package jalview.util;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignViewport;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;

import java.awt.Color;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.Set;

import org.junit.Test;

public class MappingUtilsTest
{
  private AlignViewportI dnaView;
  private AlignViewportI proteinView;

  /**
   * Simple test of mapping with no intron involved.
   */
  @Test
  public void testBuildSearchResults()
  {
    final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
    seq1.createDatasetSequence();

    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
    aseq1.createDatasetSequence();

    /*
     * Map dna bases 1-6 to protein residues 1-2
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();
    MapList map = new MapList(new int[]
    { 1, 6 }, new int[]
    { 1, 2 }, 3, 1);
    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
    Set<AlignedCodonFrame> acfList = Collections.singleton(acf);

    /*
     * Check protein residue 1 maps to codon 1-3, 2 to codon 4-6
     */
    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
    assertEquals(1, sr.getResults().size());
    Match m = sr.getResults().get(0);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(1, m.getStart());
    assertEquals(3, m.getEnd());
    sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
    assertEquals(1, sr.getResults().size());
    m = sr.getResults().get(0);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(4, m.getStart());
    assertEquals(6, m.getEnd());

    /*
     * Check inverse mappings, from codons 1-3, 4-6 to protein 1, 2
     */
    for (int i = 1; i < 7; i++)
    {
      sr = MappingUtils.buildSearchResults(seq1, i, acfList);
      assertEquals(1, sr.getResults().size());
      m = sr.getResults().get(0);
      assertEquals(aseq1.getDatasetSequence(), m.getSequence());
      int residue = i > 3 ? 2 : 1;
      assertEquals(residue, m.getStart());
      assertEquals(residue, m.getEnd());
    }
  }

  /**
   * Simple test of mapping with introns involved.
   */
  @Test
  public void testBuildSearchResults_withIntro()
  {
    final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
    seq1.createDatasetSequence();
  
    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
    aseq1.createDatasetSequence();
  
    /*
     * Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();
    MapList map = new MapList(new int[]
    { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 }, new int[]
    { 1, 2 }, 3, 1);
    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
    Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
  
    /*
     * Check protein residue 1 maps to [2, 4, 5]
     */
    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
    assertEquals(2, sr.getResults().size());
    Match m = sr.getResults().get(0);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(2, m.getStart());
    assertEquals(2, m.getEnd());
    m = sr.getResults().get(1);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(4, m.getStart());
    assertEquals(5, m.getEnd());

    /*
     * Check protein residue 2 maps to [7, 9, 11]
     */
    sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
    assertEquals(3, sr.getResults().size());
    m = sr.getResults().get(0);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(7, m.getStart());
    assertEquals(7, m.getEnd());
    m = sr.getResults().get(1);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(9, m.getStart());
    assertEquals(9, m.getEnd());
    m = sr.getResults().get(2);
    assertEquals(seq1.getDatasetSequence(), m.getSequence());
    assertEquals(11, m.getStart());
    assertEquals(11, m.getEnd());
  
    /*
     * Check inverse mappings, from codons to protein
     */
    for (int i = 1; i < 14; i++)
    {
      sr = MappingUtils.buildSearchResults(seq1, i, acfList);
      int residue = (i == 2 || i == 4 || i == 5) ? 1 : (i == 7 || i == 9
              || i == 11 ? 2 : 0);
      if (residue == 0)
      {
        assertEquals(0, sr.getResults().size());
        continue;
      }
      assertEquals(1, sr.getResults().size());
      m = sr.getResults().get(0);
      assertEquals(aseq1.getDatasetSequence(), m.getSequence());
      assertEquals(residue, m.getStart());
      assertEquals(residue, m.getEnd());
    }
  }

  /**
   * Test mapping a sequence group.
   * 
   * @throws IOException
   */
  @Test
  public void testMapSequenceGroup() throws IOException
  {
    /*
     * Set up dna and protein Seq1/2/3 with mappings (held on the protein
     * viewport).
     */
    AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
            "FASTA");
    cdna.setDataset(null);
    AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
            "FASTA");
    protein.setDataset(null);
    AlignedCodonFrame acf = new AlignedCodonFrame();
    MapList map = new MapList(new int[]
    { 1, 3 }, new int[]
    { 1, 1 }, 3, 1);
    for (int seq = 0; seq < 3; seq++)
    {
      acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
              .getSequenceAt(seq).getDatasetSequence(), map);
    }
    Set<AlignedCodonFrame> acfList = Collections.singleton(acf);

    AlignViewportI dnaView = new AlignViewport(cdna);
    AlignViewportI proteinView = new AlignViewport(protein);
    protein.setCodonFrames(acfList);

    /*
     * Select Seq1 and Seq3 in the protein
     */
    SequenceGroup sg = new SequenceGroup();
    sg.setColourText(true);
    sg.setIdColour(Color.GREEN);
    sg.setOutlineColour(Color.LIGHT_GRAY);
    sg.addSequence(protein.getSequenceAt(0), false);
    sg.addSequence(protein.getSequenceAt(2), false);

    /*
     * Verify the mapped sequence group in dna
     */
    SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
    assertTrue(mappedGroup.getColourText());
    assertSame(sg.getIdColour(), mappedGroup.getIdColour());
    assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
    assertEquals(2, mappedGroup.getSequences().size());
    assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
    assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));

