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

namespace ScienceTest.BiologyTest.PopulationGeneticsTest
{
	/// <summary>
	/// Hemophilia gene is located in chromosomeX 
	/// in non-random mating.
	/// </summary>
	public class HemoLinOpt
	{
		private string result;
		public string Result
		{
			get{return result;}
		}

		public HemoLinOpt()
		{
		}

		public void Compute() 
		{
			L.Chromosome[] Ac = new L.Chromosome[22];
			Ac[0] = new L.Chromosome();
			Ac[1] = new L.Chromosome();
			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();  

			// give hemophilia gene
			L.Gene g0 = new L.Gene();
			g0.NumberOfAllele = 2;
			g0.ChromosomeNumber = 22;
			g0.StartBase = 1200;
			g0.EndBase = 1530;
			g0.FindMutation();
			g0.From = 1;
			g0.To = 0;
			g0.ModifiedValue = 0.0;
			g0.SetMutation();

			L.Chromosome X = new L.Chromosome(g0);

			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.Mating mating = new L.Mating();
            mating.ObjectiveMating(fg,mg);

			mating.WhichFemale = 1;
			mating.WhichMale = 1;
			mating.ModifiedValue = 100.0;
			mating.SetBreedParameter();

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

			select.WhichFemale = 2;
			select.ModifiedValue = 1.0;
			select.SetDisadvantageXX();

            select.WhichMale = 1;
            select.ModifiedValue = 0.1;
            select.SetDisadvantageXY();
		
			L.PopulationEquation eq 
				= new L.PopulationEquation(mating,mut,reprod,select);

			eq.HowManyTimes  = 500000;
			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";

            foreach (double k in eq.ParentPopulation)
                result += k.ToString()+"\r\n";

			result += eq.InfantMortality();

			foreach(double k in eq.MatingFactor)
				result += Convert.ToString(k)+"\r\n";
		}
	}
}