package jalview.datamodel;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;

import java.util.List;

import org.junit.Before;
import org.junit.Test;

public class SequenceTest
{
  Sequence seq;

  @Before
  public void setUp()
  {
    seq = new Sequence("FER1", "AKPNGVL");
  }
  @Test
  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
  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
  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
  public void testAddAlignmentAnnotation()
  {
    assertNull(seq.annotation);
    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
  public void testGetStartGetEnd()
  {
    SequenceI seq = new Sequence("test", "ABCDEF");
    assertEquals(1, seq.getStart());
    assertEquals(6, seq.getEnd());

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

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

  @Test
  public void testFindPosition()
  {
    SequenceI seq = new Sequence("test", "ABCDEF");
    assertEquals(1, seq.findPosition(0));
    assertEquals(6, seq.findPosition(5));
    // assertEquals(-1, seq.findPosition(6)); // fails

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

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

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

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

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