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com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.proteinproperty;


import java.util.Collection;
import java.util.Map;

import com.hfg.bio.*;
import com.hfg.bio.seq.Protein;
import com.hfg.util.collection.OrderedMap;

//------------------------------------------------------------------------------
/**
 * Mass packaged as a protein property for ease of integration with
 * other protein properties.
 *
 * @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 Mass extends SimpleProteinProperty
{
   private KaSet mKaSet;

   private static Map sUniqueMap = new OrderedMap<>();

   public static final Mass MONOISOTOPIC       = new Mass("Monoisotopic");
   public static final Mass AVERAGE            = new Mass("Avg.");
   public static final Mass ORGANIC_AVERAGE    = new Mass("Organic Avg.");

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

   //--------------------------------------------------------------------------
   private Mass(String inName)
   {
      super(inName);

      sUniqueMap.put(inName, this);
   }

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

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

   //--------------------------------------------------------------------------
   public String getType()
   {
      return "Mass";
   }

   //--------------------------------------------------------------------------
   /**
    Determines the mass of the specified protein.
    */
   public Double calculate(Protein inProtein, SimpleProteinPropertyCalcSettings inSettings)
   {
      Double mass = null;
      switch (name())
      {
         case "Monoisotopic":
            mass = inProtein.getMonoisotopicMass(inSettings.getProteinAnalysisMode());
            break;

         case "Avg.":
            mass = inProtein.getAverageMass(inSettings.getProteinAnalysisMode());
            break;

         case "Organic Avg.":
            mass = inProtein.getOrganicAverageMass(inSettings.getProteinAnalysisMode());
            break;
      }

      return mass;
   }
}