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


import java.util.ArrayList;
import java.util.List;

import com.hfg.math.Range;

//------------------------------------------------------------------------------
/**
 1-based biological sequence location object.
 
  @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg 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 SeqLocation extends Range
{
   private String  mChainId;


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

   //--------------------------------------------------------------------------
   public SeqLocation()
   {
      super();
   }

   //--------------------------------------------------------------------------
   public SeqLocation(Integer inStart, Integer inEnd)
   {
      super(inStart, inEnd);
   }

   //--------------------------------------------------------------------------
   public SeqLocation(Range inRange)
   {
      super(inRange != null ? inRange.getStart() : null,
            inRange != null ? inRange.getEnd() : null);
   }

   //--------------------------------------------------------------------------
   public SeqLocation(String inChainId, Integer inStart, Integer inEnd)
   {
      super(inStart, inEnd);
      mChainId = inChainId;
   }


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

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

   //--------------------------------------------------------------------------
   @Override
   public SeqLocation setStart(Integer inValue)
   {
      return (SeqLocation) super.setStart(inValue);
   }

   //--------------------------------------------------------------------------
   @Override
   public SeqLocation setEnd(Integer inValue)
   {
      return (SeqLocation) super.setEnd(inValue);
   }

   //--------------------------------------------------------------------------
   public SeqLocation setChainId(String inValue)
   {
      mChainId = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String getChainId()
   {
      return mChainId;
   }

   //--------------------------------------------------------------------------
   public void addOffset(int inValue)
   {
      if (getStart() != null)
      {
         setStart(getStart() + inValue);
      }

      if (getEnd() != null)
      {
         setEnd(getEnd() + inValue);
      }
   }

   //--------------------------------------------------------------------------
   public List subtract(SeqLocation inLoc2)
   {
      List> rangeResults = super.subtract(inLoc2);

      List seqLocResults = new ArrayList<>(rangeResults.size());
      for (Range result : rangeResults)
      {
         seqLocResults.add(new SeqLocation(result.getStart(), result.getEnd()));
      }

      return seqLocResults;
   }

}