/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
 * Copyright (C) 2015 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.util;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;

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

import org.testng.annotations.Test;

public class ComparisonTest
{

  @Test(groups = { "Functional" })
  public void testIsGap()
  {
    assertTrue(Comparison.isGap('-'));
    assertTrue(Comparison.isGap('.'));
    assertTrue(Comparison.isGap(' '));
    assertFalse(Comparison.isGap('X'));
    assertFalse(Comparison.isGap('x'));
    assertFalse(Comparison.isGap('*'));
    assertFalse(Comparison.isGap('G'));
  }

  /**
   * Test for isNucleotide is that sequences in a dataset are more than 85%
   * AGCTU. Test is not case-sensitive and ignores gaps.
   */
  @Test(groups = { "Functional" })
  public void testIsNucleotide()
  {
    SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
    assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
    { seq } }));

    seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));

    seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));

    seq = new Sequence("eightyfivepercentgapped",
            "--agc--tuA--GCPV-a---gct-uA-GC---UV");
    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));

    seq = new Sequence("nineypercentgapped",
            "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));

    seq = new Sequence("allgap", "---------");
    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));

    seq = new Sequence("DNA", "ACTugGCCAG");
    SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
    /*
     * 90% DNA:
     */
    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
        seq, seq, seq, seq, seq, seq, seq2 }));
    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
        new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
        new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
    /*
     * 80% DNA:
     */
    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
        seq, seq, seq, seq, seq, seq2, seq2 }));
    assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
    { seq }, new SequenceI[] { seq, seq, seq },
        new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));

    seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
    // 12/14 = 85.7%
    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));

    assertFalse(Comparison.isNucleotide((SequenceI[]) null));
    assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
  }

  /**
   * Test percentage identity calculation for two sequences.
   */
  @Test(groups = { "Functional" })
  public void testPID_matchGaps()
  {
    String seq1 = "ABCDEF";
    String seq2 = "abcdef";
    assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);

    // comparison range defaults to length of first sequence
    seq2 = "abcdefghijklmnopqrstuvwxyz";
    assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);

    seq2 = "a---bcdef";
  }
}