/*
 * 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.datamodel;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;

import jalview.datamodel.PDBEntry.Type;
import jalview.util.MapList;

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Vector;

import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

public class SequenceTest
{
  Sequence seq;

  @BeforeMethod(alwaysRun = true)
  public void setUp()
  {
    seq = new Sequence("FER1", "AKPNGVL");
  }

  @Test(groups = { "Functional" })
  public void testInsertGapsAndGapmaps()
  {
    SequenceI aseq = seq.deriveSequence();
    aseq.insertCharAt(2, 3, '-');
    aseq.insertCharAt(6, 3, '-');
    assertEquals("Gap insertions not correct", "AK---P---NGVL",
            aseq.getSequenceAsString());
    List<int[]> gapInt = aseq.getInsertions();
    assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
    assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
    assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
    assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
  }

  @Test(groups = ("Functional"))
  public void testIsProtein()
  {
    // test Protein
    assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
    // test DNA
    assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
    // test RNA
    SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
    assertFalse(sq.isProtein());
    // change sequence, should trigger an update of cached result
    sq.setSequence("ASDFASDFADSF");
    assertTrue(sq.isProtein());
    /*
     * in situ change of sequence doesn't change hashcode :-O
     * (sequence should not expose internal implementation)
     */
    for (int i = 0; i < sq.getSequence().length; i++)
    {
      sq.getSequence()[i] = "acgtu".charAt(i % 5);
    }
    assertTrue(sq.isProtein()); // but it isn't
  }

  @Test(groups = { "Functional" })
  public void testGetAnnotation()
  {
    // initial state returns null not an empty array
    assertNull(seq.getAnnotation());
    AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
            1f);
    AlignmentAnnotation[] anns = seq.getAnnotation();
    assertEquals(1, anns.length);
    assertSame(ann, anns[0]);

    // removing all annotations reverts array to null
    seq.removeAlignmentAnnotation(ann);
    assertNull(seq.getAnnotation());
  }

  @Test(groups = { "Functional" })
  public void testGetAnnotation_forLabel()
  {
    AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
            1f);
    addAnnotation("label2", "desc2", "calcId2", 1f);
    AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
            1f);
    AlignmentAnnotation[] anns = seq.getAnnotation("label1");
    assertEquals(2, anns.length);
    assertSame(ann1, anns[0]);
    assertSame(ann3, anns[1]);
  }

  private AlignmentAnnotation addAnnotation(String label,
          String description, String calcId, float value)
  {
    final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
            description, value);
    annotation.setCalcId(calcId);
    seq.addAlignmentAnnotation(annotation);
    return annotation;
  }

  @Test(groups = { "Functional" })
  public void testGetAlignmentAnnotations_forCalcIdAndLabel()
  {
    addAnnotation("label1", "desc1", "calcId1", 1f);
    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
            1f);
    addAnnotation("label2", "desc3", "calcId3", 1f);
    AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
            1f);
    addAnnotation("label5", "desc3", null, 1f);
    addAnnotation(null, "desc3", "calcId3", 1f);

    List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
            "label2");
    assertEquals(2, anns.size());
    assertSame(ann2, anns.get(0));
    assertSame(ann4, anns.get(1));

    assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
    assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
    assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
    assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
    assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
  }

  /**
   * Tests for addAlignmentAnnotation. Note this method has the side-effect of
   * setting the sequenceRef on the annotation. Adding the same annotation twice
   * should be ignored.
   */
  @Test(groups = { "Functional" })
  public void testAddAlignmentAnnotation()
  {
    assertNull(seq.getAnnotation());
    final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
            "b", 2d);
    assertNull(annotation.sequenceRef);
    seq.addAlignmentAnnotation(annotation);
    assertSame(seq, annotation.sequenceRef);
    AlignmentAnnotation[] anns = seq.getAnnotation();
    assertEquals(1, anns.length);
    assertSame(annotation, anns[0]);

    // re-adding does nothing
    seq.addAlignmentAnnotation(annotation);
    anns = seq.getAnnotation();
    assertEquals(1, anns.length);
    assertSame(annotation, anns[0]);

