/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ 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.assertFalse;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;

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

import org.junit.Test;

import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;

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, for the case where we have no sequence
   * cross-references, so mappings are made first-served 1-1 where sequences
   * translate.
   * 
   * @throws IOException
   */
  @Test
  public void testMapProteinToCdna_noXrefs() throws IOException
  {
    List<SequenceI> protseqs = new ArrayList<SequenceI>();
    protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
    AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
    protein.setDataset(null);

    List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
    dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
    dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
    dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
    dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
    AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
    cdna.setDataset(null);

    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));

    // 3 mappings made, each from 1 to 1 sequence
    assertEquals(3, protein.getCodonFrames().size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());

    // V12345 mapped to A22222
    AlignedCodonFrame acf = protein.getCodonFrame(
            protein.getSequenceAt(0)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
    Mapping[] protMappings = acf.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().get(0)));
    assertEquals(1, mapList.getFromRanges().size());
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges().get(0)));
    assertEquals(1, mapList.getToRanges().size());

    // V12346 mapped to A33333
    acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
            acf.getdnaSeqs()[0]);

    // V12347 mapped to A11111
    acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
            acf.getdnaSeqs()[0]);

    // no mapping involving the 'extra' A44444
    assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
  }

  /**
   * 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());
  }

  /**
   * Test the method that realigns protein to match mapped codon alignment.
   */
  @Test
  public void testAlignProteinAsDna()
  {
    // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
    SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
    // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
    SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG");
    // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13]
    SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG");
    AlignmentI dna = new Alignment(new SequenceI[]
    { dna1, dna2, dna3 });
    dna.setDataset(null);

    // protein alignment will be realigned like dna
    SequenceI prot1 = new Sequence("Seq1", "CHYQ");
    SequenceI prot2 = new Sequence("Seq2", "CHYQ");
    SequenceI prot3 = new Sequence("Seq3", "CHYQ");
    AlignmentI protein = new Alignment(new SequenceI[]
    { prot1, prot2, prot3 });
    protein.setDataset(null);

    MapList map = new MapList(new int[]
    { 1, 12 }, new int[]
    { 1, 4 }, 3, 1);
    AlignedCodonFrame acf = new AlignedCodonFrame();
    acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
    acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
    acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
    protein.setCodonFrames(Collections.singleton(acf));

    /*
     * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9]
     * [8,9,10] [10,11,12] [11,12,13]
     */
    AlignmentUtils.alignProteinAsDna(protein, dna);
    assertEquals("C-H--Y-Q-", prot1.getSequenceAsString());
    assertEquals("-C--H-Y-Q", prot2.getSequenceAsString());
    assertEquals("C--H--Y-Q", prot3.getSequenceAsString());
  }

  /**
   * Test the method that tests whether a CDNA sequence translates to a protein
   * sequence
   */
  @Test
  public void testTranslatesAs()
  {
    assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
            "FPKG".toCharArray()));
    // with start codon
    assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
            3, "FPKG".toCharArray()));
    // with stop codon1
    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
            0, "FPKG".toCharArray()));
    // with stop codon2
    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(),
            0, "FPKG".toCharArray()));
    // with stop codon3
    assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
            0, "FPKG".toCharArray()));
    // with start and stop codon1
    assertTrue(AlignmentUtils.translatesAs(
            "atgtttcccaaaggtaa".toCharArray(), 3, "FPKG".toCharArray()));
    // with start and stop codon2
    assertTrue(AlignmentUtils.translatesAs(
            "atgtttcccaaaggtag".toCharArray(), 3, "FPKG".toCharArray()));
    // with start and stop codon3
    assertTrue(AlignmentUtils.translatesAs(
            "atgtttcccaaaggtga".toCharArray(), 3, "FPKG".toCharArray()));

    // wrong protein
    assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
            0,
            "FPMG".toCharArray()));
  }

  /**
   * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
   * stop codons in addition to the protein coding sequence.
   * 
   * @throws IOException
   */
  @Test
  public void testMapProteinToCdna_withStartAndStopCodons()
          throws IOException
  {
    List<SequenceI> protseqs = new ArrayList<SequenceI>();
    protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
    AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
    protein.setDataset(null);
  
