/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.analysis;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;

import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import org.testng.annotations.Test;

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(groups = { "Functional" })
  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 };
    Profile[] result = new Profile[seq1.getLength()];

    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);

    // col 0 is 100% C
    Profile col = result[0];
    assertEquals(100f, col.getPercentageIdentity(false));
    assertEquals(100f, col.getPercentageIdentity(true));
    assertEquals(4, col.getMaxCount());
    assertEquals("C", col.getModalResidue());
    assertNull(col.getCounts());

    // col 1 is 75% A
    col = result[1];
    assertEquals(75f, col.getPercentageIdentity(false));
    assertEquals(100f, col.getPercentageIdentity(true));
    assertEquals(3, col.getMaxCount());
    assertEquals("A", col.getModalResidue());

    // col 2 is 50% G 50% C or 25/25 counting gaps
    col = result[2];
    assertEquals(25f, col.getPercentageIdentity(false));
    assertEquals(50f, col.getPercentageIdentity(true));
    assertEquals(1, col.getMaxCount());
    assertEquals("CG", col.getModalResidue());

    // col 3 is 75% T 25% G
    col = result[3];
    assertEquals(75f, col.getPercentageIdentity(false));
    assertEquals(75f, col.getPercentageIdentity(true));
    assertEquals(3, col.getMaxCount());
    assertEquals("T", col.getModalResidue());
  }

  @Test(groups = { "Functional" })
  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 };
    Profile[] result = new Profile[seq1.getLength()];

    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
    Profile profile = result[0];
    assertEquals(4, profile.getCounts().getCount('C'));
    assertEquals(4, profile.getHeight());
    assertEquals(4, profile.getNonGapped());

    profile = result[1];
    assertEquals(3, profile.getCounts().getCount('A'));
    assertEquals(4, profile.getHeight());
    assertEquals(3, profile.getNonGapped());

    profile = result[2];
    assertEquals(1, profile.getCounts().getCount('C'));
    assertEquals(1, profile.getCounts().getCount('G'));
    assertEquals(4, profile.getHeight());
    assertEquals(2, profile.getNonGapped());

    profile = result[3];
    assertEquals(3, profile.getCounts().getCount('T'));
    assertEquals(1, profile.getCounts().getCount('G'));
    assertEquals(4, profile.getHeight());
    assertEquals(4, profile.getNonGapped());
  }

  @Test(groups = { "Functional" })
  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 };
    Profile[] result = new Profile[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);
  }
}