/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
 * 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);
  }
}