001package com.hfg.bio.seq.alignment;
002
003import com.hfg.bio.seq.BioSequence;
004import com.hfg.bio.seq.alignment.matrix.PSSM;
005import com.hfg.xml.XMLNode;
006
007
008//------------------------------------------------------------------------------
009/**
010 Container for the aligned subject sequence part of a pairwise sequence alignment.
011 <div>
012 @author J. Alex Taylor, hairyfatguy.com
013 </div>
014 */
015//------------------------------------------------------------------------------
016// com.hfg XML/HTML Coding Library
017//
018// This library is free software; you can redistribute it and/or
019// modify it under the terms of the GNU Lesser General Public
020// License as published by the Free Software Foundation; either
021// version 2.1 of the License, or (at your option) any later version.
022//
023// This library is distributed in the hope that it will be useful,
024// but WITHOUT ANY WARRANTY; without even the implied warranty of
025// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
026// Lesser General Public License for more details.
027//
028// You should have received a copy of the GNU Lesser General Public
029// License along with this library; if not, write to the Free Software
030// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
031//
032// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
033// [email protected]
034//------------------------------------------------------------------------------
035
036public class AlignedSubject extends AlignedSeq
037{
038   private PSSM mPSSM;
039
040   //###########################################################################
041   // CONSTRUCTORS
042   //###########################################################################
043
044   //---------------------------------------------------------------------------
045   public AlignedSubject(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)
046   {
047      super(inSeq, inAlignedSeq, inStart);
048   }
049
050   //---------------------------------------------------------------------------
051   public AlignedSubject(PSSM inPSSM, CharSequence inAlignedSeq, int inStart)
052   {
053      super(null, inAlignedSeq, inStart);
054      mPSSM = inPSSM;
055   }
056
057   //--------------------------------------------------------------------------
058   public AlignedSubject(XMLNode inXMLNode)
059   {
060      super(inXMLNode);
061   }
062
063   //###########################################################################
064   // PUBLIC METHODS
065   //###########################################################################
066
067   //---------------------------------------------------------------------------
068   public PSSM getPSSM()
069   {
070      return mPSSM;
071   }
072
073   //---------------------------------------------------------------------------
074   @Override
075   public AlignedSubject clone()
076   {
077      return (AlignedSubject) super.clone();
078   }
079}