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

import java.util.HashSet;
import java.util.Map;
import java.util.Set;

import com.hfg.chem.Charge;
import com.hfg.chem.Element;
import com.hfg.chem.IonizableGroup;
import com.hfg.chem.Molecule;
import com.hfg.xml.XMLNode;
import com.hfg.util.StringUtil;

//------------------------------------------------------------------------------
/**
 C-terminal protein group.
 
  @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 CTerminalGroup extends Molecule
{
   // This declaration has to come before the public constants below.
   private static Set sValues = new HashSet<>(5);

   //##########################################################################
   // PUBLIC FIELDS
   //##########################################################################

   public static final CTerminalGroup UNMODIFIED_C_TERMINUS = new CTerminalGroup("Unmodified", "-OH");
   public static final CTerminalGroup AMIDE                 = new CTerminalGroup("-amide", "-amide");
   public static final CTerminalGroup O_METHYL              = new CTerminalGroup("-O-methyl", "-O-methyl");


   static
   {
      UNMODIFIED_C_TERMINUS
            .addAtoms(Element.HYDROGEN, 1)
            .addAtoms(Element.OXYGEN, 1)
            .addKa(new IonizableGroup(1.0E-3, Charge.NEUTRAL))  // pKa 3.0
            .lock()
            .register();

      AMIDE.addAtoms(Element.HYDROGEN, 2)
            .addAtoms(Element.NITROGEN, 1)
            .lock()
            .register();

      O_METHYL
            .addAtoms(Element.CARBON, 1)
            .addAtoms(Element.HYDROGEN, 3)
            .addAtoms(Element.OXYGEN, 1)
            .lock()
            .register();
   }

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

   private String     mShortName;

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

   //--------------------------------------------------------------------------
   public CTerminalGroup(String inName)
   {
      super();
      setName(inName);
   }

   //--------------------------------------------------------------------------
   private CTerminalGroup(String inName, String inShortName)
   {
      this(inName);
      mShortName = inShortName;
   }

   //--------------------------------------------------------------------------
   public CTerminalGroup(String inName, Map inElementalComposition)
   {
      super(inName, inElementalComposition);
   }

   //--------------------------------------------------------------------------
   public CTerminalGroup(XMLNode inXML)
   {
      super(inXML);

      if (! inXML.getTagName().equals(HfgBioXML.CTERM_TAG))
      {
         throw new RuntimeException("Cannot construct an " + this.getClass().getSimpleName() + " from a " + inXML.getTagName() + " tag!");
      }

      XMLNode sidechainKasTag = inXML.getOptionalSubtagByName(HfgBioXML.SIDECHAIN_KAS_TAG);
      if (sidechainKasTag != null)
      {
         for (XMLNode subtag : sidechainKasTag.getXMLNodeSubtags())
         {
            addKa(new IonizableGroup(subtag));
         }
      }


      mShortName = inXML.getAttributeValue(HfgBioXML.SHORT_NAME_ATT);
   }

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

   //--------------------------------------------------------------------------
   public static CTerminalGroup[] values()
   {
      return sValues.toArray(new CTerminalGroup[sValues.size()]);
   }

   //--------------------------------------------------------------------------
   /**
    Returns the CTerminalGroup whose name matches the specified String.
    @param inString the name for the CTerminalGroup to retrieve
    @return the CTerminalGroup whose name matches the specified String
    */
   public static CTerminalGroup valueOf(String inString)
   {
      CTerminalGroup value = null;

      if (StringUtil.isSet(inString))
      {
         for (CTerminalGroup group : sValues)
         {
            if (group.name().equalsIgnoreCase(inString))
            {
               value = group;
               break;
            }
         }
      }

      return value;
   }

   //--------------------------------------------------------------------------
   /**
    Puts the CTerminalGroup into the Set of unique CTerminalGroup returned by CTerminalGroup.values().
    */
   public void register()
   {
      if (! isLocked())
      {
         throw new RuntimeException("Only locked CTerminalGroups can be added to the values list!");
      }

      sValues.add(this);
   }

   //--------------------------------------------------------------------------
   @Override
   public CTerminalGroup addAtoms(Element inElement, int inNum)
   {
      return (CTerminalGroup) super.addAtoms(inElement, inNum);
   }

   //--------------------------------------------------------------------------
   @Override
   public CTerminalGroup lock()
   {
      return (CTerminalGroup) super.lock();
   }


   //--------------------------------------------------------------------------
   @Override
   public CTerminalGroup addKa(IonizableGroup inValue)
   {
      return (CTerminalGroup) super.addKa(inValue);
   }

   //--------------------------------------------------------------------------
   public String getShortName()
   {
      return mShortName;
   }


   //--------------------------------------------------------------------------
   @Override
   public XMLNode toXMLNode()
   {
      XMLNode node = super.toXMLNode();
      node.setTagName(HfgBioXML.CTERM_TAG);

      if (StringUtil.isSet(mShortName)) node.setAttribute(HfgBioXML.SHORT_NAME_ATT, mShortName);

      return node;
   }


}