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package com.hfg.bio.seq.pattern;

import java.util.Comparator;

import com.hfg.bio.Strand;
import com.hfg.bio.seq.SeqLocation;
import com.hfg.util.CompareUtil;

//------------------------------------------------------------------------------
/**
 Container for a nucleotide pattern match.
 
 @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg 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 NucleotidePatternMatch extends SeqPatternMatch
{
   private Strand            mStrand;

   public static final Comparator LOCATION_COMPARATOR = new NucleotidePatternMatch().new LocationComparator();
   public static final Comparator MISMATCH_COMPARATOR = new NucleotidePatternMatch().new MismatchComparator();

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

   //--------------------------------------------------------------------------
   private NucleotidePatternMatch()
   {

   }

   //--------------------------------------------------------------------------
   public NucleotidePatternMatch(NucleotidePattern inPattern, String inSeq, SeqLocation inLocation)
   {
      super(inPattern, inSeq, inLocation);
   }

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

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      boolean result = false;

      if (inObj2 instanceof NucleotidePatternMatch)
      {
         NucleotidePatternMatch match2 = (NucleotidePatternMatch) inObj2;

         if (getPattern().equals(match2.getPattern())
               && getSeqLocation().equals(match2.getSeqLocation())
               && 0 == CompareUtil.compare(getStrand(), match2.getStrand()))
         {
            result = true;
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      int result = super.hashCode();

      if (getStrand() != null)
      {
         result += 31 * getStrand().hashCode();
      }

      return result;
   }

   //--------------------------------------------------------------------------
   @Override
   public NucleotidePattern getPattern()
   {
      return (NucleotidePattern) super.getPattern();
   }


   //--------------------------------------------------------------------------
   public NucleotidePatternMatch setSequence(String inValue)
   {
      return (NucleotidePatternMatch) super.setSequence(inValue);
   }


   //--------------------------------------------------------------------------
   public NucleotidePatternMatch setStrand(Strand inValue)
   {
      mStrand = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Strand getStrand()
   {
      return mStrand;
   }

   //###########################################################################
   // INNER CLASS
   //###########################################################################

   private class LocationComparator implements Comparator
   {
      //--------------------------------------------------------------------------
      public int compare(NucleotidePatternMatch inObj1, NucleotidePatternMatch inObj2)
      {
         return CompareUtil.compare(inObj1.getSeqLocation(), inObj2.getSeqLocation());
      }
   }

   //###########################################################################
   // INNER CLASS
   //###########################################################################

   private class MismatchComparator implements Comparator
   {
      //--------------------------------------------------------------------------
      public int compare(NucleotidePatternMatch inObj1, NucleotidePatternMatch inObj2)
      {
         int result = CompareUtil.compare(inObj1.getNumMismatches(), inObj2.getNumMismatches());

         if (0 == result)
         {
            result = CompareUtil.compare(inObj1.getSeqLocation(), inObj2.getSeqLocation());
         }

         return result;
      }
   }

}