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package org.broadinstitute.gatk.tools.walkers.haplotypecaller;

import htsjdk.samtools.SAMFileHeader;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.RandomDNA;
import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.util.*;

/**
 * Tests for {@link AssemblyResultSet}.
 *
 * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
 */
public class AssemblyResultSetUnitTest extends BaseTest
{
    private GenomeLocParser genomeLocParser;
    private SAMFileHeader header;

    @BeforeClass
    public void init() {
        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
    }


    @Test
    public void testEmptyResultSet() {
        final AssemblyResultSet subject = new AssemblyResultSet();

        Assert.assertEquals(subject.getHaplotypeList().size(), 0);
        Assert.assertEquals(subject.getHaplotypeCount(),0);
        Assert.assertEquals(subject.getReferenceHaplotype(),null);
        Assert.assertEquals(subject.getFullReferenceWithPadding(),null);
        Assert.assertEquals(subject.getPaddedReferenceLoc(),null);
        Assert.assertEquals(subject.getRegionForGenotyping(),null);
        Assert.assertEquals(subject.getUniqueReadThreadingGraph(10),null);
        Assert.assertFalse(subject.hasMultipleKmerSizes());
    }

    @Test
    public void testAddReferenceHaplotype() {

        final Haplotype ref = new Haplotype("ACGT".getBytes(),true);
        ref.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,ref.length() + 1 ));
        final AssemblyResultSet subject = new AssemblyResultSet();

        Assert.assertTrue(subject.add(ref));
        Assert.assertFalse(subject.add(ref));

        Assert.assertEquals(subject.getReferenceHaplotype(),ref);
        Assert.assertEquals(subject.getHaplotypeCount(),1);
        Assert.assertEquals(subject.getHaplotypeList().size(),1);
    }

    @Test(dataProvider="assemblyResults")
    public void testAddManyHaplotypes(final java.util.List<AssemblyResult> assemblyResults,
                                      final java.util.List<java.util.List<Haplotype>> haplotypes) {
        final AssemblyResultSet subject = new AssemblyResultSet();
        for (int i = 0; i < haplotypes.size(); i++) {
            final int haplotypeCountBefore = subject.getHaplotypeCount();
            final java.util.List<Haplotype> haplos = haplotypes.get(i);
            final AssemblyResult ar = assemblyResults.get(i);
            for (final Haplotype h : haplos) {
                Assert.assertTrue(subject.add(h, ar));
                Assert.assertFalse(subject.add(h,ar));
                if (h.isReference())
                    Assert.assertEquals(subject.getReferenceHaplotype(),h);
            }
            final int haplotypeCountAfter = subject.getHaplotypeCount();
            Assert.assertEquals(haplos.size(),haplotypeCountAfter - haplotypeCountBefore);
            Assert.assertTrue(subject.getMaximumKmerSize() >= ar.getKmerSize());
            Assert.assertTrue(subject.getMinimumKmerSize() <= ar.getKmerSize());
            Assert.assertEquals(subject.getUniqueReadThreadingGraph(ar.getKmerSize()), ar.getThreadingGraph());
        }
    }

    @Test(dataProvider="trimmingData")
    public void testTrimTo(final Map<Haplotype,AssemblyResult> haplotypesAndResultSets, final ActiveRegion original) {
        final AssemblyResultSet subject = new AssemblyResultSet();
        for (final Map.Entry<Haplotype,AssemblyResult> entry : haplotypesAndResultSets.entrySet())
            subject.add(entry.getKey(),entry.getValue());
        subject.setRegionForGenotyping(original);
        final GenomeLoc originalLocation = original.getExtendedLoc();
        final int length = originalLocation.size();
        final GenomeLoc newLocation = originalLocation.setStop(originalLocation.setStart(originalLocation,originalLocation.getStart() + length / 2),originalLocation.getStop() - length / 2);
        final ActiveRegion newRegion = original.trim(newLocation);

        final Map<Haplotype,Haplotype> originalHaplotypesByTrimmed = new HashMap<>(haplotypesAndResultSets.size());
        for (final Haplotype h : haplotypesAndResultSets.keySet())
            originalHaplotypesByTrimmed.put(h.trim(newRegion.getExtendedLoc()), h);

        final AssemblyResultSet trimmed = subject.trimTo(newRegion);

        Assert.assertFalse(subject.wasTrimmed());
        Assert.assertTrue(trimmed.wasTrimmed());

        for (final Haplotype h : trimmed.getHaplotypeList()) {
            Assert.assertEquals(h.getGenomeLocation(),newLocation);
            Assert.assertEquals(h.getBases().length,newLocation.size());
        }
    }

    @DataProvider(name="trimmingData")
    public Iterator<Object[]> trimmingData() {
        final ActiveRegion activeRegion = new ActiveRegion(genomeLocParser.createGenomeLoc("chr1",1000,1100),genomeLocParser,25);
        final int length = activeRegion.getExtendedLoc().size();
        final RandomDNA rnd = new RandomDNA(13); // keep it prepoducible by fixing the seed to lucky 13.
        final ActiveRegionTestDataSet actd = new ActiveRegionTestDataSet(10,new String(rnd.nextBases(length)),new String[] {
                "Civar:*1T*" }, new String[0], new byte[0], new byte[0], new byte[0]);

        final List<Haplotype> haplotypes = actd.haplotypeList();
        for (final Haplotype h : haplotypes)
            h.setGenomeLocation(activeRegion.getExtendedLoc());

        final ReadThreadingGraph rtg = new ReadThreadingGraph(10);
        for (final Haplotype h : haplotypes)
            rtg.addSequence("seq-" + Math.abs(h.hashCode()), h.getBases(), h.isReference());
        final SeqGraph seqGraph = rtg.convertToSequenceGraph();
        final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,seqGraph);
        ar.setThreadingGraph(rtg);
        final Map<Haplotype,AssemblyResult> result =
                new HashMap<>();
        for (final Haplotype h : haplotypes)
            result.put(h,ar);
        return Collections.singleton(new Object[] {result,activeRegion}).iterator();

