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