package jalview.analysis;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
import org.testng.annotations.Test;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import java.util.Hashtable;

public class AAFrequencyTest
{
  private static final String C = AAFrequency.MAXCOUNT;

  private static final String R = AAFrequency.MAXRESIDUE;

  private static final String G = AAFrequency.PID_GAPS;

  private static final String N = AAFrequency.PID_NOGAPS;

  private static final String P = AAFrequency.PROFILE;

  @Test
  public void testCalculate_noProfile()
  {
    SequenceI seq1 = new Sequence("Seq1", "CAGT");
    SequenceI seq2 = new Sequence("Seq2", "CACT");
    SequenceI seq3 = new Sequence("Seq3", "C--G");
    SequenceI seq4 = new Sequence("Seq4", "CA-t");
    SequenceI[] seqs = new SequenceI[]
    { seq1, seq2, seq3, seq4 };
    Hashtable[] result = new Hashtable[seq1.getLength()];
    
    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);

    // col 0 is 100% C
    Hashtable col = result[0];
    assertEquals(100f, (Float) col.get(G), 0.0001f);
    assertEquals(100f, (Float) col.get(N), 0.0001f);
    assertEquals(4, col.get(C));
    assertEquals("C", col.get(R));
    assertNull(col.get(P));

    // col 1 is 75% A
    col = result[1];
    assertEquals(75f, (Float) col.get(G), 0.0001f);
    assertEquals(100f, (Float) col.get(N), 0.0001f);
    assertEquals(3, col.get(C));
    assertEquals("A", col.get(R));

    // col 2 is 50% G 50% C or 25/25 counting gaps
    col = result[2];
    assertEquals(25f, (Float) col.get(G), 0.0001f);
    assertEquals(50f, (Float) col.get(N), 0.0001f);
    assertEquals(1, col.get(C));
    assertEquals("CG", col.get(R));

    // col 3 is 75% T 25% G
    col = result[3];
    assertEquals(75f, (Float) col.get(G), 0.0001f);
    assertEquals(75f, (Float) col.get(N), 0.0001f);
    assertEquals(3, col.get(C));
    assertEquals("T", col.get(R));
  }

  @Test
  public void testCalculate_withProfile()
  {
    SequenceI seq1 = new Sequence("Seq1", "CAGT");
    SequenceI seq2 = new Sequence("Seq2", "CACT");
    SequenceI seq3 = new Sequence("Seq3", "C--G");
    SequenceI seq4 = new Sequence("Seq4", "CA-t");
    SequenceI[] seqs = new SequenceI[]
    { seq1, seq2, seq3, seq4 };
    Hashtable[] result = new Hashtable[seq1.getLength()];

    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
    int[][] profile = (int[][]) result[0].get(P);
    assertEquals(4, profile[0]['C']);
    assertEquals(4, profile[1][0]); // no of seqs
    assertEquals(4, profile[1][1]); // nongapped in column

    profile = (int[][]) result[1].get(P);
    assertEquals(3, profile[0]['A']);
    assertEquals(4, profile[1][0]);
    assertEquals(3, profile[1][1]);

    profile = (int[][]) result[2].get(P);
    assertEquals(1, profile[0]['G']);
    assertEquals(1, profile[0]['C']);
    assertEquals(4, profile[1][0]);
    assertEquals(2, profile[1][1]);

    profile = (int[][]) result[3].get(P);
    assertEquals(3, profile[0]['T']);
    assertEquals(1, profile[0]['G']);
    assertEquals(4, profile[1][0]);
    assertEquals(4, profile[1][1]);
  }

  @Test
  public void testCalculate_withProfileTiming()
  {
    SequenceI seq1 = new Sequence("Seq1", "CAGT");
    SequenceI seq2 = new Sequence("Seq2", "CACT");
    SequenceI seq3 = new Sequence("Seq3", "C--G");
    SequenceI seq4 = new Sequence("Seq4", "CA-t");
    SequenceI[] seqs = new SequenceI[]
    { seq1, seq2, seq3, seq4 };
    Hashtable[] result = new Hashtable[seq1.getLength()];

    // ensure class loaded and initialized
    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
    int reps = 100000;
    long start = System.currentTimeMillis();
    for (int i = 0; i < reps; i++)
    {
      AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
    }
    System.out.println(System.currentTimeMillis() - start);
  }

  @Test
  public void testGetPercentageFormat()
  {
    assertNull(AAFrequency.getPercentageFormat(0));
    assertNull(AAFrequency.getPercentageFormat(99));
    assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
    assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
    assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
    assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());
  }
}