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



import com.hfg.setting.SettingXML;
import com.hfg.xml.XMLTag;
import com.hfg.xml.XMLTaggable;

import java.awt.Color;

//------------------------------------------------------------------------------
/**
 Standard grouping of amino acids.
 
   Basic: lysine, arginine, histidine
   Acidic: aspartic acid, glutamic acid
   Uncharged Polar: asparagine, glutamine, serine, threonine, tyrosine
   Nonpolar: glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, cysteine
 
 
 @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 StandardAAGroupingScheme extends AAGroupingSchemeImpl implements XMLTaggable
{

   private static StandardAAGroupingScheme sInstance;

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

   //--------------------------------------------------------------------------
   private StandardAAGroupingScheme()
   {
      super("Standard");

      add(new AAGroup("Acidic", 'A').setColor(Color.RED)
                .add(AminoAcid.ASPARTIC_ACID)
                .add(AminoAcid.GLUTAMIC_ACID));

      add(new AAGroup("Basic", 'B').setColor(Color.BLUE)
                .add(AminoAcid.LYSINE)
                .add(AminoAcid.ARGININE)
                .add(AminoAcid.HISTIDINE));

      add(new AAGroup("Uncharged Polar", 'U').setColor(Color.ORANGE)
            .add(AminoAcid.ASPARAGINE)
            .add(AminoAcid.GLUTAMINE)
            .add(AminoAcid.SERINE)
            .add(AminoAcid.THREONIE)
            .add(AminoAcid.TYROSINE));

      add(new AAGroup("Nonpolar", 'N').setColor(Color.GREEN)
            .add(AminoAcid.GLYCINE)
            .add(AminoAcid.ALANINE)
            .add(AminoAcid.VALINE)
            .add(AminoAcid.LEUCINE)
            .add(AminoAcid.ISOLEUCINE)
            .add(AminoAcid.PROLINE)
            .add(AminoAcid.PHENYLALANINE)
            .add(AminoAcid.METHIONINE)
            .add(AminoAcid.TRYPTOPHAN)
            .add(AminoAcid.CYSTEINE));

      add(new AAGroup("Deletion", 'D').setColor(Color.BLACK)
            .add(AminoAcid.STOP)
            .add(AminoAcid.UNDEFINED));

   }

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

   //--------------------------------------------------------------------------
   public static synchronized StandardAAGroupingScheme getInstance()
   {
      if (null == sInstance)
      {
         sInstance = new StandardAAGroupingScheme();
      }

      return sInstance;
   }

   //--------------------------------------------------------------------------
   public XMLTag toXMLTag()
   {
      XMLTag tag = new XMLTag(HfgBioXML.AA_GROUPING_SCHEME_TAG);
      tag.setAttribute(SettingXML.CLASS_ATT, getClass().getName());
      tag.setAttribute(SettingXML.INSTANCE_ATT, "true");

      return tag;
   }

}