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

import com.hfg.bio.Strand;
import com.hfg.util.CompareUtil;
import com.hfg.util.collection.OrderedMap;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;

//------------------------------------------------------------------------------
/**
 Frame for translation.
 
   @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 TranslationFrame implements Comparable
{
   private char   mLetter;
   private Strand mStrand;
   private int    mOffset;

   private static Map sValueMap = new OrderedMap(7);


   public static final TranslationFrame A = new TranslationFrame('A', Strand.PLUS, 0);
   public static final TranslationFrame B = new TranslationFrame('B', Strand.PLUS, 1);
   public static final TranslationFrame C = new TranslationFrame('C', Strand.PLUS, 2);
   public static final TranslationFrame D = new TranslationFrame('D', Strand.MINUS, 0);
   public static final TranslationFrame E = new TranslationFrame('E', Strand.MINUS, 1);
   public static final TranslationFrame F = new TranslationFrame('F', Strand.MINUS, 2);


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

   //---------------------------------------------------------------------------
   private TranslationFrame(char inLetter, Strand inStrand, int inOffset)
   {
      mLetter = inLetter;
      mStrand = inStrand;
      mOffset = inOffset;

      sValueMap.put(mLetter, this);
   }

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

   //---------------------------------------------------------------------------
   public static Collection values()
   {
      return sValueMap.values();
   }

   //---------------------------------------------------------------------------
   public static Collection values(Strand inStrand)
   {
      List values = new ArrayList(3);
      for (TranslationFrame frame : sValueMap.values())
      {
         if (frame.getStrand().equals(inStrand))
         {
            values.add(frame);
         }
      }

      return values;
   }

   //---------------------------------------------------------------------------
   public static TranslationFrame valueOf(String inStringValue)
   {
      TranslationFrame frame = null;
      if (inStringValue != null)
      {
         if (1 == inStringValue.length())
         {
            frame = sValueMap.get(inStringValue.toUpperCase().charAt(0));
         }

         // Maybe it was a number formatted as a string.
         if (null == frame)
         {
            try
            {
               String intString = inStringValue.trim();
               if (intString.startsWith("+"))
               {
                  intString = intString.substring(1);
               }

               int intValue = Integer.parseInt(intString);
               frame = valueOf(intValue);
            }
            catch (Exception e)
            {
               // Ignore
            }
         }
      }

      return frame;
   }

   //---------------------------------------------------------------------------
   public static TranslationFrame valueOf(char inCharValue)
   {
      TranslationFrame value = sValueMap.get(Character.toUpperCase(inCharValue));

      if (null == value)
      {
         // Maybe it was a number formatted as a char.
         try
         {
            int intValue = Integer.parseInt(inCharValue + "");
            value = valueOf(intValue);
         }
         catch (Exception e)
         {
            // Ignore
         }
      }

      return value;
   }

   //---------------------------------------------------------------------------
   public static TranslationFrame valueOf(int inIntValue)
   {
      TranslationFrame outFrame = null;

      if (inIntValue < 0)
      {
         inIntValue = (- inIntValue) + 3;
      }
      for (TranslationFrame frame : sValueMap.values())
      {
         if (frame.toInt() == inIntValue)
         {
            outFrame = frame;
         }
      }

      return outFrame;
   }

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

   //---------------------------------------------------------------------------
   public int getOffset()
   {
      return mOffset;
   }

   //---------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return mLetter + "";
   }

   //---------------------------------------------------------------------------
   public int toChar()
   {
      return mLetter;
   }

   //---------------------------------------------------------------------------
   public int toInt()
   {
      return mLetter - 'A' + 1;
   }

   //---------------------------------------------------------------------------
   public int compareTo(TranslationFrame inObj2)
   {
      return (inObj2 != null ? CompareUtil.compare(toChar(), inObj2.toChar()) : -1);
   }
}