com.hfg.bio.seq.Exon Maven / Gradle / Ivy

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com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.seq;

import java.awt.*;

import com.hfg.bio.Strand;

//------------------------------------------------------------------------------
/**
 * An exon in a gene.
 *
 * @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 Exon implements Comparable
{

   //##########################################################################
   // PRIVATE FIELDS
   //##########################################################################

   private int    mStartLocation;
   private int    mEndLocation;
   private Strand mStrand;
   private Color  mColor;

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

   //--------------------------------------------------------------------------
   public Exon(int inStart, int inEnd)
   {
      mStartLocation = inStart;
      mEndLocation   = inEnd;
   }

   //--------------------------------------------------------------------------
   public Exon(int inStart, int inEnd, Strand inStrand)
   {
      mStartLocation = inStart;
      mEndLocation   = inEnd;
      mStrand = inStrand;
   }


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

   //--------------------------------------------------------------------------
   public int getStartLocation()
   {
      return mStartLocation;
   }

   //--------------------------------------------------------------------------
   public int getEndLocation()
   {
      return mEndLocation;
   }


   //--------------------------------------------------------------------------
   public int getLeft()
   {
      return Math.min(mStartLocation, mEndLocation);
   }

   //--------------------------------------------------------------------------
   public int getRight()
   {
      return Math.max(mStartLocation, mEndLocation);
   }



   //--------------------------------------------------------------------------
   public Strand getStrand()
   {
      return mStrand;
   }

   //--------------------------------------------------------------------------
   public void setStrand(Strand inValue)
   {
      mStrand = inValue;
   }



   //--------------------------------------------------------------------------
   public Exon setColor(Color inValue)
   {
      mColor = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public Color getColor()
   {
      return mColor;
   }

   //--------------------------------------------------------------------------
   public int compareTo(Object o2)
   {
      Exon exon2 = (Exon) o2;

      int returnValue = 0;

      if (mStartLocation > exon2.mStartLocation)
      {
         returnValue = 1;
      }
      else if (mStartLocation < exon2.mStartLocation)
      {
         returnValue = -1;
      }
      else
      {
         if (mEndLocation > exon2.mEndLocation)
         {
            returnValue = 1;
         }
         else if (mEndLocation < exon2.mEndLocation)
         {
            returnValue = -1;
         }
      }

      return returnValue;
   }

}