using System.Collections.Generic;

using System.Linq;

using Phantom.PositionCollections;

using Xunit;



namespace UnitTests.Phantom.PositionCollections

{

    public sealed class AlleleBlockTests

    {



        [Fact]

        public void GetPloidyFromGenotypes_DotIsIgnored()

        {

            var genotypes = new[] { Genotype.GetGenotype("."), Genotype.GetGenotype("1|2"), Genotype.GetGenotype("0/2") };

            var ploidy = AlleleBlock.GetMaxPloidy(genotypes);

            Assert.Equal(2, ploidy);

        }



        [Fact]

        public void GetAlleleBlockToSampleHaplotype_AsExpected()

        {

            var genotypeBlock1 = new GenotypeBlock(new[] { "1|2", "1/1", "0|1", "./1" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock2 = new GenotypeBlock(new[] { "0/1", "0|0", "1|1", "1|1" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock3 = new GenotypeBlock(new[] { "0|1", "1|1", "0/0" }.Select(Genotype.GetGenotype).ToArray(), 1);

            var genotypeToSample =

                new Dictionary<GenotypeBlock, List<int>>

                {

                    {genotypeBlock1, new List<int> {0, 1}},

                    {genotypeBlock2, new List<int> {2}},

                    {genotypeBlock3, new List<int> {3}}

                };

            var indexOfUnsupportedVars = Enumerable.Repeat(new HashSet<int>(), 4).ToArray();

            var starts = Enumerable.Range(100, 4).ToArray();

            var functionBlockRanges = starts.Select(x => x + 2).ToList();





            var alleleBlockToSampleHaplotype = AlleleBlock.GetAlleleBlockToSampleHaplotype(genotypeToSample,

                indexOfUnsupportedVars, starts, functionBlockRanges, out _);

            var expectedBlock1 = new AlleleBlock(0, new[] { 1, 1, 0 }, 0, 0);

            var expectedBlock2 = new AlleleBlock(0, new[] { 2, 1, 1 }, 0, 0);

            var expectedBlock3 = new AlleleBlock(2, new[] { 1, 1 }, 1, 0);

            var expectedBlock4 = new AlleleBlock(1, new[] { 1, 1 }, 0, 1);

            var expectedBlock5 = new AlleleBlock(1, new[] { 0, 1 }, 0, 1);



            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock1));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock1]

                .SequenceEqual(new[] { new SampleHaplotype(0, 0), new SampleHaplotype(1, 0) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock2));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock2]

                .SequenceEqual(new[] { new SampleHaplotype(0, 1), new SampleHaplotype(1, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock3));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock3]

                .SequenceEqual(new[] { new SampleHaplotype(2, 0), new SampleHaplotype(2, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock4));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock4].SequenceEqual(new[] { new SampleHaplotype(3, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock5));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock5].SequenceEqual(new[] { new SampleHaplotype(3, 0) }));

        }





        [Fact]

        public void GetAlleleBlockToSampleHaplotype_AlleleBlock_WithInternalRefPositions_SplitIfOutOfRange()

        {

            var genotypeBlock1 = new GenotypeBlock(new[] { "1|2", "0/0", "0|0", "1/1" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock2 = new GenotypeBlock(new[] { "1/1", "0|0", "1|1" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock3 = new GenotypeBlock(new[] { "1|2", "0|0", "1|1" }.Select(Genotype.GetGenotype).ToArray(), 1);

            var genotypeToSample =

                new Dictionary<GenotypeBlock, List<int>>

                {

                    {genotypeBlock1, new List<int> {0}},

                    {genotypeBlock2, new List<int> {1}},

                    {genotypeBlock3, new List<int> {2}}

                };

            var indexOfUnsupportedVars = Enumerable.Repeat(new HashSet<int>(), genotypeBlock1.Genotypes.Length).ToArray();



            var starts = new[] { 100, 102, 103, 104 };

            var functionBlockRanges = starts.Select(x => x + 2).ToList();



            var alleleBlockToSampleHaplotype = AlleleBlock.GetAlleleBlockToSampleHaplotype(genotypeToSample,

                indexOfUnsupportedVars, starts, functionBlockRanges, out _);

            var expectedBlock1 = new AlleleBlock(1, new[] { 1, 0, 1 }, 0, 0);

            var expectedBlock2 = new AlleleBlock(1, new[] { 2, 0, 1 }, 0, 0);



            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock1));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock1].SequenceEqual(new[] { new SampleHaplotype(2, 0) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock2));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock2].SequenceEqual(new[] { new SampleHaplotype(2, 1) }));

        }



        [Fact]

        public void GetAlleleBlockToSampleHaplotype_AlleleBlock_OneAlleleIsRef_EachTime()

