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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 com.hfg.bio.AminoAcid;
import com.hfg.bio.HfgBioXML;
import com.hfg.util.CompareUtil;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Reduced (and denatured) protein analysis mode.
 
  @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 ReducedAnalysisMode extends ProteinAnalysisMode
{
   private AminoAcid mAlkylatedCys;



   //---------------------------------------------------------------------------
   public ReducedAnalysisMode()
   {
      super("Reduced");
   }

   //---------------------------------------------------------------------------
   public ReducedAnalysisMode(XMLTag inXMLNode)
   {
      this();

      XMLTag alkylatedCysTag = inXMLNode.getOptionalSubtagByName(HfgBioXML.AA_TAG);
      if (alkylatedCysTag != null)
      {
         setAlkylatedCysteine(new AminoAcid(alkylatedCysTag));
      }
   }

   //--------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return toXMLTag().toXML();
   }

   //--------------------------------------------------------------------------
   @Override
   public XMLTag toXMLTag()
   {
      XMLTag tag = super.toXMLTag();

      if (mAlkylatedCys != null)
      {
         tag.addSubtag(mAlkylatedCys.toXMLNode());
      }

      return tag;
   }

   //--------------------------------------------------------------------------
   public ReducedAnalysisMode setAlkylatedCysteine(AminoAcid inAA)
   {
      mAlkylatedCys = inAA;
      return this;
   }

   //--------------------------------------------------------------------------
   public AminoAcid getAlkylatedCysteine()
   {
      return mAlkylatedCys;
   }

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      return (inObj2 instanceof ReducedAnalysisMode
              && 0 == CompareUtil.compare(getAlkylatedCysteine(), ((ReducedAnalysisMode) inObj2).getAlkylatedCysteine()));
   }
}