com.hfg.bio.AAGroupingSchemeImpl Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of com_hfg Show documentation
com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import com.hfg.util.CompareUtil;
import com.hfg.util.collection.CollectionUtil;

//------------------------------------------------------------------------------
/**
 Base class for amino acid grouping schemes.
 
 @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 abstract class AAGroupingSchemeImpl implements AAGroupingScheme, Comparable
{
   private String        mName;
   private List mAAGroups;

   // Cached values
   private Map mAAMap;
   private Map mCharMap;


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

   //--------------------------------------------------------------------------
   public AAGroupingSchemeImpl(String inName)
   {
      mName = inName;
   }

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

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

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

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

   //--------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      int hashCode = 0;
      if (CollectionUtil.hasValues(getAAGroups()))
      {
         for (AAGroup group : getAAGroups())
         {
            hashCode += 31 * group.hashCode();
         }
      }

      return hashCode;
   }

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

   //--------------------------------------------------------------------------
   public List getAAGroups()
   {
      return Collections.unmodifiableList(mAAGroups);
   }

   //--------------------------------------------------------------------------
   public AAGroup getAAGroup(AminoAcid inAA)
   {
      return getAAMap().get(inAA);
   }

   //--------------------------------------------------------------------------
   public AAGroup getAAGroup(Character inResidue)
   {
      return getCharMap().get(inResidue);
   }

   //##########################################################################
   // PROTECTED METHODS
   //##########################################################################

   //--------------------------------------------------------------------------
   protected AAGroupingSchemeImpl add(AAGroup inAAGroup)
   {
      if (null == mAAGroups)
      {
         mAAGroups = new ArrayList<>(10);
      }

      mAAGroups.add(inAAGroup);

      // Force the maps to get rebuilt.
      mAAMap = null;
      mCharMap = null;

      return this;
   }

   //--------------------------------------------------------------------------
   private Map getAAMap()
   {
      if (null == mAAMap)
      {
         Map map = new HashMap<>(30);
         for (AAGroup group : mAAGroups)
         {
            for (AminoAcid aa : group.getAminoAcids())
            {
               map.put(aa, group);
            }
         }

         mAAMap = map;
      }

      return mAAMap;
   }

   //--------------------------------------------------------------------------
   private Map getCharMap()
   {
      if (null == mCharMap)
      {
         Map map = new HashMap<>(30);
         for (AAGroup group : mAAGroups)
         {
            for (Character residue : group.getResidues())
            {
               map.put(residue, group);
            }
         }

         mCharMap = map;
      }

      return mCharMap;
   }
}