    List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
    // start + SAR:
    dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
    // = EIQ + stop
    dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
    // = start +EIQ + stop
    dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
    dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
    AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
    cdna.setDataset(null);
  
    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));

    // 3 mappings made, each from 1 to 1 sequence
    assertEquals(3, protein.getCodonFrames().size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
  
    // V12345 mapped from A22222
    AlignedCodonFrame acf = protein.getCodonFrame(
            protein.getSequenceAt(0)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
    Mapping[] protMappings = acf.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().get(0)));
    assertEquals(1, mapList.getFromRanges().size());
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges().get(0)));
    assertEquals(1, mapList.getToRanges().size());

    // V12346 mapped from A33333 starting position 4
    acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
    protMappings = acf.getProtMappings();
    assertEquals(1, protMappings.length);
    mapList = protMappings[0].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 4, 12 }, mapList.getFromRanges().get(0)));
    assertEquals(1, mapList.getFromRanges().size());
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges().get(0)));
    assertEquals(1, mapList.getToRanges().size());
  
    // V12347 mapped to A11111 starting position 4
    acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
    protMappings = acf.getProtMappings();
    assertEquals(1, protMappings.length);
    mapList = protMappings[0].getMap();
    assertEquals(3, mapList.getFromRatio());
    assertEquals(1, mapList.getToRatio());
    assertTrue(Arrays.equals(new int[]
    { 4, 12 }, mapList.getFromRanges().get(0)));
    assertEquals(1, mapList.getFromRanges().size());
    assertTrue(Arrays.equals(new int[]
    { 1, 3 }, mapList.getToRanges().get(0)));
    assertEquals(1, mapList.getToRanges().size());
  
    // no mapping involving the 'extra' A44444
    assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
  }

  /**
   * Test mapping of protein to cDNA, for the case where we have some sequence
   * cross-references. Verify that 1-to-many mappings are made where
   * cross-references exist and sequences are mappable.
   * 
   * @throws IOException
   */
  @Test
  public void testMapProteinToCdna_withXrefs() throws IOException
  {
    List<SequenceI> protseqs = new ArrayList<SequenceI>();
    protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
    AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
    protein.setDataset(null);
  
    List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
    dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
    dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
    dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
    dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
    dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ
    AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5]));
    cdna.setDataset(null);
  
    // Xref A22222 to V12345 (should get mapped)
    dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
    // Xref V12345 to A44444 (should get mapped)
    protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
    // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
    dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
    // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
    // it should get paired up with the unmapped A33333
    // A11111 should be mapped to V12347
    // A55555 is spare and has no xref so is not mapped

    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));

    // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7
    assertEquals(3, protein.getCodonFrames().size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());

    // one mapping for each of the first 4 cDNA sequences
    assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
    assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size());
    assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size());
  
    // V12345 mapped to A22222 and A44444
    AlignedCodonFrame acf = protein.getCodonFrame(
            protein.getSequenceAt(0)).get(0);
    assertEquals(2, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
    assertEquals(cdna.getSequenceAt(3).getDatasetSequence(),
            acf.getdnaSeqs()[1]);
  
    // V12346 mapped to A33333
    acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
  
    // V12347 mapped to A11111
    acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
  
    // no mapping involving the 'extra' A55555
    assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty());
  }

  /**
   * Test mapping of protein to cDNA, for the case where we have some sequence
   * cross-references. Verify that once we have made an xref mapping we don't
   * also map un-xrefd sequeces.
   * 
   * @throws IOException
   */
  @Test
  public void testMapProteinToCdna_prioritiseXrefs() throws IOException
  {
    List<SequenceI> protseqs = new ArrayList<SequenceI>();
    protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
    protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
    AlignmentI protein = new Alignment(
            protseqs.toArray(new SequenceI[protseqs.size()]));
    protein.setDataset(null);
  
    List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
    dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
    dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
    AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
            .size()]));
    cdna.setDataset(null);
  
    // Xref A22222 to V12345 (should get mapped)
    // A11111 should then be mapped to the unmapped V12346
    dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345"));
  
    assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna));
  
