/*
 * 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.datamodel;

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

import jalview.util.MapList;

import java.util.Arrays;

import org.testng.annotations.Test;

public class AlignedCodonFrameTest
{

  /**
   * Test the method that locates the first aligned sequence that has a mapping.
   */
  @Test(groups = { "Functional" })
  public void testFindAlignedSequence()
  {
    AlignmentI cdna = new Alignment(new SequenceI[] {});
    final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
    seq1.createDatasetSequence();
    cdna.addSequence(seq1);
    final Sequence seq2 = new Sequence("Seq2", "-TA-GG-GG");
    seq2.createDatasetSequence();
    cdna.addSequence(seq2);

    AlignmentI aa = new Alignment(new SequenceI[] {});
    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
    aseq1.createDatasetSequence();
    aa.addSequence(aseq1);
    final Sequence aseq2 = new Sequence("Seq2", "-LY-");
    aseq2.createDatasetSequence();
    aa.addSequence(aseq2);

    /*
     * Mapping from first DNA sequence to second AA sequence.
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();

    assertNull(acf.findAlignedSequence(seq1, aa));

    MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
    acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);

    /*
     * DNA seq1 maps to AA seq2
     */
    assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
            .getSequenceAt(0).getDatasetSequence(), aa));

    assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
            .getSequenceAt(1).getDatasetSequence(), cdna));
  }

  /**
   * Test the method that locates the mapped codon for a protein position.
   */
  @Test(groups = { "Functional" })
  public void testGetMappedRegion()
  {
    // introns lower case, exons upper case
    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
    seq1.createDatasetSequence();
    final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
    seq2.createDatasetSequence();

    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
    aseq1.createDatasetSequence();
    final Sequence aseq2 = new Sequence("Seq2", "-LY-");
    aseq2.createDatasetSequence();

    /*
     * First with no mappings
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();

    assertNull(acf.getMappedRegion(seq1, aseq1, 1));

    /*
     * Set up the mappings for the exons (upper-case bases)
     */
    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
        1, 2 }, 3, 1);
    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
    map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
            3, 1);
    acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);

    assertEquals("[2, 4]",
            Arrays.toString(acf.getMappedRegion(seq1, aseq1, 1)));
    assertEquals("[6, 6, 8, 9]",
            Arrays.toString(acf.getMappedRegion(seq1, aseq1, 2)));
    assertEquals("[1, 2, 4, 4]",
            Arrays.toString(acf.getMappedRegion(seq2, aseq2, 1)));
    assertEquals("[5, 5, 7, 8]",
            Arrays.toString(acf.getMappedRegion(seq2, aseq2, 2)));

    /*
     * No mapping from sequence 1 to sequence 2
     */
    assertNull(acf.getMappedRegion(seq1, aseq2, 1));
  }

  @Test(groups = { "Functional" })
  public void testGetMappedCodon()
  {
    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
    seq1.createDatasetSequence();
    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
    aseq1.createDatasetSequence();

    /*
     * First with no mappings
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();

    assertNull(acf.getMappedCodon(seq1.getDatasetSequence(), 0));

    /*
     * Set up the mappings for the exons (upper-case bases)
     */
    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
        1, 2 }, 3, 1);
    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);

    assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
            aseq1.getDatasetSequence(), 1)));
    assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
            aseq1.getDatasetSequence(), 2)));
  }

  /**
   * Test for the case where sequences have start > 1
   */
  @Test(groups = { "Functional" })
  public void testGetMappedCodon_forSubSequences()
  {
    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
    seq1.createDatasetSequence();

    final Sequence aseq1 = new Sequence("Seq1", "-P-R", 12, 13);
    aseq1.createDatasetSequence();

    /*
     * Set up the mappings for the exons (upper-case bases)
     */
    AlignedCodonFrame acf = new AlignedCodonFrame();
    MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
            new int[] { 12, 13 }, 3, 1);
    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);

    assertEquals("[G, T, A]", Arrays.toString(acf.getMappedCodon(
            aseq1.getDatasetSequence(), 12)));
    assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
            aseq1.getDatasetSequence(), 13)));
  }

  @Test(groups = { "Functional" })
  public void testCouldReplaceSequence()
  {
    SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
    SequenceI seq2 = new Sequence("Seq2", "PG");
    SequenceI seq1proxy = new SequenceDummy("Seq1");

    // map to region within sequence is ok
    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
            17));
    // map to region overlapping sequence is ok
    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 5,
            10));
    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 21,
            26));
    // map to region before sequence is not ok
    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 4,
            9));
    // map to region after sequence is not ok
    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 22,
            27));

    /*
     * test should fail if name doesn't match
     */
    seq1proxy.setName("Seq1a");
    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
            17));
    seq1proxy.setName("Seq1");
    seq1.setName("Seq1a");
    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
            17));
  }

  @Test(groups = { "Functional" })
  public void testIsRealisableWith()
  {
    SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
    SequenceI seq2 = new Sequence("Seq2", "PG");
    SequenceI seq1proxy = new SequenceDummy("Seq1");
    seq1.createDatasetSequence();
    seq2.createDatasetSequence();
    MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
            3, 1);
    AlignedCodonFrame acf = new AlignedCodonFrame();
    acf.addMap(seq1proxy, seq2, mapList);

    /*
     * Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
     * This is 'realisable' from real sequence Seq1
     */
    assertTrue(acf.isRealisableWith(seq1));

    /*
     * test should fail if name doesn't match
     */
    seq1proxy.setName("Seq1a");
    assertFalse(acf.isRealisableWith(seq1));
    seq1proxy.setName("Seq1");
    seq1.setName("Seq1a");
    assertFalse(acf.isRealisableWith(seq1));
    seq1.setName("Seq1");

    /*
     * test should fail if no sequence overlap with mapping of bases 7-12
     * use artificial start/end values to test this
     */
    seq1.setStart(1);
    seq1.setEnd(6);
    // seq1 precedes mapped region:
    assertFalse(acf.isRealisableWith(seq1));
    seq1.setEnd(7);
    // seq1 includes first mapped base:
    assertTrue(acf.isRealisableWith(seq1));
    seq1.setStart(13);
    seq1.setEnd(18);
    // seq1 follows mapped region:
    assertFalse(acf.isRealisableWith(seq1));
    seq1.setStart(12);
    // seq1 includes last mapped base:
    assertTrue(acf.isRealisableWith(seq1));
  }
}