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com.hfg xml, html, svg, and bioinformatics utility library
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package com.hfg.bio.seq.translation;

import java.io.InputStream;

import com.hfg.exception.ProgrammingException;
import com.hfg.util.StringUtil;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Standard translation table for mapping codons to amino acids.
 
  @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------

public class StandardTranslationTable implements TranslationTable
{
   private CodonTable mCodonTable;

   private static StandardTranslationTable sInstance;

   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################

   //---------------------------------------------------------------------------
   private StandardTranslationTable()
   {
      String rsrc = "codondata/standard.cod.xml";

      InputStream stream = getClass().getResourceAsStream(rsrc);
      if (null == stream)
      {
         throw new ProgrammingException("The rsrc " + StringUtil.singleQuote(rsrc) + " couldn't be found!?");
      }

      try
      {
         mCodonTable = new CodonTable(new XMLTag(stream));
      }
      catch (Exception e)
      {
         throw new ProgrammingException(e);
      }
   }

   //###########################################################################
   // PUBLIC METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   public static synchronized StandardTranslationTable getInstance()
   {
      if (null == sInstance)
      {
         sInstance = new StandardTranslationTable();
      }

      return sInstance;
   }

   //---------------------------------------------------------------------------
   /**
    Converts the specified codon (3 nucleotides) into a character representing
    the corresponding amino acid.
    @param inCodon 3-letter nucleotide (DNA or RNA) string to be translated
    @return single letter amino acid
    */
   public char translateCodon(String inCodon)
   {
      return mCodonTable.translateCodon(inCodon);
   }
}