    // an identical but different annotation can be added
    final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
            "b", 2d);
    seq.addAlignmentAnnotation(annotation2);
    anns = seq.getAnnotation();
    assertEquals(2, anns.length);
    assertSame(annotation, anns[0]);
    assertSame(annotation2, anns[1]);
  }

  @Test(groups = { "Functional" })
  public void testGetStartGetEnd()
  {
    SequenceI sq = new Sequence("test", "ABCDEF");
    assertEquals(1, sq.getStart());
    assertEquals(6, sq.getEnd());

    sq = new Sequence("test", "--AB-C-DEF--");
    assertEquals(1, sq.getStart());
    assertEquals(6, sq.getEnd());

    sq = new Sequence("test", "----");
    assertEquals(1, sq.getStart());
    assertEquals(0, sq.getEnd()); // ??
  }

  /**
   * Tests for the method that returns an alignment column position (base 1) for
   * a given sequence position (base 1).
   */
  @Test(groups = { "Functional" })
  public void testFindIndex()
  {
    SequenceI sq = new Sequence("test", "ABCDEF");
    assertEquals(0, sq.findIndex(0));
    assertEquals(1, sq.findIndex(1));
    assertEquals(5, sq.findIndex(5));
    assertEquals(6, sq.findIndex(6));
    assertEquals(6, sq.findIndex(9));

    sq = new Sequence("test", "-A--B-C-D-E-F--");
    assertEquals(2, sq.findIndex(1));
    assertEquals(5, sq.findIndex(2));
    assertEquals(7, sq.findIndex(3));

    // before start returns 0
    assertEquals(0, sq.findIndex(0));
    assertEquals(0, sq.findIndex(-1));

    // beyond end returns last residue column
    assertEquals(13, sq.findIndex(99));

  }

  /**
   * Tests for the method that returns a dataset sequence position (base 1) for
   * an aligned column position (base 0).
   */
  @Test(groups = { "Functional" })
  public void testFindPosition()
  {
    SequenceI sq = new Sequence("test", "ABCDEF");
    assertEquals(1, sq.findPosition(0));
    assertEquals(6, sq.findPosition(5));
    // assertEquals(-1, seq.findPosition(6)); // fails

    sq = new Sequence("test", "AB-C-D--");
    assertEquals(1, sq.findPosition(0));
    assertEquals(2, sq.findPosition(1));
    // gap position 'finds' residue to the right (not the left as per javadoc)
    assertEquals(3, sq.findPosition(2));
    assertEquals(3, sq.findPosition(3));
    assertEquals(4, sq.findPosition(4));
    assertEquals(4, sq.findPosition(5));
    // returns 1 more than sequence length if off the end ?!?
    assertEquals(5, sq.findPosition(6));
    assertEquals(5, sq.findPosition(7));

    sq = new Sequence("test", "--AB-C-DEF--");
    assertEquals(1, sq.findPosition(0));
    assertEquals(1, sq.findPosition(1));
    assertEquals(1, sq.findPosition(2));
    assertEquals(2, sq.findPosition(3));
    assertEquals(3, sq.findPosition(4));
    assertEquals(3, sq.findPosition(5));
    assertEquals(4, sq.findPosition(6));
    assertEquals(4, sq.findPosition(7));
    assertEquals(5, sq.findPosition(8));
    assertEquals(6, sq.findPosition(9));
    assertEquals(7, sq.findPosition(10));
    assertEquals(7, sq.findPosition(11));
  }

  @Test(groups = { "Functional" })
  public void testDeleteChars()
  {
    SequenceI sq = new Sequence("test", "ABCDEF");
    assertEquals(1, sq.getStart());
    assertEquals(6, sq.getEnd());
    sq.deleteChars(2, 3);
    assertEquals("ABDEF", sq.getSequenceAsString());
    assertEquals(1, sq.getStart());
    assertEquals(5, sq.getEnd());

    sq = new Sequence("test", "ABCDEF");
    sq.deleteChars(0, 2);
    assertEquals("CDEF", sq.getSequenceAsString());
    assertEquals(3, sq.getStart());
    assertEquals(6, sq.getEnd());
  }

  @Test(groups = { "Functional" })
  public void testInsertCharAt()
  {
    // non-static methods:
    SequenceI sq = new Sequence("test", "ABCDEF");
    sq.insertCharAt(0, 'z');
    assertEquals("zABCDEF", sq.getSequenceAsString());
    sq.insertCharAt(2, 2, 'x');
    assertEquals("zAxxBCDEF", sq.getSequenceAsString());

