package jalview.commands;

import static org.junit.Assert.assertEquals;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

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

/**
 * Unit tests for EditCommand
 * 
 * @author gmcarstairs
 *
 */
public class EditCommandTest
{

  private EditCommand testee;

  private SequenceI[] seqs;

  private Alignment al;

  @Before
  public void setUp()
  {
    testee = new EditCommand();
    seqs = new SequenceI[4];
    seqs[0] = new Sequence("seq0", "abcdefghjk");
    seqs[1] = new Sequence("seq1", "fghjklmnopq");
    seqs[2] = new Sequence("seq2", "qrstuvwxyz");
    seqs[3] = new Sequence("seq3", "1234567890");
    al = new Alignment(seqs);
    al.setGapCharacter('?');
  }

  /**
   * Test inserting gap characters
   */
  @Test
  public void testAppendEdit_insertGap()
  {
    // set a non-standard gap character to prove it is actually used
    testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true);
    assertEquals("abcd???efghjk", seqs[0].getSequenceAsString());
    assertEquals("fghj???klmnopq", seqs[1].getSequenceAsString());
    assertEquals("qrst???uvwxyz", seqs[2].getSequenceAsString());
    assertEquals("1234???567890", seqs[3].getSequenceAsString());

    // todo: test for handling out of range positions?
  }

  /**
   * Test deleting characters from sequences. Note the deleteGap() action does
   * not check that only gap characters are being removed.
   */
  @Test
  public void testAppendEdit_deleteGap()
  {
    testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true);
    assertEquals("abcdhjk", seqs[0].getSequenceAsString());
    assertEquals("fghjnopq", seqs[1].getSequenceAsString());
    assertEquals("qrstxyz", seqs[2].getSequenceAsString());
    assertEquals("1234890", seqs[3].getSequenceAsString());
  }

  /**
   * Test a cut action. The command should store the cut characters to support
   * undo.
   */
  @Test
  public void testCut()
  {
    Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al);
    testee.cut(ec, new AlignmentI[]
    { al });
    assertEquals("abcdhjk", seqs[0].getSequenceAsString());
    assertEquals("fghjnopq", seqs[1].getSequenceAsString());
    assertEquals("qrstxyz", seqs[2].getSequenceAsString());
    assertEquals("1234890", seqs[3].getSequenceAsString());

    assertEquals("efg", new String(ec.string[0]));
    assertEquals("klm", new String(ec.string[1]));
    assertEquals("uvw", new String(ec.string[2]));
    assertEquals("567", new String(ec.string[3]));
    // TODO: case where whole sequence is deleted as nothing left; etc
  }

  /**
   * Test a Paste action, where this adds sequences to an alignment.
   */
  @Test
  @Ignore
  // TODO fix so it works
  public void testPaste_addToAlignment()
  {
    SequenceI[] newSeqs = new SequenceI[2];
    newSeqs[0] = new Sequence("newseq0", "ACEFKL");
    newSeqs[1] = new Sequence("newseq1", "JWMPDH");

    Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al);
    testee.paste(ec, new AlignmentI[]
    { al });
    assertEquals(6, al.getSequences().size());
    assertEquals("1234567890", seqs[3].getSequenceAsString());
    assertEquals("ACEFKL", seqs[4].getSequenceAsString());
    assertEquals("JWMPDH", seqs[5].getSequenceAsString());
  }

  /**
   * Test insertGap followed by undo command
   */
  @Test
  public void testUndo_insertGap()
  {
    // Edit ec = testee.new Edit(Action.INSERT_GAP, seqs, 4, 3, '?');
    testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true);
    // check something changed
    assertEquals("abcd???efghjk", seqs[0].getSequenceAsString());
    testee.undoCommand(new AlignmentI[]
    { al });
    assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
    assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
    assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
    assertEquals("1234567890", seqs[3].getSequenceAsString());
  }

  /**
   * Test deleteGap followed by undo command
   */
  @Test
  public void testUndo_deleteGap()
  {
    testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true);
    // check something changed
    assertEquals("abcdhjk", seqs[0].getSequenceAsString());
    testee.undoCommand(new AlignmentI[]
    { al });
    // deleteGap doesn't 'remember' deleted characters, only gaps get put back
    assertEquals("abcd???hjk", seqs[0].getSequenceAsString());
    assertEquals("fghj???nopq", seqs[1].getSequenceAsString());
    assertEquals("qrst???xyz", seqs[2].getSequenceAsString());
    assertEquals("1234???890", seqs[3].getSequenceAsString());
  }

  /**
   * Test several commands followed by an undo command
   */
  @Test
  public void testUndo_multipleCommands()
  {
    // delete positions 3/4/5 (counting from 1)
    testee.appendEdit(Action.DELETE_GAP, seqs, 2, 3, al, true);
    assertEquals("abfghjk", seqs[0].getSequenceAsString());
    assertEquals("1267890", seqs[3].getSequenceAsString());

    // insert 2 gaps after the second residue
    testee.appendEdit(Action.INSERT_GAP, seqs, 2, 2, al, true);
    assertEquals("ab??fghjk", seqs[0].getSequenceAsString());
    assertEquals("12??67890", seqs[3].getSequenceAsString());

    // delete positions 4/5/6
    testee.appendEdit(Action.DELETE_GAP, seqs, 3, 3, al, true);
    assertEquals("ab?hjk", seqs[0].getSequenceAsString());
    assertEquals("12?890", seqs[3].getSequenceAsString());

    // undo edit commands
    testee.undoCommand(new AlignmentI[]
    { al });
    assertEquals("ab?????hjk", seqs[0].getSequenceAsString());
    assertEquals("12?????890", seqs[3].getSequenceAsString());
  }

  /**
   * Unit test for JAL-1594 bug: click and drag sequence right to insert gaps -
   * undo did not remove them all.
   */
  @Test
  public void testUndo_multipleInsertGaps()
  {
    testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true);
    testee.appendEdit(Action.INSERT_GAP, seqs, 5, 1, al, true);
    testee.appendEdit(Action.INSERT_GAP, seqs, 6, 1, al, true);

    // undo edit commands
    testee.undoCommand(new AlignmentI[]
    { al });
    assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
    assertEquals("1234567890", seqs[3].getSequenceAsString());

  }

  /**
   * Test cut followed by undo command
   */
  @Test
  public void testUndo_cut()
  {
    testee.appendEdit(Action.CUT, seqs, 4, 3, al, true);
    // check something changed
    assertEquals("abcdhjk", seqs[0].getSequenceAsString());
    testee.undoCommand(new AlignmentI[]
    { al });
    assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
    assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
    assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
    assertEquals("1234567890", seqs[3].getSequenceAsString());
  }

  /**
   * Test the replace command (used to manually edit a sequence)
   */
  @Test
  public void testReplace()
  {
    // seem to need a dataset sequence on the edited sequence here
    seqs[1].setDatasetSequence(seqs[1]);
    new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[]
    { seqs[1] }, 4, 8, al);
    assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
    assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
    assertEquals("1234567890", seqs[3].getSequenceAsString());
    seqs[1] = new Sequence("seq1", "fghjZXYnopq");

  }
}