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

import java.util.Map;

import com.hfg.util.collection.CollectionUtil;

//------------------------------------------------------------------------------
/**
 Elemental composition and mass tracking object.
 
  @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding 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 OrganicMatterImpl extends MatterImpl implements OrganicMatter, Cloneable
{

   //##########################################################################
   // PRIVATE FIELDS
   //##########################################################################

   private Double                  mOrganicAverageMass;

   private boolean                 mOrganicAverageMassIsUserSet;

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

   //--------------------------------------------------------------------------
   public OrganicMatterImpl()
   {
      super();
   }

   //--------------------------------------------------------------------------
   public OrganicMatterImpl(Map inMap)
   {
      super(inMap);
   }

   //--------------------------------------------------------------------------
   public OrganicMatterImpl(OrganicMatter inInitialValue)
   {
      super(inInitialValue);

      if (inInitialValue != null)
      {
         setOrganicAverageMass(inInitialValue.getOrganicAverageMass());
      }
   }

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

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj)
   {
      boolean result = false;

      if (inObj != null
         && inObj instanceof OrganicMatterImpl)
      {
         result = (0 == compareTo((OrganicMatterImpl) inObj));
      }

      return result;
   }

   //--------------------------------------------------------------------------
   @Override
   public OrganicMatterImpl add(Matter inValue, int inCount)
   {
      if (inValue != null)
      {
         super.add(inValue, inCount);

         if (mOrganicAverageMassIsUserSet
             || (null == inValue.getElementalComposition()
                 && ((inValue instanceof OrganicMatter
                      && ((OrganicMatter)inValue).getOrganicAverageMass() != null)
                    || inValue.getAverageMass() != null)))
         {
            setOrganicAverageMass((mOrganicAverageMassIsUserSet ? mOrganicAverageMass : CollectionUtil.hasValues(getElementalComposition()) ? getOrganicAverageMass() : 0.0)
                  + (inValue instanceof OrganicMatter ?
                        ((((OrganicMatter)inValue).getOrganicAverageMass() != null ? ((OrganicMatter)inValue).getOrganicAverageMass() : inValue.getAverageMass()) * inCount) :
                        inValue.getAverageMass() * inCount));
         }
      }

      return this;
   }

   //--------------------------------------------------------------------------
   @Override
   public OrganicMatterImpl remove(Matter inValue)
   {
      return remove(inValue, 1);
   }

   //--------------------------------------------------------------------------
   @Override
   public OrganicMatterImpl remove(Matter inValue, int inCount)
   {
      // This will call add() with a negative count
      return (OrganicMatterImpl) super.remove(inValue, inCount);
   }

   //--------------------------------------------------------------------------
   /**
    If the elemental composition is known, use setElementalComposition() and
    the masses will be derived automatically; this method is for use in those
    (hopefully) rare times when the mass is known but not the elemental composition.
    @param inValue the mass to use as the organic average mass for this object
    @return this OrganicMatterImpl object to enable method chaining
    */
   public OrganicMatterImpl setOrganicAverageMass(Double inValue)
   {
      mOrganicAverageMass = inValue;

      mOrganicAverageMassIsUserSet = (inValue != null && calculateOrganicMassFromElementalComposition() != mOrganicAverageMass);

      return this;
   }

   //--------------------------------------------------------------------------
   public Double getOrganicAverageMass()
   {
      if (null == mOrganicAverageMass)
      {
         calculateMassFromElementalComposition();
      }

      return mOrganicAverageMass;
   }


   //--------------------------------------------------------------------------
   @Override
   public OrganicMatterImpl clone()
   {
      return (OrganicMatterImpl) super.clone();
   }


   //--------------------------------------------------------------------------
   @Override
   public void clearCalculatedProperties()
   {
      super.clearCalculatedProperties();
      if (! mOrganicAverageMassIsUserSet) mOrganicAverageMass = null;
   }

   //##########################################################################
   // PROTECTED METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   @Override
   protected void calculateMassFromElementalComposition()
   {
      super.calculateMassFromElementalComposition();

      if (! mOrganicAverageMassIsUserSet)
      {
         mOrganicAverageMass = calculateOrganicMassFromElementalComposition();
      }
   }


   //--------------------------------------------------------------------------
   @Override
   protected boolean massesAreUserSet()
   {
      return (super.massesAreUserSet() || mOrganicAverageMassIsUserSet);
   }

   //##########################################################################
   // PRIVATE METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   private double calculateOrganicMassFromElementalComposition()
   {
      double organicAvg = 0.0;

      Map elementalCompositionMap = getElementalComposition();
      if (elementalCompositionMap != null)
      {
         for (Element element : elementalCompositionMap.keySet())
         {
            float count = elementalCompositionMap.get(element);

            Double elementalAvgMass = element.getAverageMass();
            Double elementalOrgAvgMass = element.getOrganicAverageMass();

            organicAvg += count * (elementalOrgAvgMass != null ? elementalOrgAvgMass : elementalAvgMass != null ? elementalAvgMass : element.getMonoisotopicMass());
         }

      }

      return organicAvg;
   }
}