/*
 * 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.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import org.junit.Before;
import org.junit.Test;

/**
 * Test the alignment -> Mapping routines
 * 
 * @author jimp
 * 
 */
public class TestAlignSeq
{

  SequenceI s1, s2, s3;

  /**
   * @throws java.lang.Exception
   */
  @Before
  public void setUp() throws Exception
  {
    s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
    s1.setStart(3);
    s2 = new Sequence("Seq2", "ASDFA");
    s2.setStart(5);
    s3 = new Sequence("Seq1", "SDFAQQQSSS");

  }

  @Test
  /**
   * simple test that mapping from alignment corresponds identical positions.
   */
  public void TestGetMappingForS1()
  {
    jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq
            .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
    System.out.println("s1: " + as.getAStr1());
    System.out.println("s2: " + as.getAStr2());

    Mapping s1tos2 = as.getMappingFromS1(false);
    System.out.println(s1tos2.getMap().toString());
    for (int i = s2.getStart(); i < s2.getEnd(); i++)
    {
      System.out.println("Position in s2: " + i
              + " maps to position in s1: " + s1tos2.getPosition(i));
      assertTrue("", s2.getCharAt(i) == s1.getCharAt(s1tos2.getPosition(i)));
    }
  }

  @Test
  public void testExtractGaps()
  {
    assertNull(AlignSeq.extractGaps(null, null));
    assertNull(AlignSeq.extractGaps(". -", null));
    assertNull(AlignSeq.extractGaps(null, "AB-C"));

    assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
  }
}