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package com.hfg.bio.seq.pattern;

import com.hfg.bio.seq.SeqLocation;

//------------------------------------------------------------------------------
/**
 Container for a sequence 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 abstract class SeqPatternMatch
{
   private SeqPattern   mPattern;
   private String       mSequence;
   private SeqLocation  mSeqLocation;
   private int          mNumMismatches;

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

   //--------------------------------------------------------------------------
   protected SeqPatternMatch()
   {

   }

   //--------------------------------------------------------------------------
   public SeqPatternMatch(SeqPattern inPattern, String inSeq, SeqLocation inLocation)
   {
      mPattern = inPattern;
      mSequence = inSeq;
      mSeqLocation = inLocation;
   }

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

   //--------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return mSequence + " " + mSeqLocation;
   }

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

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

         if (getPattern().equals(match2.getPattern())
               && getSeqLocation().equals(match2.getSeqLocation()))
         {
            result = true;
         }
      }

      return result;
   }

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

      result += 31 * getSeqLocation().hashCode();

      return result;
   }

   //--------------------------------------------------------------------------
   public SeqPattern getPattern()
   {
      return mPattern;
   }


   //--------------------------------------------------------------------------
   public String getSequence()
   {
      return mSequence;
   }

   //--------------------------------------------------------------------------
   public SeqPatternMatch setSequence(String inValue)
   {
      mSequence = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public SeqLocation getSeqLocation()
   {
      return mSeqLocation;
   }


   //--------------------------------------------------------------------------
   public SeqPatternMatch setNumMismatches(int inValue)
   {
      mNumMismatches = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public int getNumMismatches()
   {
      return mNumMismatches;
   }


}