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



import com.hfg.util.CompareUtil;

//------------------------------------------------------------------------------
/**
 Seeds are the tail ends of local sequence alignments.

 @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 AlignmentSeed implements Comparable
{
   private int   mX;
   private int   mY;
   private float mCumulativeScore;


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

   //---------------------------------------------------------------------------
   public AlignmentSeed(int inX, int inY, float inScore)
   {
      mX = inX;
      mY = inY;
      mCumulativeScore = inScore;
   }

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

   //---------------------------------------------------------------------------
   public int getX()
   {
      return mX;
   }

   //---------------------------------------------------------------------------
   public int getY()
   {
      return mY;
   }

   //---------------------------------------------------------------------------
   public float getScore()
   {
      return mCumulativeScore;
   }

   //---------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return String.format("[%d,%d]: %.2f", mX, mY, mCumulativeScore);
   }

   //---------------------------------------------------------------------------
   public int compareTo(AlignmentSeed inObj2)
   {
      int result = 1;

      if (inObj2 != null)
      {
         // Sort by score high to low
         result = - CompareUtil.compare(getScore(), inObj2.getScore());

         if (0 == result)
         {
            result = CompareUtil.compare(getX(), inObj2.getX());

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

      return result;
   }

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

      if (inObj2 != null
          && inObj2 instanceof AlignmentSeed)
      {
         AlignmentSeed seed2 = (AlignmentSeed) inObj2;
         result = (0 == compareTo(seed2));
      }

      return result;
   }

   //---------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      return (31 * mX) + (31 * mY) + (31 * Float.floatToIntBits(mCumulativeScore));
   }
}