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


import java.math.BigDecimal;
import java.math.MathContext;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;

import com.hfg.bio.AminoAcid;
import com.hfg.bio.seq.AminoAcidComposition;
import com.hfg.bio.seq.Protein;

//------------------------------------------------------------------------------
/**
 A₂₈₀ extinction coefficient packaged as a protein property for ease of integration with
 other protein properties.
 
   Uses residue coefficients from  Pace, C.N. et. al. (1995). "How to measure and predict the molar absorption coefficient of a protein."
   Protein Science, 4, 2411-2423.
 
 
 @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 ExtinctionCoeff extends SimpleProteinProperty
{
   private static Map sUniqueMap = new HashMap<>();

   protected static final String TYPE = "Extinction Coeff.";

   public static final ExtinctionCoeff PROPERTY = new ExtinctionCoeff("Extinction Coeff.", "Extinction Coefficient at A280");

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

   //---------------------------------------------------------------------------
   private ExtinctionCoeff(String inName, String inDescription)
   {
      super(inName);
      setDescription(inDescription);

      sUniqueMap.put(inName, this);
   }

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

   //---------------------------------------------------------------------------
   public static Collection values()
   {
      return sUniqueMap.values();
   }

   //--------------------------------------------------------------------------
   @Override
   public String getType()
   {
      return TYPE;
   }

   //---------------------------------------------------------------------------
   public Integer calculate(Protein inProtein)
   {
      return calculate(inProtein, null);
   }

   //---------------------------------------------------------------------------
   @Override
   public Integer calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
   {
      double value = getRawValue(inProtein, inSettings);

      // To get to 3 sig. figs. ...
      int length = ((int)value + "").length();
      if (length > 3)
      {
         BigDecimal bd = new BigDecimal(value);
         bd = bd.round(new MathContext(3));
         value = bd.doubleValue();
      }

      return (int) value;
   }


   //--------------------------------------------------------------------------
   protected int getRawValue(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
   {
      int rawValue = 0;
      if (inProtein.length() > 0)
      {
         if (null == inSettings)
         {
            inSettings = new SimpleProteinPropertyCalcSettings();
         }

         AminoAcidComposition aaComposition = inProtein.getAminoAcidComposition();

         Integer numDisulfideBonds = null;

         // Only consider disulfide bonds if were in native mode
         if (inSettings.getProteinAnalysisMode().equals(ProteinAnalysisMode.NATIVE))
         {
            numDisulfideBonds = inProtein.getTotalNumDisulfideBonds();
            // If the number of disulfide bonds has not been specified, assume that all cysteines are disulfide-linked.
            if (null == numDisulfideBonds)
            {
               numDisulfideBonds = (aaComposition.get(AminoAcid.CYSTEINE) / 2);
            }
         }

         rawValue = aaComposition.get(AminoAcid.TRYPTOPHAN) * 5500
                + aaComposition.get(AminoAcid.TYROSINE) * 1490
                + (numDisulfideBonds != null ? numDisulfideBonds * 125 : 0);
      }

      return rawValue;
   }

}