package jalview.datamodel;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;

import java.io.IOException;
import java.util.Iterator;

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

/**
 * Unit tests for Alignment datamodel.
 * 
 * @author gmcarstairs
 *
 */
public class AlignmentTest
{
  // @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 TEST_DATA2 = 
          ">TEST21 test21\n" +
          "AC-GG--CUC-CAA-CT\n" +
          ">TEST22 test22\n" +
          "-CG-TTA--ACG---AAGT\n";

  private static final String TEST_DATA3 = 
          ">TEST31 test31\n" +
          "K-QY--L\n" +
          ">TEST32 test32\n" +
          "-R-FP-W-\n";

  private static final String TEST_DATA4 = 
          ">TEST41 test41\n" +
          "GCTCGUCGTACT\n" +
          ">TEST42 test42\n" +
          "GGGTCAGGCAGT\n";
  // @formatter:on

  private Alignment al;

  /*
   * Read in Stockholm format test data including secondary structure
   * annotations.
   */
  @Before
  public void setUp() throws IOException
  {
    al = new FormatAdapter().readFile(TEST_DATA,
            AppletFormatAdapter.PASTE, "STH");
    int i = 0;
    for (AlignmentAnnotation ann : al.getAlignmentAnnotation())
    {
      ann.setCalcId("CalcIdFor"
              + al.getSequenceAt(i).getName());
      i++;
    }
  }

  /**
   * Test method that returns annotations that match on calcId.
   */
  @Test
  public void testFindAnnotation_byCalcId()
  {
    Iterable<AlignmentAnnotation> anns = al
            .findAnnotation("CalcIdForD.melanogaster.2");
    Iterator<AlignmentAnnotation> iter = anns.iterator();
    assertTrue(iter.hasNext());
    AlignmentAnnotation ann = iter.next();
    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
    assertFalse(iter.hasNext());
  }

  /**
   * Tests for method that checks for alignment 'mappability'.
   * 
   * @throws IOException
   */
  @Test
  public void testIsMappableTo() throws IOException
  {
    al = new FormatAdapter().readFile(TEST_DATA2,
            AppletFormatAdapter.PASTE, "FASTA");
    al.setDataset(null);

    // not mappable to self
    assertFalse(al.isMappableTo(al));

    // dna mappable to protein and vice versa
    AlignmentI alp = new FormatAdapter().readFile(TEST_DATA3,
            AppletFormatAdapter.PASTE, "FASTA");
    alp.setDataset(null);
    assertTrue(al.isMappableTo(alp));
    assertTrue(alp.isMappableTo(al));
    assertFalse(alp.isMappableTo(alp));

    // not mappable if any sequence length mismatch
    alp.getSequenceAt(1).setSequence("-R--FP-");
    alp.getSequenceAt(1).setDatasetSequence(new Sequence("", "RFP"));
    assertFalse(alp.isMappableTo(al));
    assertFalse(al.isMappableTo(alp));

    // not mappable if number of sequences differs
    alp.deleteSequence(1);
    assertFalse(alp.isMappableTo(al));
    assertFalse(al.isMappableTo(alp));
  }

  /**
   * Tests for realigning as per a supplied alignment.
   * 
   * @throws IOException
   */
  @Test
  public void testAlignAs_dnaAsDna() throws IOException
  {
    // aligned cDNA:
    Alignment al1 = new FormatAdapter().readFile(TEST_DATA2,
            AppletFormatAdapter.PASTE, "FASTA");
    al1.setDataset(null);
    // unaligned cDNA:
    Alignment al2 = new FormatAdapter().readFile(TEST_DATA4,
            AppletFormatAdapter.PASTE, "FASTA");
    al2.setDataset(null);

    al2.alignAs(al1);
    assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0)
            .getSequenceAsString());
    assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1)
            .getSequenceAsString());
  }

  /**
   * Aligning protein from cDNA yet to be implemented.
   * 
   * @throws IOException
   */
  @Test
  public void testAlignAs_proteinAsCdna() throws IOException
  {
    // aligned cDNA:
    Alignment al1 = new FormatAdapter().readFile(TEST_DATA2,
            AppletFormatAdapter.PASTE, "FASTA");
    al1.setDataset(null);
    // unaligned cDNA:
    Alignment al2 = new FormatAdapter().readFile(TEST_DATA3,
            AppletFormatAdapter.PASTE, "FASTA");
    al2.setDataset(null);

    try
    {
      al2.alignAs(al1);
      fail("No exception thrown");
    } catch (UnsupportedOperationException e)
    {
      // expected;
    }
  }

  /**
   * Test aligning cdna as per protein alignment.
   * 
   * @throws IOException
   */
  @Test
  public void testAlignAs_cdnaAsProtein() throws IOException
  {
    // aligned cDNA:
    Alignment al1 = new FormatAdapter().readFile(TEST_DATA2,
            AppletFormatAdapter.PASTE, "FASTA");
    al1.setDataset(null);
    // unaligned cDNA:
    Alignment al2 = new FormatAdapter().readFile(TEST_DATA3,
            AppletFormatAdapter.PASTE, "FASTA");
    al2.setDataset(null);

    al1.alignAs(al2);
    assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0)
            .getSequenceAsString());
    assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
            .getSequenceAsString());
  }
}