/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
 * Copyright (C) 2014 The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
import jalview.analysis.AlignmentUtils.MappingResult;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;

import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Map;

import org.junit.Test;

public class AlignmentUtilsTests 
{
  // @formatter:off
  private static final String TEST_DATA = 
          "# STOCKHOLM 1.0\n" +
          "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
          "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
          "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
          "D.melanogaster.1          G.AGCC.CU...AUGAUCGA\n" +
          "#=GR D.melanogaster.1 SS  ................((((\n" +
          "D.melanogaster.2          C.AUUCAACU.UAUGAGGAU\n" +
          "#=GR D.melanogaster.2 SS  ................((((\n" +
          "D.melanogaster.3          G.UGGCGCU..UAUGACGCA\n" +
          "#=GR D.melanogaster.3 SS  (.(((...(....(((((((\n" +
          "//";

  private static final String AA_SEQS_1 = 
          ">Seq1Name\n" +
          "K-QY--L\n" +
          ">Seq2Name\n" +
          "-R-FP-W-\n";

  private static final String CDNA_SEQS_1 = 
          ">Seq1Name\n" +
          "AC-GG--CUC-CAA-CT\n" +
          ">Seq2Name\n" +
          "-CG-TTA--ACG---AAGT\n";

  private static final String CDNA_SEQS_2 = 
          ">Seq1Name\n" +
          "GCTCGUCGTACT\n" +
          ">Seq2Name\n" +
          "GGGTCAGGCAGT\n";
  // @formatter:on

  public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");

  @Test
  public void testExpandFlanks()
  {
    AlignmentI al = new Alignment(new Sequence[] {});
    for (int i=4;i<14;i+=3)
    {
      SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
      al.addSequence(s1);
    }
    System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
    for (int flnk=-1;flnk<25; flnk++)
    {
      AlignmentI exp;
      System.out.println("\nFlank size: "+flnk);
      System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
      if (flnk==-1) {
        for (SequenceI sq:exp.getSequences())
      {
          String ung = sq.getSequenceAsString().replaceAll("-+", "");
          assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
      }
      }
    }
    }    

  /**
   * Test method that returns a map of lists of sequences by sequence name.
   * 
   * @throws IOException
   */
  @Test
  public void testGetSequencesByName() throws IOException
  {
    final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
            + ">Seq1Name\nABCD\n";
    AlignmentI al = loadAlignment(data, "FASTA");
    Map<String, List<SequenceI>> map = AlignmentUtils
            .getSequencesByName(al);
    assertEquals(2, map.keySet().size());
    assertEquals(2, map.get("Seq1Name").size());
    assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
    assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
    assertEquals(1, map.get("Seq2Name").size());
    assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString());
  }
  /**
   * 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 of protein to cDNA.
   * 
   * @throws IOException
   */
  @Test
  public void testMapProteinToCdna() throws IOException
  {
    // protein: Human + Mouse, 3 residues
    AlignmentI protein = loadAlignment(
            ">Human\nKQY\n>Mouse\nAFP\n>Worm\nRST\n",
            "FASTA");
    // cDNA: Mouse, Human, Mouse, 9 bases
    // @formatter:off
    String dnaData = 
            ">Mouse\nGAAATCCAG\n" + 
            ">Human\nTTCGATTAC\n" + 
            ">Mouse\nGTCGTTTGC\n" + 
            ">Mouse\nGTCGTTTGCgac\n" + // not mapped - wrong length 
            ">Fly\nGTCGTTTGC\n"; // not mapped - no name match
    // @formatter:on
    AlignmentI cdna1 = loadAlignment(
            dnaData,
            "FASTA");
    MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna1);
    assertEquals(mapped, MappingResult.Mapped);

    /*
     * Check two mappings (one for Mouse, one for Human)
     */
    assertEquals(2, protein.getCodonFrames().size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());

    /*
     * Inspect mapping for Human protein
     */
    AlignedCodonFrame humanMapping = protein.getCodonFrame(
            protein.getSequenceAt(0)).get(0);
    assertEquals(1, humanMapping.getdnaSeqs().length);
    assertEquals(cdna1.getSequenceAt(1).getDatasetSequence(),
            humanMapping.getdnaSeqs()[0]);
    Mapping[] protMappings = humanMapping.getProtMappings();
    assertEquals(1, protMappings.length);
    MapList mapList = protMappings[0].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 1, 9 }, mapList.getFromRanges()));
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges()));