    // for static method see StringUtilsTest
  }

  /**
   * Test the method that returns an array of aligned sequence positions where
   * the array index is the data sequence position (both base 0).
   */
  @Test(groups = { "Functional" })
  public void testGapMap()
  {
    SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
    sq.createDatasetSequence();
    assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
  }

  /**
   * Test the method that gets sequence features, either from the sequence or
   * its dataset.
   */
  @Test(groups = { "Functional" })
  public void testGetSequenceFeatures()
  {
    SequenceI sq = new Sequence("test", "GATCAT");
    sq.createDatasetSequence();

    assertNull(sq.getSequenceFeatures());

    /*
     * SequenceFeature on sequence
     */
    SequenceFeature sf = new SequenceFeature();
    sq.addSequenceFeature(sf);
    SequenceFeature[] sfs = sq.getSequenceFeatures();
    assertEquals(1, sfs.length);
    assertSame(sf, sfs[0]);

    /*
     * SequenceFeature on sequence and dataset sequence; returns that on
     * sequence
     * 
     * Note JAL-2046: spurious: we have no use case for this at the moment.
     * This test also buggy - as sf2.equals(sf), no new feature is added
     */
    SequenceFeature sf2 = new SequenceFeature();
    sq.getDatasetSequence().addSequenceFeature(sf2);
    sfs = sq.getSequenceFeatures();
    assertEquals(1, sfs.length);
    assertSame(sf, sfs[0]);

    /*
     * SequenceFeature on dataset sequence only
     * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
     */
    sq.setSequenceFeatures(null);
    assertNull(sq.getDatasetSequence().getSequenceFeatures());

    /*
     * Corrupt case - no SequenceFeature, dataset's dataset is the original
     * sequence. Test shows no infinite loop results.
     */
    sq.getDatasetSequence().setSequenceFeatures(null);
    /**
     * is there a usecase for this ? setDatasetSequence should throw an error if
     * this actually occurs.
     */
    try
    {
      sq.getDatasetSequence().setDatasetSequence(sq); // loop!
      Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
    } catch (IllegalArgumentException e)
    {
      // TODO Jalview error/exception class for raising implementation errors
      assertTrue(e.getMessage().toLowerCase()
              .contains("implementation error"));
    }
    assertNull(sq.getSequenceFeatures());
  }

  /**
   * Test the method that returns an array, indexed by sequence position, whose
   * entries are the residue positions at the sequence position (or to the right
   * if a gap)
   */
  @Test(groups = { "Functional" })
  public void testFindPositionMap()
  {
    /*
     * Note: Javadoc for findPosition says it returns the residue position to
     * the left of a gapped position; in fact it returns the position to the
     * right. Also it returns a non-existent residue position for a gap beyond
     * the sequence.
     */
    Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
    int[] map = sq.findPositionMap();
    assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
            Arrays.toString(map));
  }

  /**
   * Test for getSubsequence
   */
  @Test(groups = { "Functional" })
  public void testGetSubsequence()
  {
    SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
    sq.createDatasetSequence();

    // positions are base 0, end position is exclusive
    SequenceI subseq = sq.getSubSequence(2, 4);

    assertEquals("CD", subseq.getSequenceAsString());
    // start/end are base 1 positions
    assertEquals(3, subseq.getStart());
    assertEquals(4, subseq.getEnd());
    // subsequence shares the full dataset sequence
    assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
  }

  /**
   * test createDatasetSequence behaves to doc
   */
  @Test(groups = { "Functional" })
  public void testCreateDatasetSequence()
  {
    SequenceI sq = new Sequence("my", "ASDASD");
    assertNull(sq.getDatasetSequence());
    SequenceI rds = sq.createDatasetSequence();
    assertNotNull(rds);
    assertNull(rds.getDatasetSequence());
    assertEquals(sq.getDatasetSequence(), rds);
  }