    /*
     * Verify mapping sequence group from dna to protein
     */
    sg.clear();
    sg.addSequence(cdna.getSequenceAt(1), false);
    sg.addSequence(cdna.getSequenceAt(0), false);
    mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
    assertTrue(mappedGroup.getColourText());
    assertSame(sg.getIdColour(), mappedGroup.getIdColour());
    assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
    assertEquals(2, mappedGroup.getSequences().size());
    assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
    assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
  }

  /**
   * Helper method to load an alignment and ensure dataset sequences are set up.
   * 
   * @param data
   * @param format
   *          TODO
   * @return
   * @throws IOException
   */
  protected AlignmentI loadAlignment(final String data, String format)
          throws IOException
  {
    Alignment a = new FormatAdapter().readFile(data,
            AppletFormatAdapter.PASTE, format);
    a.setDataset(null);
    return a;
  }

  /**
   * Test mapping a column selection in protein to its dna equivalent
   * 
   * @throws IOException
   */
  @Test
  public void testMapColumnSelection_proteinToDna() throws IOException
  {
    setupMappedAlignments();
  
    ColumnSelection colsel = new ColumnSelection();

    /*
     * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
     * in dna respectively, overall 0-4
     */
    colsel.addElement(0);
    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
            proteinView, dnaView);
    assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());

    /*
     * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
     */
    colsel.clear();
    colsel.addElement(1);
    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
    assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());

    /*
     * Column 2 in protein picks up gaps only - no mapping
     */
    colsel.clear();
    colsel.addElement(2);
    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
    assertEquals("[]", cs.getSelected().toString());

    /*
     * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
     * 6-9, 6-10, 5-8 respectively, overall to 5-10
     */
    colsel.clear();
    colsel.addElement(3);
    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
    assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());

    /*
     * Combine selection of columns 1 and 3 to get a discontiguous mapped
     * selection
     */
    colsel.clear();
    colsel.addElement(1);
    colsel.addElement(3);
    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
    assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
            .toString());
  }

  /**
   * @throws IOException
   */
  protected void setupMappedAlignments() throws IOException
  {
    /*
     * Set up dna and protein Seq1/2/3 with mappings (held on the protein
     * viewport). Lower case for introns.
     */
    AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n"
            + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n",
            "FASTA");
    cdna.setDataset(null);
    AlignmentI protein = loadAlignment(
            ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n",
            "FASTA");
    protein.setDataset(null);
    AlignedCodonFrame acf = new AlignedCodonFrame();
    MapList map = new MapList(new int[]
    { 1, 3, 6, 6, 8, 9 }, new int[]
    { 1, 2 }, 3, 1);
    acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
            .getSequenceAt(0).getDatasetSequence(), map);
    map = new MapList(new int[]
    { 1, 1, 3, 4, 5, 7 }, new int[]
    { 1, 2 }, 3, 1);
    acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
            .getSequenceAt(1).getDatasetSequence(), map);
    map = new MapList(new int[]
    { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[]
    { 1, 2 }, 3, 1);
    acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
            .getSequenceAt(2).getDatasetSequence(), map);
    Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
  
    dnaView = new AlignViewport(cdna);
    proteinView = new AlignViewport(protein);
    protein.setCodonFrames(acfList);
  }

  /**
   * Test mapping a column selection in dna to its protein equivalent
   * 
   * @throws IOException
   */
  @Test
  public void testMapColumnSelection_dnaToProtein() throws IOException
  {
    setupMappedAlignments();
  
    ColumnSelection colsel = new ColumnSelection();
  
    /*
     * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
     * in protein.
     */
    colsel.addElement(0);
    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
            proteinView);
    assertEquals("[0, 1]", cs.getSelected().toString());

    /*
     * Columns 3-5 in dna map to the first residues in protein Seq1, Seq2, and
     * the first two in Seq3. Overall to columns 0, 1, 3 (col2 is all gaps).
     */
    colsel.addElement(3);
    colsel.addElement(4);
    colsel.addElement(5);
    cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
    assertEquals("[0, 1, 3]", cs.getSelected().toString());
  }

  /**
   * Tests for the method that converts a series of [start, end] ranges to
   * single positions
   */
  @Test
  public void testFlattenRanges()
  {
    assertEquals("[1, 2, 3, 4]",
            Arrays.toString(MappingUtils.flattenRanges(new int[]
            { 1, 4 })));
    assertEquals("[1, 2, 3, 4]",
            Arrays.toString(MappingUtils.flattenRanges(new int[]
            { 1, 2, 3, 4 })));
    assertEquals("[1, 2, 3, 4]",
            Arrays.toString(MappingUtils.flattenRanges(new int[]
            { 1, 1, 2, 2, 3, 3, 4, 4 })));
    assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
            Arrays.toString(MappingUtils.flattenRanges(new int[]
            { 1, 4, 7, 9, 12, 12 })));
    // unpaired start position is ignored:
    assertEquals("[1, 2, 3, 4, 7, 8, 9, 12]",
            Arrays.toString(MappingUtils.flattenRanges(new int[]
            { 1, 4, 7, 9, 12, 12, 15 })));
  }
}