com.hfg.bio.seq.translation.Codon 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.translation;

import com.hfg.util.StringUtil;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Codon container.
 
  @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 Codon
{
   private String     mTriplet;
   private Character  mAA;
   private boolean    mContainsDegenerateBases;
   private CodonUsage mCodonUsage;

   public static final String XML_CODON       = "Codon";
   public static final String XML_AA_ATT      = "aa";
   public static final String XML_TRIPLET_ATT = "triplet";

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

   //---------------------------------------------------------------------------
   public Codon(String inTriplet)
   {
      if (! StringUtil.isSet(inTriplet)
          || 3 != inTriplet.length())
      {
         throw new RuntimeException("Codons must be three nucleotides long!");
      }

      setTriplet(inTriplet);
   }

   //---------------------------------------------------------------------------
   public Codon(XMLTag inXMLTag)
   {
      inXMLTag.verifyTagName(XML_CODON);

      setTriplet(inXMLTag.getAttributeValue(XML_TRIPLET_ATT));

      String aa = inXMLTag.getAttributeValue(XML_AA_ATT);
      {
         if (StringUtil.isSet(aa))
         {
            if (aa.length() > 1)
            {
               throw new RuntimeException("The specified aa value " + StringUtil.singleQuote(aa) + " is longer than 1 character!");
            }

            mAA = aa.charAt(0);
         }
      }

      XMLTag codonUsageTag = inXMLTag.getOptionalSubtagByName(CodonUsage.XML_CODON_USAGE);
      if (codonUsageTag != null)
      {
         mCodonUsage = new CodonUsage(codonUsageTag);
      }
   }


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

   //---------------------------------------------------------------------------
   public Codon setAA(Character inValue)
   {
      mAA = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public Character getAA()
   {
      return mAA;
   }

   //---------------------------------------------------------------------------
   public Codon setCodonUsage(CodonUsage inValue)
   {
      mCodonUsage = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public CodonUsage getCodonUsage()
   {
      return mCodonUsage;
   }

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

   //---------------------------------------------------------------------------
   public XMLTag toXMLTag()
   {
      XMLTag tag = new XMLTag(XML_CODON);
      tag.setAttribute(XML_TRIPLET_ATT, mTriplet);
      if (mAA != null)
      {
         tag.setAttribute(XML_AA_ATT, mAA);
      }

      if (mCodonUsage != null)
      {
         tag.addSubtag(mCodonUsage.toXMLTag());
      }

      return tag;
   }

   //---------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      boolean result = false;
      if (inObj2 != null
          && inObj2 instanceof Codon)
      {
         Codon codon2 = (Codon) inObj2;

         result = toString().equals(codon2.toString());
      }

      return result;
   }

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

   //---------------------------------------------------------------------------
   public boolean containsDegenerateBases()
   {
      return mContainsDegenerateBases;
   }

   //###########################################################################
   // PRIVATE METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   private void setTriplet(String inValue)
   {
      mTriplet = inValue.toUpperCase().replaceAll("U", "T"); // Force everything into uppercase DNA

      mContainsDegenerateBases = false;
      for (Character nucleotide : mTriplet.toCharArray())
      {
         if (! "ATGC".contains(nucleotide + ""))
         {
            mContainsDegenerateBases = true;
            break;
         }
      }
   }

}