/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
 * Copyright (C) 2014 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.schemes;

import static org.junit.Assert.*;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import java.io.IOException;
import java.util.Map;
import java.util.Vector;

import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;

public class DnaCodonTests
{

  @Test
  public void testAmbiguityCodeGeneration()
  {
    assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
  }

  @Test
  public void testAmbiguityCodon()
  {
    for (String ac : ResidueProperties.ambiguityCodes.keySet())
    {
      assertTrue("Couldn't resolve GGN as glycine codon",
              ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
    }
  }

  @Test
  public void regenerateCodonTable()
  {
    for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
            .entrySet())
    {
      System.out.println("ResidueProperties.codonHash2.set(\""
              + codon.getKey() + "\", \"" + codon.getValue() + "\");");
    }
  }

  @Test
  public void checkOldCodonagainstNewCodonTable()
  {
    // note - this test will be removed once the old codon table (including
    // Vectors) is removed
    String additional = "", failtrans = "", differentTr = "";
    for (Object aa : ResidueProperties.codonHash.keySet())
    {
      String amacid = (String) aa;
      for (Object codons : ((Vector) ResidueProperties.codonHash
              .get(amacid)))
      {
        String codon = (String) codons;
        String trans = ResidueProperties.codonTranslate(codon);
        String oldtrans = ResidueProperties._codonTranslate(codon);
        if (trans == null)
        {
          additional += "\nOld translation table includes additional codons for "
                  + amacid + " : " + codon;
        }
        if (oldtrans == null)
        {
          failtrans += ("\nold translation routine failed for old translation entry (aa was "
                  + amacid + " codon was " + codon + ")");
        }
        if (!oldtrans.equals(trans))
        {
          differentTr += ("\nDifferent translation for old and new routines: "
                  + amacid
                  + " "
                  + codon
                  + " => expected "
                  + oldtrans
                  + " and got " + trans);
        }
      }
    }
    assertTrue("" + additional + "\n" + failtrans + "\n" + differentTr,
            additional.length() == 0 && failtrans.length() == 0
                    && differentTr.length() == 0);
  }
}