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

Show more of this group Show more artifacts with this name
Show all versions of com_hfg Show documentation
com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.seq;



import java.util.Arrays;

import com.hfg.exception.ProgrammingException;
import com.hfg.util.StringBuilderPlus;

//------------------------------------------------------------------------------
/**
 Container for sequence quality scores.
 
 @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 SeqQualityScores implements Cloneable
{
   private SeqQualityScoreScheme mScheme;
   private String mQualityString;
   private short[] mQualityScores;

   private static final String sQualityChars = "!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~";
   private static SeqQualityScoreScheme sDefaultScheme = SeqQualityScoreScheme.sanger;

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

   //---------------------------------------------------------------------------
   public SeqQualityScores(String inEncodedQualityString)
   {
      this(inEncodedQualityString, sDefaultScheme);
   }

   //---------------------------------------------------------------------------
   public SeqQualityScores(String inEncodedQualityString, SeqQualityScoreScheme inScheme)
   {
      mQualityString = inEncodedQualityString;
      mScheme = inScheme;
   }

   //---------------------------------------------------------------------------
   public SeqQualityScores(short[] inQualityScores)
   {
      this(inQualityScores, sDefaultScheme);
   }

   //---------------------------------------------------------------------------
   public SeqQualityScores(short[] inQualityScores, SeqQualityScoreScheme inScheme)
   {
      mQualityScores = inQualityScores;
      mScheme = inScheme;
   }

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

   //--------------------------------------------------------------------------
   @Override
   public SeqQualityScores clone()
   {
      SeqQualityScores theClone;
      try
      {
         theClone = (SeqQualityScores) super.clone();
      }
      catch (CloneNotSupportedException e)
      {
         throw new ProgrammingException(e);
      }

      theClone.mQualityScores = Arrays.copyOfRange(mQualityScores, 0, mQualityScores.length);

      return theClone;
   }

   //---------------------------------------------------------------------------
   public SeqQualityScoreScheme getScheme()
   {
      return mScheme;
   }

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

   //---------------------------------------------------------------------------
   public String getEncodedQualityString()
   {
      if (null == mQualityString
            && mQualityScores != null)
      {
         mQualityString = encodeScores(mQualityScores);
      }

      return mQualityString;
   }

   //---------------------------------------------------------------------------
   public short[] getQualityScores()
   {
      if (null == mQualityScores
            && mQualityString != null)
      {
         mQualityScores = decodeScores(mQualityString);
      }

      return mQualityScores;
   }

   //---------------------------------------------------------------------------
   private static String encodeScores(short[] inScores)
   {
      StringBuilderPlus buffer = new StringBuilderPlus();
      for (short score : inScores)
      {
         buffer.append(sQualityChars.charAt(score));
      }

      return buffer.toString();
   }

   //---------------------------------------------------------------------------
   private static short[] decodeScores(String inScoreString)
   {
      short[] scores = new short[inScoreString.length()];
      for (int index = 0; index < inScoreString.length(); index++)
      {
         char scoreChar = inScoreString.charAt(index);

         scores[index] = (short) sQualityChars.indexOf(scoreChar);
      }

      return scores;
   }
}