  /**
   * Test for deriveSequence applied to a sequence with a dataset
   */
  @Test(groups = { "Functional" })
  public void testDeriveSequence_existingDataset()
  {
    Sequence sq = new Sequence("Seq1", "CD");
    sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
    sq.getDatasetSequence().addSequenceFeature(
            new SequenceFeature("", "", 1, 2, 0f, null));
    sq.setStart(3);
    sq.setEnd(4);

    sq.setDescription("Test sequence description..");
    sq.setVamsasId("TestVamsasId");
    sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));

    sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
    sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
    sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
    sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));

    sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
    sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
    sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
    sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));

    // these are the same as ones already added
    DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
    DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");

    List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
        pdb2pdb });

    sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
    sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
    sq.getDatasetSequence().addDBRef(
            new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
    sq.getDatasetSequence().addDBRef(
            new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing

    PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
    PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
    PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
            "filePath/test2");
    PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
            "filePath/test2");
    sq.getDatasetSequence().addPDBId(pdbe1a);
    sq.getDatasetSequence().addPDBId(pdbe1b);
    sq.getDatasetSequence().addPDBId(pdbe2a);
    sq.getDatasetSequence().addPDBId(pdbe2b);

    /*
     * test we added pdb entries to the dataset sequence
     */
    Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
            .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
            "PDB Entries were not found on dataset sequence.");

    /*
     * we should recover a pdb entry that is on the dataset sequence via PDBEntry
     */
    Assert.assertEquals(pdbe1a,
            sq.getDatasetSequence().getPDBEntry("1PDB"),
            "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
    ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
    System.out.println(">>>>>> " + sq.getSequenceAsString().length());
    annotsList.add(new Annotation("A", "A", 'X', 0.1f));
    annotsList.add(new Annotation("A", "A", 'X', 0.1f));
    Annotation[] annots = annotsList.toArray(new Annotation[0]);
    sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
            "Test annot description", annots));
    sq.getDatasetSequence().addAlignmentAnnotation(
            new AlignmentAnnotation("Test annot", "Test annot description",
                    annots));
    Assert.assertEquals(sq.getDescription(), "Test sequence description..");
    Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
                                                   // sequence
    Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
    Assert.assertNotNull(sq.getAnnotation());
    Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
    Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
                                                                        // as
                                                                        // sq.getDBRefs()
    Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
            4);
    Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());

    Sequence derived = (Sequence) sq.deriveSequence();

    Assert.assertEquals(derived.getDescription(),
            "Test sequence description..");
    Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
    Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
    Assert.assertNotNull(derived.getAnnotation());
    Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
    Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
    Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
            .size(), 4);
    Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());

    assertEquals("CD", derived.getSequenceAsString());
    assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());

    assertNull(sq.sequenceFeatures);
    assertNull(derived.sequenceFeatures);
    // derived sequence should access dataset sequence features
    assertNotNull(sq.getSequenceFeatures());
    assertArrayEquals(sq.getSequenceFeatures(),
            derived.getSequenceFeatures());

    /*
     *  verify we have primary db refs *just* for PDB IDs with associated
     *  PDBEntry objects
     */

    assertEquals(primRefs, sq.getPrimaryDBRefs());
    assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());

    assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());

  }

  /**
   * Test for deriveSequence applied to an ungapped sequence with no dataset
   */
  @Test(groups = { "Functional" })
  public void testDeriveSequence_noDatasetUngapped()
  {
    SequenceI sq = new Sequence("Seq1", "ABCDEF");
    assertEquals(1, sq.getStart());
    assertEquals(6, sq.getEnd());
    SequenceI derived = sq.deriveSequence();
    assertEquals("ABCDEF", derived.getSequenceAsString());
    assertEquals("ABCDEF", derived.getDatasetSequence()
            .getSequenceAsString());
  }

  /**
   * Test for deriveSequence applied to a gapped sequence with no dataset
   */
  @Test(groups = { "Functional" })
  public void testDeriveSequence_noDatasetGapped()
  {
    SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
    assertEquals(1, sq.getStart());
    assertEquals(6, sq.getEnd());
    assertNull(sq.getDatasetSequence());
    SequenceI derived = sq.deriveSequence();
    assertEquals("AB-C.D EF", derived.getSequenceAsString());
    assertEquals("ABCDEF", derived.getDatasetSequence()
            .getSequenceAsString());
  }

