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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.bio.seq.BioSequence;
import com.hfg.bio.seq.alignment.matrix.PSSM;
import com.hfg.xml.XMLNode;


//------------------------------------------------------------------------------
/**
 Container for the aligned subject sequence part of a pairwise sequence alignment.
 
 @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 AlignedSubject extends AlignedSeq
{
   private PSSM mPSSM;

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

   //---------------------------------------------------------------------------
   public AlignedSubject(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)
   {
      super(inSeq, inAlignedSeq, inStart);
   }

   //---------------------------------------------------------------------------
   public AlignedSubject(PSSM inPSSM, CharSequence inAlignedSeq, int inStart)
   {
      super(null, inAlignedSeq, inStart);
      mPSSM = inPSSM;
   }

   //--------------------------------------------------------------------------
   public AlignedSubject(XMLNode inXMLNode)
   {
      super(inXMLNode);
   }

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

   //---------------------------------------------------------------------------
   public PSSM getPSSM()
   {
      return mPSSM;
   }

   //---------------------------------------------------------------------------
   @Override
   public AlignedSubject clone()
   {
      return (AlignedSubject) super.clone();
   }
}