package jalview.datamodel;

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

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" +
          "//";
  // @formatter:on


  private Alignment al;

  /*
   * Read in Stockholm format test data including secondary structure
   * annotations.
   */
  @Before
  public void setUp() throws IOException
  {
    al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
            AppletFormatAdapter.PASTE, "STH");
    for (int i = 0; i < al.getSequencesArray().length; ++i)
    {
      al.getSequenceAt(i).setDatasetSequence(
              al.getSequenceAt(i).createDatasetSequence());
      al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]);
      al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor"
              + al.getSequenceAt(i).getName());
    }
  }

  /**
   * 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());
  }
}