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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.exception.ProgrammingException;

/**
 Container for pairwise sequence alignment gap penalties.

 @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 GapPenalties implements Cloneable
{
   private Float mOpenPenalty;
   private Float mExtensionPenalty;


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

   //---------------------------------------------------------------------------
   @Override
   public GapPenalties clone()
   {
      GapPenalties cloneObj = null;
      try
      {
         cloneObj = (GapPenalties) super.clone();
      }
      catch (CloneNotSupportedException e)
      {
         throw new ProgrammingException(e);
      }

      return cloneObj;
   }

   //---------------------------------------------------------------------------
   public GapPenalties setOpenPenalty(Float inValue)
   {
      mOpenPenalty = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Float getOpenPenalty()
   {
      return mOpenPenalty;
   }

   //---------------------------------------------------------------------------
   public GapPenalties setExtensionPenalty(Float inValue)
   {
      mExtensionPenalty = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Float getExtensionPenalty()
   {
      return mExtensionPenalty;
   }

   //---------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return String.format("[%.1f, %.1f]", mOpenPenalty, mExtensionPenalty);
   }
}