package com.hfg.bio.seq;

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

import com.hfg.bio.AminoAcid;
import com.hfg.chem.Element;
import com.hfg.bio.HfgBioXML;
import com.hfg.chem.Molecule;
import com.hfg.util.CompareUtil;
import com.hfg.util.StringUtil;
import com.hfg.xml.XMLNode;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 * Biological protein sequence cross-link types.
 *
 * @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
// jataylor@hairyfatguy.com
//------------------------------------------------------------------------------


public class ProteinXLinkType extends Molecule
{
   // This declaration has to come before the public constants below.
   private static Set<ProteinXLinkType> sValues = new HashSet<>();

   public static final ProteinXLinkType DISULFIDE;

   /**
    Lysine-arginine protein cross-linking product common with aging of collagen and crystallin.
    Sjöberg, Johan Svantesson, and Sven Bulterijs. 2009. “Characteristics, Formation, and Pathophysiology of Glucosepane: A Major Protein Cross-Link.”
            Rejuvenation Research 12 (2) (April): 137–148. doi:10.1089/rej.2009.0846.
    */
   public static final ProteinXLinkType GLUCOSEPANE;

   static
   {
      Map<Element, Float> elementalComp = new HashMap<>();
      elementalComp.put(Element.HYDROGEN, -2f);

      DISULFIDE = new ProteinXLinkType("Disulfide", elementalComp)
            .addDonor(AminoAcid.CYSTEINE)
            .addAcceptor(AminoAcid.CYSTEINE)
            .lock()
            .register();


      elementalComp = new HashMap<>();
      elementalComp.put(Element.CARBON, 6f);
      elementalComp.put(Element.OXYGEN, 2f);
      elementalComp.put(Element.HYDROGEN, 4f);

      GLUCOSEPANE = new ProteinXLinkType("Glucosepane", elementalComp)
            .addDonor(AminoAcid.LYSINE)
            .addAcceptor(AminoAcid.ARGININE)
            .lock()
            .register();

   }


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

   private Set<AminoAcid> mDonorSpecificity;
   private Set<AminoAcid> mAcceptorSpecificity;


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

   //--------------------------------------------------------------------------
   private ProteinXLinkType(String inName,
                            Map<Element, Float> inElementalComposition)
   {
      super(inName, inElementalComposition);
   }

   //--------------------------------------------------------------------------
   public ProteinXLinkType(String inName,
                           Map<Element, Float> inElementalComposition,
                           Set<AminoAcid> inDonorSpecificity,
                           Set<AminoAcid> inAcceptorSpecificity)
   {
      this(inName, inElementalComposition);
      mDonorSpecificity = inDonorSpecificity;
      mAcceptorSpecificity = inAcceptorSpecificity;
   }

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

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

      XMLNode donorsTag = inXML.getRequiredSubtagByName(HfgBioXML.DONORS_TAG);
      for (XMLNode subtag : donorsTag.getXMLNodeSubtags())
      {
         addDonor(new AminoAcid(subtag));
      }

      XMLNode acceptorsTag = inXML.getRequiredSubtagByName(HfgBioXML.ACCEPTORS_TAG);
      for (XMLNode subtag : acceptorsTag.getXMLNodeSubtags())
      {
         addAcceptor(new AminoAcid(subtag));
      }
   }


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

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

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

      return value;
   }

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

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

      sValues.add(this);

      return this;
   }

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

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

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

      return result;
   }

   //--------------------------------------------------------------------------
   public int compareTo(Object inObj)
   {
      int result = -1;

      if (inObj != null)
      {
         if (inObj instanceof ProteinXLinkType)
         {
            ProteinXLinkType xLinkType2 = (ProteinXLinkType) inObj;

            result = CompareUtil.compare(mAcceptorSpecificity, xLinkType2.mAcceptorSpecificity);
            if (0 == result)
            {
               result = CompareUtil.compare(mDonorSpecificity, xLinkType2.mDonorSpecificity);
               if (0 == result)
               {
                  result = super.compareTo(inObj);
               }
            }
         }
         else
         {
            result = CompareUtil.compare(hashCode(), inObj.hashCode());
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   public boolean isAcceptableSite(AminoAcid inDonor, AminoAcid inAcceptor)
   {
      return mDonorSpecificity.contains(inDonor) && mAcceptorSpecificity.contains(inAcceptor);
   }

   //--------------------------------------------------------------------------
   public XMLNode toXMLNode()
   {
      XMLNode node = super.toXMLNode();
      node.setTagName(HfgBioXML.XLINK_TYPE_TAG);

      XMLNode donorsTag = new XMLTag(HfgBioXML.DONORS_TAG);
      node.addSubtag(donorsTag);
      for (AminoAcid aa : mDonorSpecificity)
      {
         donorsTag.addSubtag(aa.toXMLNode());
      }

      XMLNode acceptorsTag = new XMLTag(HfgBioXML.ACCEPTORS_TAG);
      node.addSubtag(acceptorsTag);
      for (AminoAcid aa : mAcceptorSpecificity)
      {
         acceptorsTag.addSubtag(aa.toXMLNode());
      }

      return node;
   }

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

   //--------------------------------------------------------------------------
   private ProteinXLinkType addDonor(AminoAcid inDonor)
   {
      if (null == mDonorSpecificity)
      {
         mDonorSpecificity = new HashSet<>();
      }

      mDonorSpecificity.add(inDonor);

      return this;
   }

   //--------------------------------------------------------------------------
   private ProteinXLinkType addAcceptor(AminoAcid inAcceptor)
   {
      if (null == mAcceptorSpecificity)
      {
         mAcceptorSpecificity = new HashSet<>();
      }

      mAcceptorSpecificity.add(inAcceptor);

      return this;
   }
}