    // 2 protein mappings made
    assertEquals(2, protein.getCodonFrames().size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
  
    // one mapping for each of the cDNA sequences
    assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
    assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size());
  
    // V12345 mapped to A22222
    AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
            .get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
  
    // V12346 mapped to A11111
    acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
    assertEquals(1, acf.getdnaSeqs().length);
    assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
            acf.getdnaSeqs()[0]);
  }

  /**
   * Test the method that shows or hides sequence annotations by type(s) and
   * selection group.
   */
  @Test
  public void testShowOrHideSequenceAnnotations()
  {
    SequenceI seq1 = new Sequence("Seq1", "AAA");
    SequenceI seq2 = new Sequence("Seq2", "BBB");
    SequenceI seq3 = new Sequence("Seq3", "CCC");
    Annotation[] anns = new Annotation[]
    { new Annotation(2f) };
    AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
            anns);
    ann1.setSequenceRef(seq1);
    AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
            anns);
    ann2.setSequenceRef(seq2);
    AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
            anns);
    AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
    ann4.setSequenceRef(seq1);
    AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
    ann5.setSequenceRef(seq2);
    AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
    AlignmentI al = new Alignment(new SequenceI[] {seq1, seq2, seq3});
    al.addAnnotation(ann1); // Structure for Seq1
    al.addAnnotation(ann2); // Structure for Seq2
    al.addAnnotation(ann3); // Structure for no sequence
    al.addAnnotation(ann4); // Temp for seq1
    al.addAnnotation(ann5); // Temp for seq2
    al.addAnnotation(ann6); // Temp for no sequence
    List<String> types = new ArrayList<String>();
    List<SequenceI> scope = new ArrayList<SequenceI>();

    /*
     * Set all sequence related Structure to hidden (ann1, ann2)
     */
    types.add("Structure");
    AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
            false);
    assertFalse(ann1.visible);
    assertFalse(ann2.visible);
    assertTrue(ann3.visible); // not sequence-related, not affected
    assertTrue(ann4.visible); // not Structure, not affected
    assertTrue(ann5.visible); // "
    assertTrue(ann6.visible); // not sequence-related, not affected

    /*
     * Set Temp in {seq1, seq3} to hidden
     */
    types.clear();
    types.add("Temp");
    scope.add(seq1);
    scope.add(seq3);
    AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
            false);
    assertFalse(ann1.visible); // unchanged
    assertFalse(ann2.visible); // unchanged
    assertTrue(ann3.visible); // not sequence-related, not affected
    assertFalse(ann4.visible); // Temp for seq1 hidden
    assertTrue(ann5.visible); // not in scope, not affected
    assertTrue(ann6.visible); // not sequence-related, not affected

    /*
     * Set Temp in all sequences to hidden
     */
    types.clear();
    types.add("Temp");
    scope.add(seq1);
    scope.add(seq3);
    AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
            false);
    assertFalse(ann1.visible); // unchanged
    assertFalse(ann2.visible); // unchanged
    assertTrue(ann3.visible); // not sequence-related, not affected
    assertFalse(ann4.visible); // Temp for seq1 hidden
    assertFalse(ann5.visible); // Temp for seq2 hidden
    assertTrue(ann6.visible); // not sequence-related, not affected

    /*
     * Set all types in {seq1, seq3} to visible
     */
    types.clear();
    scope.clear();
    scope.add(seq1);
    scope.add(seq3);
    AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
            true);
    assertTrue(ann1.visible); // Structure for seq1 set visible
    assertFalse(ann2.visible); // not in scope, unchanged
    assertTrue(ann3.visible); // not sequence-related, not affected
    assertTrue(ann4.visible); // Temp for seq1 set visible
    assertFalse(ann5.visible); // not in scope, unchanged
    assertTrue(ann6.visible); // not sequence-related, not affected

    /*
     * Set all types in all scope to hidden
     */
    AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
            false);
    assertFalse(ann1.visible);
    assertFalse(ann2.visible);
    assertTrue(ann3.visible); // not sequence-related, not affected
    assertFalse(ann4.visible);
    assertFalse(ann5.visible);
    assertTrue(ann6.visible); // not sequence-related, not affected
  }
}