  @Test(groups = { "Functional" })
  public void testCopyConstructor_noDataset()
  {
    SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
    seq1.setDescription("description");
    seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
            1.3d));
    seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
            12.4f, "group"));
    seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
    seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));

    SequenceI copy = new Sequence(seq1);

    assertNull(copy.getDatasetSequence());

    verifyCopiedSequence(seq1, copy);

    // copy has a copy of the DBRefEntry
    // this is murky - DBrefs are only copied for dataset sequences
    // where the test for 'dataset sequence' is 'dataset is null'
    // but that doesn't distinguish it from an aligned sequence
    // which has not yet generated a dataset sequence
    // NB getDBRef looks inside dataset sequence if not null
    DBRefEntry[] dbrefs = copy.getDBRefs();
    assertEquals(1, dbrefs.length);
    assertFalse(dbrefs[0] == seq1.getDBRefs()[0]);
    assertTrue(dbrefs[0].equals(seq1.getDBRefs()[0]));
  }

  @Test(groups = { "Functional" })
  public void testCopyConstructor_withDataset()
  {
    SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
    seq1.createDatasetSequence();
    seq1.setDescription("description");
    seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
            1.3d));
    // JAL-2046 - what is the contract for using a derived sequence's
    // addSequenceFeature ?
    seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
            12.4f, "group"));
    seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
    // here we add DBRef to the dataset sequence:
    seq1.getDatasetSequence().addDBRef(
            new DBRefEntry("EMBL", "1.2", "AZ12345"));

    SequenceI copy = new Sequence(seq1);

    assertNotNull(copy.getDatasetSequence());
    assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());

    verifyCopiedSequence(seq1, copy);

    // getDBRef looks inside dataset sequence and this is shared,
    // so holds the same dbref objects
    DBRefEntry[] dbrefs = copy.getDBRefs();
    assertEquals(1, dbrefs.length);
    assertSame(dbrefs[0], seq1.getDBRefs()[0]);
  }

  /**
   * Helper to make assertions about a copied sequence
   * 
   * @param seq1
   * @param copy
   */
  protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
  {
    // verify basic properties:
    assertEquals(copy.getName(), seq1.getName());
    assertEquals(copy.getDescription(), seq1.getDescription());
    assertEquals(copy.getStart(), seq1.getStart());
    assertEquals(copy.getEnd(), seq1.getEnd());
    assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());

    // copy has a copy of the annotation:
    AlignmentAnnotation[] anns = copy.getAnnotation();
    assertEquals(1, anns.length);
    assertFalse(anns[0] == seq1.getAnnotation()[0]);
    assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
    assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
    assertEquals(anns[0].score, seq1.getAnnotation()[0].score);

    // copy has a copy of the sequence feature:
    SequenceFeature[] sfs = copy.getSequenceFeatures();
    assertEquals(1, sfs.length);
    if (seq1.getDatasetSequence() != null
            && copy.getDatasetSequence() == seq1.getDatasetSequence())
    {
      assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
    }
    else
    {
      assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
    }
    assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));

    // copy has a copy of the PDB entry
    Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
    assertEquals(1, pdbs.size());
    assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
    assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
  }

  @Test(groups = "Functional")
  public void testGetCharAt()
  {
    SequenceI sq = new Sequence("", "abcde");
    assertEquals('a', sq.getCharAt(0));
    assertEquals('e', sq.getCharAt(4));
    assertEquals(' ', sq.getCharAt(5));
    assertEquals(' ', sq.getCharAt(-1));
  }

  /**
   * Tests for adding (or updating) dbrefs
   * 
   * @see DBRefEntry#updateFrom(DBRefEntry)
   */
  @Test(groups = { "Functional" })
  public void testAddDBRef()
  {
    SequenceI sq = new Sequence("", "abcde");
    assertNull(sq.getDBRefs());
    DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
    sq.addDBRef(dbref);
    assertEquals(1, sq.getDBRefs().length);
    assertSame(dbref, sq.getDBRefs()[0]);

    /*
     * change of version - new entry
     */
    DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
    sq.addDBRef(dbref2);
    assertEquals(2, sq.getDBRefs().length);
    assertSame(dbref, sq.getDBRefs()[0]);
    assertSame(dbref2, sq.getDBRefs()[1]);

