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

import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;


//------------------------------------------------------------------------------
/**
 * Table of amino acid frequency data.
 * 
 *  @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 AminoAcidFreqTable
{
   private Map mFreqMap;

   /**
    Amino acid frequencies in mammalian proteins.
    Based on data from ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian.*.protein.faa.gz on 2014.09.15
    */
   public static final AminoAcidFreqTable MAMMALIAN = new AminoAcidFreqTable();


   static
   {
      Map freqMap = new HashMap();
      freqMap.put(AminoAcid.ALANINE,       0.0694f);
      freqMap.put(AminoAcid.ARGININE,      0.0569f);
      freqMap.put(AminoAcid.ASPARAGINE,    0.0539f);
      freqMap.put(AminoAcid.ASPARTIC_ACID, 0.0481f);
      freqMap.put(AminoAcid.CYSTEINE,      0.0219f);
      freqMap.put(AminoAcid.GLUTAMIC_ACID, 0.0713f);
      freqMap.put(AminoAcid.GLUTAMINE,     0.0481f);
      freqMap.put(AminoAcid.GLYCINE,       0.0648f);
      freqMap.put(AminoAcid.HISTIDINE,     0.0261f);
      freqMap.put(AminoAcid.ISOLEUCINE,    0.0434f);
      freqMap.put(AminoAcid.LEUCINE,       0.0991f);
      freqMap.put(AminoAcid.LYSINE,        0.0577f);
      freqMap.put(AminoAcid.METHIONINE,    0.0217f);
      freqMap.put(AminoAcid.PHENYLALANINE, 0.0361f);
      freqMap.put(AminoAcid.PROLINE,       0.0632f);
      freqMap.put(AminoAcid.SERINE,        0.0844f);
      freqMap.put(AminoAcid.THREONIE,      0.0534f);
      freqMap.put(AminoAcid.TRYPTOPHAN,    0.0119f);
      freqMap.put(AminoAcid.TYROSINE,      0.0262f);
      freqMap.put(AminoAcid.VALINE,        0.0602f);
      freqMap.put(AminoAcid.UNDEFINED,     0.0002f);

      MAMMALIAN.mFreqMap = Collections.unmodifiableMap(freqMap);
   }


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

   //--------------------------------------------------------------------------
   private AminoAcidFreqTable()
   {

   }

   //--------------------------------------------------------------------------
   public AminoAcidFreqTable(Map inData)
   {
      mFreqMap = Collections.unmodifiableMap(inData);
   }

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

   //--------------------------------------------------------------------------
   public Set keySet()
   {
      return mFreqMap.keySet();
   }

   //--------------------------------------------------------------------------
   public Float get(AminoAcid inAA)
   {
      return mFreqMap.get(inAA);
   }
}