    /*
     * Inspect mappings for Mouse protein
     */
    AlignedCodonFrame mouseMapping1 = protein.getCodonFrame(
            protein.getSequenceAt(1)).get(0);
    assertEquals(2, mouseMapping1.getdnaSeqs().length);
    assertEquals(cdna1.getSequenceAt(0).getDatasetSequence(),
            mouseMapping1.getdnaSeqs()[0]);
    assertEquals(cdna1.getSequenceAt(2).getDatasetSequence(),
            mouseMapping1.getdnaSeqs()[1]);
    protMappings = mouseMapping1.getProtMappings();
    assertEquals(2, protMappings.length);
    for (int i = 0; i < 2; i++)
    {
      mapList = protMappings[i].getMap();
      assertEquals(3, mapList.getFromRatio());
      assertEquals(1, mapList.getToRatio());
      assertTrue(Arrays.equals(new int[]
      { 1, 9 }, mapList.getFromRanges()));
      assertTrue(Arrays.equals(new int[]
      { 1, 3 }, mapList.getToRanges()));
    }
  }

  /**
   * Test mapping of protein to cDNA which may include start and/or stop codons.
   * 
   * @throws IOException
   */
  @Test
  public void testMapProteinToCdna_stopStartCodons() throws IOException
  {
    // protein: Human + Mouse, 3 residues
    AlignmentI protein = loadAlignment(
            ">Human\nKQY\n>Mouse\nAFP\n>Worm\nRST\n", "FASTA");
    // @formatter:off
    String dnaData = 
            ">Mouse\natgGAAATCCAG\n" + // Mouse with start codon
            ">Human\nTTCGATtactaa\n" + // Human with stop codon TAA
            ">Mouse\nGTCGTTTGctaG\n" + // Mouse with stop codon TAG 
            ">Human\nGTCGTTTgctGa\n" + // Human with stop codon TGA
            ">Mouse\nATGGTCGTTTGCtag\n"; // Mouse with start and stop codons 
    // @formatter:on
    AlignmentI cdna1 = loadAlignment(
            dnaData,
            "FASTA");
    MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna1);
    assertEquals(mapped, MappingResult.Mapped);

    /*
     * Check two mappings (one for Mouse, one for Human)
     */
    assertEquals(2, protein.getCodonFrames().size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());

    /*
     * Inspect mapping for Human protein - should map to 2nd and 4th cDNA seqs
     */
    AlignedCodonFrame humanMapping = protein.getCodonFrame(
            protein.getSequenceAt(0)).get(0);
    assertEquals(2, humanMapping.getdnaSeqs().length);
    assertEquals(cdna1.getSequenceAt(1).getDatasetSequence(),
            humanMapping.getdnaSeqs()[0]);
    assertEquals(cdna1.getSequenceAt(3).getDatasetSequence(),
            humanMapping.getdnaSeqs()[1]);
    Mapping[] protMappings = humanMapping.getProtMappings();
    // two mappings, both to cDNA with stop codon
    assertEquals(2, protMappings.length);
    MapList mapList = protMappings[0].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 1, 9 }, mapList.getFromRanges()));
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges()));
    mapList = protMappings[1].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 1, 9 }, mapList.getFromRanges()));
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges()));

    /*
     * Inspect mapping for Mouse protein - should map to 1st/3rd/5th cDNA seqs
     */
    AlignedCodonFrame mouseMapping = protein.getCodonFrame(
            protein.getSequenceAt(1)).get(0);
    assertEquals(3, mouseMapping.getdnaSeqs().length);
    assertEquals(cdna1.getSequenceAt(0).getDatasetSequence(),
            mouseMapping.getdnaSeqs()[0]);
    assertEquals(cdna1.getSequenceAt(2).getDatasetSequence(),
            mouseMapping.getdnaSeqs()[1]);
    assertEquals(cdna1.getSequenceAt(4).getDatasetSequence(),
            mouseMapping.getdnaSeqs()[2]);

    // three mappings
    protMappings = mouseMapping.getProtMappings();
    assertEquals(3, protMappings.length);

    // first mapping to cDNA with start codon
    mapList = protMappings[0].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 4, 12 }, mapList.getFromRanges()));
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges()));

    // second mapping to cDNA with stop codon
    mapList = protMappings[1].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 1, 9 }, mapList.getFromRanges()));
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges()));

    // third mapping to cDNA with start and stop codon
    mapList = protMappings[2].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 4, 12 }, mapList.getFromRanges()));
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges()));
  }

  /**
   * Test for the alignSequenceAs method that takes two sequences and a mapping.
   */
  @Test
  public void testAlignSequenceAs_withMapping_noIntrons()
  {
    MapList map = new MapList(new int[]
    { 1, 6 }, new int[]
    { 1, 2 }, 3, 1);

