using System;
using System.Collections.Generic;
using System.Text;
using DNAModule.Sunweaver.Commands.Abstracts;
using DNAModule.Sunweaver.DataPrototypes;

namespace DNAModule.Sunweaver
{
    public class CoduleTranslocationMutation : AdvancedCoduleMutation
    {
        public CoduleTranslocationMutation(int minLength, int maxLength, double probability)
            : base(minLength, maxLength, probability)
        {
        }

        public CoduleTranslocationMutation()
            : base()
        {
        }

        public override void mutate(Codule c, int index1, int index2, int length)
        {
            //index 1
            if (length < 1)
            {
                length = 1;
            }
            if (index1 + length > c.BasePairs.Count)
            {
                index1 = c.BasePairs.Count - length;
            }
            if (index1 < 0)
            {
                index1 = 0;
            }
            if (index1 + length > c.BasePairs.Count)
            {
                length = c.BasePairs.Count - index1;
            }

            //index 2
            if (index2 + length > c.BasePairs.Count)
            {
                index2 = c.BasePairs.Count - length;
            }
            if (index2 < 0)
            {
                index2 = 0;
            }
            
            //mutate
            List<BasePair> temp = new List<BasePair>();

            temp.AddRange(c.BasePairs.GetRange(index1, length));
            c.BasePairs.InsertRange(index2, temp);
            c.BasePairs.RemoveRange(index1, length);
        }
    }
}