    /*
     * matches existing entry - not added
     */
    sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
    assertEquals(2, sq.getDBRefs().length);

    /*
     * different source = new entry
     */
    DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
    sq.addDBRef(dbref3);
    assertEquals(3, sq.getDBRefs().length);
    assertSame(dbref3, sq.getDBRefs()[2]);

    /*
     * different ref = new entry
     */
    DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
    sq.addDBRef(dbref4);
    assertEquals(4, sq.getDBRefs().length);
    assertSame(dbref4, sq.getDBRefs()[3]);

    /*
     * matching ref with a mapping - map updated
     */
    DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
    Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
        1, 1 }, 3, 1));
    dbref5.setMap(map);
    sq.addDBRef(dbref5);
    assertEquals(4, sq.getDBRefs().length);
    assertSame(dbref4, sq.getDBRefs()[3]);
    assertSame(map, dbref4.getMap());

    /*
     * 'real' version replaces "0" version
     */
    dbref2.setVersion("0");
    DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
            dbref2.getAccessionId());
    sq.addDBRef(dbref6);
    assertEquals(4, sq.getDBRefs().length);
    assertSame(dbref2, sq.getDBRefs()[1]);
    assertEquals("3", dbref2.getVersion());

    /*
     * 'real' version replaces "source:0" version
     */
    dbref3.setVersion("Uniprot:0");
    DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
            dbref3.getAccessionId());
    sq.addDBRef(dbref7);
    assertEquals(4, sq.getDBRefs().length);
    assertSame(dbref3, sq.getDBRefs()[2]);
    assertEquals("3", dbref2.getVersion());
  }

  @Test(groups = { "Functional" })
  public void testGetPrimaryDBRefs_peptide()
  {
    SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);

    // no dbrefs
    List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
    assertTrue(primaryDBRefs.isEmpty());

    // empty dbrefs
    sq.setDBRefs(new DBRefEntry[] {});
    primaryDBRefs = sq.getPrimaryDBRefs();
    assertTrue(primaryDBRefs.isEmpty());

    // primary - uniprot
    DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
    sq.addDBRef(upentry1);

    // primary - uniprot with congruent map
    DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
    upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
            new int[] { 10, 22 }, 1, 1)));
    sq.addDBRef(upentry2);

    // primary - uniprot with map of enclosing sequence
    DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
    upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
            new int[] { 8, 24 }, 1, 1)));
    sq.addDBRef(upentry3);

    // not primary - uniprot with map of sub-sequence (5')
    DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
    upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
            new int[] { 10, 18 }, 1, 1)));
    sq.addDBRef(upentry4);

    // not primary - uniprot with map that overlaps 3'
    DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
    upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
            new int[] { 12, 22 }, 1, 1)));
    sq.addDBRef(upentry5);

    // not primary - uniprot with map to different coordinates frame
    DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
    upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
            new int[] { 112, 118 }, 1, 1)));
    sq.addDBRef(upentry6);

    // not primary - dbref to 'non-core' database
    DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
    sq.addDBRef(upentry7);

    // primary - type is PDB
    DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
    sq.addDBRef(pdbentry);

    // not primary - PDBEntry has no file
    sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));

    // not primary - no PDBEntry
    sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));

    // add corroborating PDB entry for primary DBref -
    // needs to have a file as well as matching ID
    // note PDB ID is not treated as case sensitive
    sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
            .toString()));

    // not valid DBRef - no file..
    sq.addPDBId(new PDBEntry("1AAA", null, null, null));

    primaryDBRefs = sq.getPrimaryDBRefs();
    assertEquals(4, primaryDBRefs.size());
    assertTrue("Couldn't find simple primary reference (UNIPROT)",
            primaryDBRefs.contains(upentry1));
    assertTrue("Couldn't find mapped primary reference (UNIPROT)",
            primaryDBRefs.contains(upentry2));
    assertTrue("Couldn't find mapped context reference (UNIPROT)",
            primaryDBRefs.contains(upentry3));
    assertTrue("Couldn't find expected PDB primary reference",
            primaryDBRefs.contains(pdbentry));
  }

  @Test(groups = { "Functional" })
  public void testGetPrimaryDBRefs_nucleotide()
  {
    SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);

    // primary - Ensembl
    DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
    sq.addDBRef(dbr1);

