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

import java.awt.Color;
import java.util.Collection;
import java.util.Collections;
import java.util.Set;

import com.hfg.exception.UnmodifyableObjectException;
import com.hfg.util.CompareUtil;
import com.hfg.util.collection.CollectionUtil;
import com.hfg.util.collection.OrderedSet;

//------------------------------------------------------------------------------
/**
 Amino acid group. Used with AAGroupingScheme.
 
 @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 AAGroup implements Comparable
{
   private Set mAAs;
   private String         mName;
   private Character      mLetter;
   private boolean        mLocked;
   private Color          mColor;

   // Cached values
   private Set mResidues;
   private Integer        mHashCode;

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

   //--------------------------------------------------------------------------
   public AAGroup(String inName, Character inLetter)
   {
      setName(inName);
      mLetter = inLetter;
   }

   //--------------------------------------------------------------------------
   public AAGroup(String inName, Character inLetter, Collection inAAs)
   {
      this(inName, inLetter);

      if (inAAs != null)
      {
         mAAs = new OrderedSet<>(inAAs);
      }
   }

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

   //--------------------------------------------------------------------------
   public void setName(String inValue)
   {
      if (mLocked) throw new UnmodifyableObjectException(mName + " is locked and cannot be modified!");
      mName = inValue;
   }

   //--------------------------------------------------------------------------
   public String name()
   {
      return mName;
   }

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      return (inObj2 != null
              && inObj2 instanceof AAGroup
              && 0 == compareTo((AAGroup) inObj2));
   }

   //--------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      if (null == mHashCode)
      {
         int hashCode = 0;
         if (CollectionUtil.hasValues(getResidues()))
         {
            for (Character residue : getResidues())
            {
               hashCode += 31 * residue.hashCode();
            }
         }

         mHashCode = hashCode;
      }

      return mHashCode;
   }

   //--------------------------------------------------------------------------
   @Override
   public int compareTo(AAGroup inObj2)
   {
      return CompareUtil.compare(getResidues(), inObj2.getResidues());
   }

   //--------------------------------------------------------------------------
   public Character getLetter()
   {
      return mLetter;
   }

   //--------------------------------------------------------------------------
   public AAGroup setColor(Color inValue)
   {
      mColor = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Color getColor()
   {
      return mColor;
   }

   //--------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return name();
   }

   //--------------------------------------------------------------------------
   public AAGroup add(AminoAcid inAA)
   {
      if (mLocked) throw new UnmodifyableObjectException(mName + " is locked and cannot be modified!");

      if (inAA != null)
      {
         if (null == mAAs)
         {
            mAAs = new OrderedSet<>(26);
         }

         if (mAAs.add(inAA))
         {
            clearCachedValues();
         }
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public Set getAminoAcids()
   {
      return Collections.unmodifiableSet(mAAs);
   }

   //--------------------------------------------------------------------------
   public Set getResidues()
   {
      if (null == mResidues
          && CollectionUtil.hasValues(mAAs))
      {
         OrderedSet residues = new OrderedSet<>(mAAs.size());
         for (AminoAcid aa : mAAs)
         {
            residues.add(aa.getOneLetterCode());
         }

         mResidues = residues;
      }

      return mResidues;
   }

   //--------------------------------------------------------------------------
   public boolean contains(Character inResidue)
   {
      Set residues = getResidues();
      return (residues != null
              && residues.contains(inResidue));
   }

   //--------------------------------------------------------------------------
   public boolean contains(AminoAcid inAA)
   {
      return (mAAs != null
              && mAAs.contains(inAA));
   }

   //--------------------------------------------------------------------------
   public boolean isLocked()
   {
      return mLocked;
   }

   //--------------------------------------------------------------------------
   public void lock()
   {
      mLocked = true;
   }

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

   //--------------------------------------------------------------------------
   private void clearCachedValues()
   {
      mResidues = null;
      mHashCode = null;
   }
}