(fg,mg);
			L.Selection select = new L.Selection(fg,mg);

			L.PopulationEquation eq = new L.PopulationEquation(mating,mut,reprod, select); // non-random mating

			eq.HowManyTimes  = 50000;
			eq.Compute();

			foreach(double k in eq.AdultFemalePopulation)
				result += Convert.ToString(k)+"\r\n";
			result += "------\r\n";
			foreach(double k in eq.AdultMalePopulation)
				result += Convert.ToString(k)+"\r\n";

			result += eq.InfantMortality();

			for(int k = 0; k < 9; k++)
			{
				for(int i = 0; i < 9; i++)
				{
					double kk = eq.MatingFactor[k,i];
					result += Convert.ToString(kk)+"\t";
				}
				result += "\r\n";
			}
		}
	}
}