com.hfg.bio.seq.format.feature.BasicSeqFeatureLocation Maven / Gradle / Ivy

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

import com.hfg.bio.Strand;
import com.hfg.exception.UnimplementedMethodException;
import com.hfg.math.Range;
import com.hfg.util.CompareUtil;


//------------------------------------------------------------------------------
/**
 A basic implementation of the SeqFeatureLocation interface.
 
  @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 BasicSeqFeatureLocation implements SeqFeatureLocation
{
   private Range mIntRange;

   private Strand mStrand;

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

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

   //--------------------------------------------------------------------------
   public BasicSeqFeatureLocation(int inStart, int inEnd)
   {
      mIntRange = new Range<>(inStart, inEnd);
   }


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

   //--------------------------------------------------------------------------
   public BasicSeqFeatureLocation setStrand(Strand inValue)
   {
      mStrand = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Strand getStrand()
   {
      if (null == mStrand)
      {
         mStrand = (mIntRange.getStart() <= mIntRange.getEnd() ? Strand.FORWARD : Strand.REVERSE);
      }

      return mStrand;
   }

   //--------------------------------------------------------------------------
   @Override
   public void append(String inAdditionalLocationData)
   {
      throw new UnimplementedMethodException();
   }

   //---------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      return (inObj2 != null
              && inObj2 instanceof SeqFeatureLocation
              && 0 == compareTo(inObj2));
   }

   //---------------------------------------------------------------------------
   @Override
   public int compareTo(Object inObj2)
   {
      int result = 1;

      if (inObj2 != null
          && inObj2 instanceof SeqFeatureLocation)
      {
         SeqFeatureLocation seqLoc2 = (SeqFeatureLocation) inObj2;

         result = CompareUtil.compare(toIntRange(), seqLoc2.toIntRange());
         if (0 == result)
         {
            result = CompareUtil.compare(toString(), inObj2.toString());
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   @Override
   public Range toIntRange()
   {
      return mIntRange;
   }

   //--------------------------------------------------------------------------
   @Override
   public String eval(String inSequence)
   {
      return inSequence.subSequence(toIntRange().getStart(), toIntRange().getEnd()).toString();
   }
}