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

import com.hfg.setting.SettingXML;
import com.hfg.util.CompareUtil;
import com.hfg.xml.XMLTag;
import com.hfg.xml.XMLTaggable;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;

//------------------------------------------------------------------------------
/**
 * Enum-like sequence strand class
 *
 * @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 final class Strand implements Serializable, XMLTaggable, Comparable
{

   private char   mSymbol;
   private String mName;
   private int    mIndex;

   private static List sList = new ArrayList(3);

   public static final Strand FORWARD    = new Strand('+', "Forward");
   public static final Strand PLUS       = Strand.FORWARD;
   public static final Strand SENSE      = Strand.FORWARD;
   public static final Strand REVERSE    = new Strand('-', "Reverse");
   public static final Strand MINUS      = Strand.REVERSE;
   public static final Strand ANITSENSE  = Strand.REVERSE;


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

   //--------------------------------------------------------------------------
   private Strand(char inSymbol, String inName)
   {
      mSymbol = inSymbol;
      mName = inName;
      mIndex = sList.size();
      sList.add(this);
   }

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

   //--------------------------------------------------------------------------
   public final char getSymbol()
   {
      return mSymbol;
   }

   //--------------------------------------------------------------------------
   public final String getName()
   {
      return mName;
   }

   //--------------------------------------------------------------------------
   @Override
   public final String toString()
   {
      return mName;
   }

   //--------------------------------------------------------------------------
   @Override
   public final int hashCode()
   {
      return super.hashCode();
   }

   //--------------------------------------------------------------------------
   @Override
   public final boolean equals(Object inObj2)
   {
      return (0 == compareTo(inObj2));
   }

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

      if (inObj2 != null
            && inObj2 instanceof Strand)
      {
         Strand strand2 = (Strand) inObj2;

         result = CompareUtil.compare(mIndex, strand2.mIndex);
      }

      return result;
   }

   //--------------------------------------------------------------------------
   public XMLTag toXMLTag()
   {
      XMLTag tag = new XMLTag(HfgBioXML.STRAND_TAG);
      tag.setAttribute(SettingXML.CLASS_ATT, getClass().getName());
      tag.setAttribute(SettingXML.ENUM_ATT, "true");
      tag.setContent(getName());

      return tag;
   }

   //--------------------------------------------------------------------------
   public static Strand valueOf(String inValue)
   {
      Strand strand = null;

      if (inValue != null)
      {
         if (inValue.equalsIgnoreCase("+")
             || inValue.equalsIgnoreCase("plus")
             || inValue.equalsIgnoreCase("sense")
             || inValue.equalsIgnoreCase("f")
             || inValue.equalsIgnoreCase("forward"))
         {
            strand = Strand.FORWARD;
         }
         else if (inValue.equalsIgnoreCase("-")
             || inValue.equalsIgnoreCase("minus")
             || inValue.equalsIgnoreCase("antisense")
             || inValue.equalsIgnoreCase("r")
             || inValue.equalsIgnoreCase("reverse"))
         {
            strand = Strand.REVERSE;
         }
         else
         {
            throw new RuntimeException("'" + inValue + "' is not a recognized Strand value.");
         }
      }

      return strand;
   }

   //--------------------------------------------------------------------------
   /**
    * This method is called after de-serialization, allowing the object
    * to nominate a replacement object to be used in the output
    * graph instead of this object. We don't want multiple objects of each type
    * to exist in a target VM, so instances replace themselves with
    * local objects.
    */
   private Object readResolve()
   {
      return sList.get(mIndex);
   }
}