        {

            var genotypeBlock1 = new GenotypeBlock(new[] { "1|0", "0|1", "1|0", "0|1" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock2 = new GenotypeBlock(new[] { "1/1", "0|1", "1|0" }.Select(Genotype.GetGenotype).ToArray(), 1);

            var genotypeBlock3 = new GenotypeBlock(new[] { "0|0", "1|0", "0|1", "0|0" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock4 = new GenotypeBlock(new[] { "0|1", "1|0", "1|0" }.Select(Genotype.GetGenotype).ToArray());



            var genotypeToSample =

                new Dictionary<GenotypeBlock, List<int>>

                {

                    {genotypeBlock1, new List<int> {0}},

                    {genotypeBlock2, new List<int> {1}},

                    {genotypeBlock3, new List<int> {2}},

                    {genotypeBlock4, new List<int> {3}}

                };

            var indexOfUnsupportedVars = Enumerable.Repeat(new HashSet<int>(), genotypeBlock1.Genotypes.Length).ToArray();



            var starts = new[] { 100, 101, 102, 104 };

            var functionBlockRanges = starts.Select(x => x + 2).ToList();



            var alleleBlockToSampleHaplotype = AlleleBlock.GetAlleleBlockToSampleHaplotype(genotypeToSample,

                indexOfUnsupportedVars, starts, functionBlockRanges, out _);

            var expectedBlock1 = new AlleleBlock(0, new[] { 1, 0, 1 }, 0, 0);

            var expectedBlock2 = new AlleleBlock(0, new[] { 0, 1, 0 }, 0, 0);

            var expectedBlock3 = new AlleleBlock(1, new[] { 1, 0 }, 0, 0);

            var expectedBlock4 = new AlleleBlock(1, new[] { 1, 1 }, 0, 0);

            var expectedBlock5 = new AlleleBlock(1, new[] { 0, 0 }, 0, 0);



            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock1));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock1].SequenceEqual(new[] { new SampleHaplotype(0, 0) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock2));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock2].SequenceEqual(new[] { new SampleHaplotype(0, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock3));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock3].SequenceEqual(new[] { new SampleHaplotype(1, 0) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock4));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock4].SequenceEqual(new[] { new SampleHaplotype(1, 1), new SampleHaplotype(3, 0) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock5));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock5].SequenceEqual(new[] { new SampleHaplotype(3, 1) }));

        }



        [Fact]

        public void GetAlleleBlockToSampleHaplotype_AwareOfTrimmedRefPositions()

        {

            var genotypeBlock1 = new GenotypeBlock(new[] { "0|0", "1|1", "1|1", "0|0" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock2 = new GenotypeBlock(new[] { "0|0", "1|1", "1|1" }.Select(Genotype.GetGenotype).ToArray());

            var genotypeBlock3 = new GenotypeBlock(new[] { "1|1", "1|1", "0|0" }.Select(Genotype.GetGenotype).ToArray(), 1);

            var genotypeBlock4 = new GenotypeBlock(new[] { "1|1", "1|1" }.Select(Genotype.GetGenotype).ToArray(), 1);

            var genotypeToSample =

                new Dictionary<GenotypeBlock, List<int>>

                {

                    {genotypeBlock1, new List<int> {0}},

                    {genotypeBlock2, new List<int> {1}},

                    {genotypeBlock3, new List<int> {2}},

                    {genotypeBlock4, new List<int> {3}}

                };

            var indexOfUnsupportedVars = Enumerable.Repeat(new HashSet<int>(), 4).ToArray();

            var starts = Enumerable.Range(100, 4).ToArray();

            var functionBlockRanges = starts.Select(x => x + 2).ToList();





            var alleleBlockToSampleHaplotype = AlleleBlock.GetAlleleBlockToSampleHaplotype(genotypeToSample,

                indexOfUnsupportedVars, starts, functionBlockRanges, out _);

            var expectedBlock1 = new AlleleBlock(1, new[] { 1, 1 }, 1, 1);

            var expectedBlock2 = new AlleleBlock(1, new[] { 1, 1 }, 1, 0);

            var expectedBlock3 = new AlleleBlock(1, new[] { 1, 1 }, 0, 1);

            var expectedBlock4 = new AlleleBlock(1, new[] { 1, 1 }, 0, 0);



            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock1));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock1]

                .SequenceEqual(new[] { new SampleHaplotype(0, 0), new SampleHaplotype(0, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock2));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock2]

                .SequenceEqual(new[] { new SampleHaplotype(1, 0), new SampleHaplotype(1, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock3));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock3]

                .SequenceEqual(new[] { new SampleHaplotype(2, 0), new SampleHaplotype(2, 1) }));

            Assert.True(alleleBlockToSampleHaplotype.ContainsKey(expectedBlock4));

            Assert.True(alleleBlockToSampleHaplotype[expectedBlock4]

                .SequenceEqual(new[] { new SampleHaplotype(3, 0), new SampleHaplotype(3, 1) }));

        }

    }

}