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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.seq.Protein;

//------------------------------------------------------------------------------
/**
 Percent extinction coefficient (ml/mg cm^-1) at A₂₈₀
 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 PctExtinctionCoeff extends SimpleProteinProperty
{
   private static Map sUniqueMap = new HashMap<>();

   public static final PctExtinctionCoeff PROPERTY = new PctExtinctionCoeff("Pct. Extinction Coeff.", "Pct. Extinction Coefficient (ml/mg per cm) at A280");

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

   //---------------------------------------------------------------------------
   private PctExtinctionCoeff(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 ExtinctionCoeff.TYPE;
   }

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

   //---------------------------------------------------------------------------
   @Override
   public Float calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
   {
      Float returnValue = 0.0f;

      if (inProtein.length() > 0)
      {
         if (null == inSettings)
         {
            inSettings = new SimpleProteinPropertyCalcSettings();
         }

         double value = ExtinctionCoeff.PROPERTY.getRawValue(inProtein, inSettings) / inProtein.getAverageMass(inSettings.getProteinAnalysisMode());

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

         returnValue = (float) value;
      }

      return returnValue;
   }

}