    // not primary - Ensembl 'transcript' mapping of sub-sequence
    DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
    dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
            new int[] { 1, 11 }, 1, 1)));
    sq.addDBRef(dbr2);

    // primary - EMBL with congruent map
    DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
    dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
            new int[] { 10, 34 }, 1, 1)));
    sq.addDBRef(dbr3);

    // not primary - to non-core database
    DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
    sq.addDBRef(dbr4);

    // not primary - to protein
    DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
    sq.addDBRef(dbr5);

    List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
    assertEquals(2, primaryDBRefs.size());
    assertTrue(primaryDBRefs.contains(dbr1));
    assertTrue(primaryDBRefs.contains(dbr3));
  }

  /**
   * Test the method that updates the list of PDBEntry from any new DBRefEntry
   * for PDB
   */
  @Test(groups = { "Functional" })
  public void testUpdatePDBIds()
  {
    PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
    seq.addPDBId(pdbe1);
    seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
    seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
    seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
    seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
    // 7 is not a valid chain code:
    seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));

    seq.updatePDBIds();
    List<PDBEntry> pdbIds = seq.getAllPDBEntries();
    assertEquals(4, pdbIds.size());
    assertSame(pdbe1, pdbIds.get(0));
    // chain code got added to 3A6S:
    assertEquals("B", pdbe1.getChainCode());
    assertEquals("1A70", pdbIds.get(1).getId());
    // 4BQGA is parsed into id + chain
    assertEquals("4BQG", pdbIds.get(2).getId());
    assertEquals("a", pdbIds.get(2).getChainCode());
    assertEquals("2GIS7", pdbIds.get(3).getId());
    assertNull(pdbIds.get(3).getChainCode());
  }

  /**
   * Test the method that either adds a pdbid or updates an existing one
   */
  @Test(groups = { "Functional" })
  public void testAddPDBId()
  {
    PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
    seq.addPDBId(pdbe);
    assertEquals(1, seq.getAllPDBEntries().size());
    assertSame(pdbe, seq.getPDBEntry("3A6S"));
    assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive

    // add the same entry
    seq.addPDBId(pdbe);
    assertEquals(1, seq.getAllPDBEntries().size());
    assertSame(pdbe, seq.getPDBEntry("3A6S"));

    // add an identical entry
    seq.addPDBId(new PDBEntry("3A6S", null, null, null));
    assertEquals(1, seq.getAllPDBEntries().size());
    assertSame(pdbe, seq.getPDBEntry("3A6S"));

    // add a different entry
    PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
    seq.addPDBId(pdbe2);
    assertEquals(2, seq.getAllPDBEntries().size());
    assertSame(pdbe, seq.getAllPDBEntries().get(0));
    assertSame(pdbe2, seq.getAllPDBEntries().get(1));

    // update pdbe with chain code, file, type
    PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
    seq.addPDBId(pdbe3);
    assertEquals(2, seq.getAllPDBEntries().size());
    assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
    assertEquals("3A6S", pdbe.getId()); // unchanged
    assertEquals("A", pdbe.getChainCode()); // updated
    assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
    assertEquals("filepath", pdbe.getFile()); // updated
    assertSame(pdbe2, seq.getAllPDBEntries().get(1));

    // add with a different file path
    PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
    seq.addPDBId(pdbe4);
    assertEquals(3, seq.getAllPDBEntries().size());
    assertSame(pdbe4, seq.getAllPDBEntries().get(2));

    // add with a different chain code
    PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
    seq.addPDBId(pdbe5);
    assertEquals(4, seq.getAllPDBEntries().size());
    assertSame(pdbe5, seq.getAllPDBEntries().get(3));
  }

  @Test(
    groups = { "Functional" },
    expectedExceptions = { IllegalArgumentException.class })
  public void testSetDatasetSequence_toSelf()
  {
    seq.setDatasetSequence(seq);
  }

  @Test(
    groups = { "Functional" },
    expectedExceptions = { IllegalArgumentException.class })
  public void testSetDatasetSequence_cascading()
  {
    SequenceI seq2 = new Sequence("Seq2", "xyz");
    seq2.createDatasetSequence();
    seq.setDatasetSequence(seq2);
  }
}