    }




    @DataProvider(name="assemblyResults")
    public java.util.Iterator<Object[]> assemblyResults() {
        final int size = THREE_KS_GRAPH_AND_HAPLOTYPES.length * (1 + TEN_KS_GRAPH_AND_HAPLOTYPES.length);
        final Object[][] result = new Object[size][];

        for (int i = 0; i < THREE_KS_GRAPH_AND_HAPLOTYPES.length; i++) {
            final ReadThreadingGraph rtg = new ReadThreadingGraph((String) THREE_KS_GRAPH_AND_HAPLOTYPES[i][0]);
            final AssemblyResult ar = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,rtg.convertToSequenceGraph());
            ar.setThreadingGraph(rtg);
            final Object[] haplotypeStrings = (Object[]) THREE_KS_GRAPH_AND_HAPLOTYPES[i][1];
            final Haplotype[] haplotypes = new Haplotype[haplotypeStrings.length];
            for (int j = 0; j < haplotypeStrings.length; j++) {
                haplotypes[j] = new Haplotype(((String)haplotypeStrings[j]).getBytes(),j == 0);
                haplotypes[j].setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,haplotypes[j].length() + 1));
            }
            result[i] = new Object[] { Collections.singletonList(ar),Arrays.asList(Arrays.asList(haplotypes))};
            for (int j = 0; j < TEN_KS_GRAPH_AND_HAPLOTYPES.length; j++) {
                final ReadThreadingGraph rtg10 = new ReadThreadingGraph((String) TEN_KS_GRAPH_AND_HAPLOTYPES[j][0]);
                final AssemblyResult ar10 = new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION,rtg10.convertToSequenceGraph());
                ar10.setThreadingGraph(rtg10);
                final Object[] haplotypeStrings10 = (Object[]) TEN_KS_GRAPH_AND_HAPLOTYPES[j][1];
                final Haplotype[] haplotype10 = new Haplotype[haplotypeStrings10.length];
                for (int k = 0; k < haplotypeStrings10.length; k++) {
                    haplotype10[k] = new Haplotype(((String)haplotypeStrings10[k]).getBytes(),false);
                    haplotype10[k].setGenomeLocation(genomeLocParser.createGenomeLoc("chr1", 1, haplotype10[k].length() + 1));
                }

                result[THREE_KS_GRAPH_AND_HAPLOTYPES.length + i * TEN_KS_GRAPH_AND_HAPLOTYPES.length + j] = new Object[] { Arrays.asList(ar,ar10),
                        Arrays.asList( Arrays.asList(haplotypes), Arrays.asList(haplotype10)) };
            }
        }
        return Arrays.asList(result).iterator();
    }


    private static final Object[][] THREE_KS_GRAPH_AND_HAPLOTYPES = new Object[][] {
            {"[ks=3]{REF: ACT}",new Object[] {"ACT"}},
            {"[ks=3]{REF: ACT(3) -> T(1)      ->      G(2) -> A}" +
                    "{ (3) -> A -> G ->          (2) }" +
                    "{  (1) -> A -> G ->  (2) }",new Object[] {"ACTTGA","ACTAGGA","ACTTAGGA"}},
            {"[ks=3]{REF: ACT -> C(1) -> G}{ACT -> C(1) -> G}{ACT -> C(1) -> G}", new Object[] {"ACTCG"}} ,
            {"[ks=3]{REF: ACT -> A(1) -> G -> A(2) -> C -> G -> T }" +
                    "{A(1) -> T -> A(2) }", new Object[] {"ACTAGACGT","ACTATACGT"}}  ,
            {"[ks=3]{REF: ACT -> A -> T(2) -> C -> A -> G -> T -> A -> C -> G -> T -> A(1) -> T}" +
                    "{ ACT -> A -> T(2) -> C -> T -> A -> C -> G -> T -> A(1) -> T}",
                           new Object[] {"ACTATCAGTACGTAT","ACTATCTACGTAT"}} ,
            {"[ks=3]{REF: ACT -> A -> T    -> C -> A -> G -> T -> A -> C -> G -> T -> A    -> T}",
                           new Object[] {"ACTATCAGTACGTAT"}},
            {"[ks=3]{REF: ACT -> A -> T(1) }" +
                    "{ ACT -> A -> T(1) }", new Object[] {"ACTAT"}},
            {"[ks=3]{REF: TTT -> A(1) -> C -> T(2)}{ A(1) -> T(2) } ", new Object[] {"TTTACT","TTTAT"}}
    };

    private static final Object[][] TEN_KS_GRAPH_AND_HAPLOTYPES = new Object[][] {
            {"[ks=10]{ACTAGTAAAT -> A -> T -> A -> A -> T -> A", new Object[] {"ACTAGTAAATATAATA"}},
            {"[ks=10]{ATAGTAATAA(1) -> A -> C -> T -> A(2) -> C}{ (1) -> C -> C -> C -> A(2) -> C}",
                    new Object[] {"ATAGTAATAAACTAC","ATAGTAATAACCCAC"}},

    };

}