    /*
     * No existing gaps in dna:
     */
    checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
            "---GGG---AAA");

    /*
     * Now introduce gaps in dna but ignore them when realigning.
     */
    checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
            "---GGG---AAA");

    /*
     * Now include gaps in dna when realigning. First retaining 'mapped' gaps
     * only, i.e. those within the exon region.
     */
    checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
            "---G-G--G---A--A-A");

    /*
     * Include all gaps in dna when realigning (within and without the exon
     * region). The leading gap, and the gaps between codons, are subsumed by
     * the protein alignment gap.
     */
    checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", true, true, map,
            "---G-GG---AA-A-");

    /*
     * Include only unmapped gaps in dna when realigning (outside the exon
     * region). The leading gap, and the gaps between codons, are subsumed by
     * the protein alignment gap.
     */
    checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
            "---GGG---AAA-");
  }

  /**
   * Test for the alignSequenceAs method that takes two sequences and a mapping.
   */
  @Test
  public void testAlignSequenceAs_withMapping_withIntrons()
  {
    /*
     * Exons at codon 2 (AAA) and 4 (TTT)
     */
    MapList map = new MapList(new int[]
    { 4, 6, 10, 12 }, new int[]
    { 1, 2 }, 3, 1);

    /*
     * Simple case: no gaps in dna
     */
    checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
            "GGG---AAACCCTTTGGG");

    /*
     * Add gaps to dna - but ignore when realigning.
     */
    checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
            false, false, map, "GGG---AAACCCTTTGGG");

    /*
     * Add gaps to dna - include within exons only when realigning.
     */
    checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
            true, false, map, "GGG---A--A---ACCCT-TTGGG");

    /*
     * Include gaps outside exons only when realigning.
     */
    checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
            false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");

    /*
     * Include gaps following first intron if we are 'preserving mapped gaps'
     */
    checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
            true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");

    /*
     * Include all gaps in dna when realigning.
     */
    checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
            true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
  }

  /**
   * Test for the case where not all of the protein sequence is mapped to cDNA.
   */
  @Test
  public void testAlignSequenceAs_withMapping_withUnmappedProtein()
  {
    
    /*
     * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
     */
    final MapList map = new MapList(new int[]
    { 4, 6, 10, 12 }, new int[]
    { 1, 1, 3, 3 }, 3, 1);
    

    /*
     * Expect alignment does nothing (aborts realignment). Change this test
     * first if different behaviour wanted.
     */
    checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false,
            false, map, "GGGAAACCCTTTGGG");
  }

  /**
   * Helper method that performs and verifies the method under test.
   * 
   * @param dnaSeq
   * @param proteinSeq
   * @param preserveMappedGaps
   * @param preserveUnmappedGaps
   * @param map
   * @param expected
   */
  protected void checkAlignSequenceAs(final String dnaSeq,
          final String proteinSeq, final boolean preserveMappedGaps,
          final boolean preserveUnmappedGaps, MapList map,
          final String expected)
  {
    SequenceI dna = new Sequence("Seq1", dnaSeq);
    dna.createDatasetSequence();
    SequenceI protein = new Sequence("Seq1", proteinSeq);
    protein.createDatasetSequence();
    AlignedCodonFrame acf = new AlignedCodonFrame();
    acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);

    AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-',
            preserveMappedGaps, preserveUnmappedGaps);
    assertEquals(expected, dna.getSequenceAsString());
  }

  /**
   * Test for the alignSequenceAs method where we preserve gaps in introns only.
   */
  @Test
  public void testAlignSequenceAs_keepIntronGapsOnly()
  {

    /*
     * Intron GGGAAA followed by exon CCCTTT
     */
    MapList map = new MapList(new int[]
    { 7, 12 }, new int[]
    { 1, 2 }, 3, 1);
    
    checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL",
            false, true, map, "GG-G-AA-ACCCTTT");
  }

  /**
   * Test for the method that generates an aligned translated sequence from one
   * mapping.
   */
  @Test
  public void testGetAlignedTranslation_dnaLikeProtein()
  {
    // dna alignment will be replaced
    SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
    dna.createDatasetSequence();
    // protein alignment will be 'applied' to dna
    SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
    protein.createDatasetSequence();
    MapList map = new MapList(new int[]
    { 1, 12 }, new int[]
    { 1, 4 }, 3, 1);
    AlignedCodonFrame acf = new AlignedCodonFrame();
    acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);

    final SequenceI aligned = AlignmentUtils
                .getAlignedTranslation(protein, '-', acf);
    assertEquals("---TGCCAT---TAC------CAG---", aligned.getSequenceAsString());
    assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
  }
}