using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;

namespace Sunweaver.Mutations
{
    /// <summary>
    /// Functions to mutate a codule or chromosome.  Mutation types are:
    /// Point - Change a single BasePair to another BasePair
    /// Insertion - Insert a stream of new BasePairs in to the middle of a stream of BasePairs.
    /// Deletion - Delete a sequence of BasePairs in the middle of a stream of BasePairs.
    /// Reversal - Reverse a sequence of BasePairs in the middle of a stream of BasePairs.
    /// </summary>
    public static class Mutator
    {
        public static void PointMutation(ref Codule codule, BasePair mutateTo, int bpIndex)
        {
            if(bpIndex < 0 || bpIndex >= codule.BasePairs.Count)
            {
                throw new Exception("Point mutation index is out of range of the codule's base pairs.");
            }

            codule.BasePairs[bpIndex] = mutateTo;
        }

        public static void InsertionMutation(ref Codule codule, IEnumerable<BasePair> insertDNA, int bpIndex)
        {
            // bpIndex is the index before which to insert insertDNA.
            if (bpIndex < 0 || bpIndex > codule.BasePairs.Count)
            {
                throw new Exception("Point mutation index is out of range of the codule's base pairs.");
            }

            codule.BasePairs.InsertRange(bpIndex, insertDNA);
        }

        public static void DeletionMutation(ref Codule codule, int bpStartIndex, int bpCount)
        {
            if (bpStartIndex < 0 || bpStartIndex >= codule.BasePairs.Count)
            {
                throw new Exception("Point mutation index is out of range of the codule's base pairs.");
            }

            if (bpStartIndex + bpCount > codule.BasePairs.Count)
            {
                throw new Exception("Point mutation index is out of range of the codule's base pairs.");
            }

            codule.BasePairs.RemoveRange(bpStartIndex, bpCount);
        }

        public static void ReversalMutation(ref Codule codule, int bpStartIndex, int bpCount)
        {
            if (bpStartIndex < 0 || bpStartIndex >= codule.BasePairs.Count)
            {
                throw new Exception("Point mutation index is out of range of the codule's base pairs.");
            }

            if (bpStartIndex + bpCount > codule.BasePairs.Count)
            {
                throw new Exception("Point mutation index is out of range of the codule's base pairs.");
            }

            codule.BasePairs.Reverse(bpStartIndex, bpCount);
        }

        public static void MoveMutation(ref Codule codule, int exciseLocation, int length, int insertionLocation)
        {
            if (exciseLocation < 0 || exciseLocation >= codule.BasePairs.Count)
            {
                throw new Exception("Translocation mutation index is out of range of the codule's base pairs.");
            }

            if (length < 0 || exciseLocation + length > codule.BasePairs.Count)
            {
                throw new Exception("Translocation mutation's length is part the end of the codule.");
            }

            if (insertionLocation < 0 || insertionLocation > codule.BasePairs.Count - length)
            {
                throw new Exception("Translocation mutation's insertionLocation is outside a valid range.");
            }

            var excised = codule.BasePairs.GetRange(exciseLocation, length);
            codule.BasePairs.RemoveRange(exciseLocation, length);

            codule.BasePairs.InsertRange(insertionLocation, excised);
        }




        public static void InsertionMutation(ref Chromosome chromosome, IList<BasePair> insertDNA, int bpIndex)
        {
            if (bpIndex < 0 || bpIndex >= chromosome.TotalBasePairs)
            {
                throw new Exception("Insertion mutation index is out of range of the chromosome's base pairs.");
            }

            for (int i = 0; i < chromosome.Codules.Values.Count; ++i)
            {
                var codule = chromosome.Codules.Values.ElementAt(i);

                if (bpIndex < codule.BasePairs.Count)
                {
                    InsertionMutation(ref codule, insertDNA, bpIndex);
                    return;
                }
                else
                {
                    bpIndex -= codule.BasePairs.Count;
                }
            }
        }


        public static void PointMutation(ref Chromosome chromosome, BasePair mutateTo, int bpIndex)
        {
            if (bpIndex < 0 || bpIndex >= chromosome.TotalBasePairs)
            {
                throw new Exception("Point mutation index is out of range of the chromosome's base pairs.");
            }

            for (int i = 0; i < chromosome.Codules.Values.Count; ++i)
            {
                var codule = chromosome.Codules.Values.ElementAt(i);

                if (bpIndex < codule.BasePairs.Count)
                {
                    PointMutation(ref codule, mutateTo, bpIndex);
                    return;
                }
                else
                {
                    bpIndex -= codule.BasePairs.Count;
                }
            }
        }

        public static void PointMutation(ref Chromosome chromosome, Func<int, int> getRandomIndex = null)
        {
            PointMutation(ref chromosome,
                DNASystem.RandomBasePair(getRandomIndex ?? DNASystem.rand.Next),
                getRandomIndex(chromosome.TotalBasePairs));
        }
    }
}