/*
 * 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 java.util.Arrays;
import java.util.List;
import java.util.Vector;

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 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);
    AlignmentAnnotation ann2 = 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()
  {
    AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
            1f);
    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
            1f);
    AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
            1f);
    AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
            1f);
    AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
    AlignmentAnnotation ann6 = 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
     */
    SequenceFeature sf2 = new SequenceFeature();
    sq.getDatasetSequence().addSequenceFeature(sf2);
    sfs = sq.getSequenceFeatures();
    assertEquals(1, sfs.length);
    assertSame(sf, sfs[0]);

    /*
     * SequenceFeature on dataset sequence only
     */
    sq.setSequenceFeatures(null);
    sfs = sq.getSequenceFeatures();
    assertEquals(1, sfs.length);
    assertSame(sf2, sfs[0]);

    /*
     * Corrupt case - no SequenceFeature, dataset's dataset is the original
     * sequence. Test shows no infinite loop results.
     */
    sq.getDatasetSequence().setSequenceFeatures(null);
    sq.getDatasetSequence().setDatasetSequence(sq); // loop!
    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 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);

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

  /**
   * 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));
    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));
  }
}