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


import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;

import com.hfg.bio.taxonomy.NCBITaxon;
import com.hfg.util.CompareUtil;
import com.hfg.util.io.StreamUtil;
import com.hfg.xml.XMLNode;

//------------------------------------------------------------------------------
/**
 * Biological DNA or RNA sequence.
 *
 * @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 NucleicAcid extends BioSequencePlusImpl
{
   //##########################################################################
   // PRIVATE FIELDS
   //##########################################################################

   private SeqQualityScores mQualityScores;


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

   //--------------------------------------------------------------------------
   public NucleicAcid()
   {
      super();
   }

   //--------------------------------------------------------------------------
   public NucleicAcid(XMLNode inXML)
   {
      super(inXML);
   }

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

   //--------------------------------------------------------------------------
   @Override
   public NucleicAcid clone()
   {
      clearCalculatedProperties();

      NucleicAcid theClone = (NucleicAcid) super.clone();

      if (mQualityScores != null)
      {
         theClone.mQualityScores = mQualityScores.clone();
      }

      return theClone;
   }

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

      if (this == inObj2)
      {
         result = 0;
      }
      else if (inObj2 != null
               && inObj2 instanceof NucleicAcid)
      {
         NucleicAcid nucleicAcid2 = (NucleicAcid) inObj2;

         // First compare the lengths
         result = CompareUtil.compare(length(), nucleicAcid2.length());

         if (0 == result)
         {
            // Second compare the sequences themselves
            result = CompareUtil.compare(getSequence(), nucleicAcid2.getSequence());
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   public BioSequenceType getType()
   {
      return BioSequenceType.NUCLEIC_ACID;
   }

   //--------------------------------------------------------------------------
   @Override
   public NucleicAcid setID(String inValue)
   {
      return (NucleicAcid) super.setID(inValue);
   }

   //--------------------------------------------------------------------------
   @Override
   public NucleicAcid setDescription(CharSequence inValue)
   {
      return (NucleicAcid) super.setDescription(inValue);
   }


   //--------------------------------------------------------------------------
   @Override
   public NucleicAcid setNCBITaxon(NCBITaxon inValue)
   {
      return (NucleicAcid) super.setNCBITaxon(inValue);
   }

   //--------------------------------------------------------------------------
   @Override
   public NucleicAcid setSequence(CharSequence inValue)
   {
      return (NucleicAcid) super.setSequence(inValue);
   }

   //--------------------------------------------------------------------------
   public String getComplementSequence()
   {
      String outRevCompSeq = null;

      try
      {
         outRevCompSeq = StreamUtil.inputStreamToString(getComplementSequenceStream());
      }
      catch (IOException e)
      {
         throw new RuntimeException(e);
      }

      return outRevCompSeq;
   }

   //--------------------------------------------------------------------------
   public String getReverseSequence()
   {
      String outRevCompSeq = null;

      try
      {
         outRevCompSeq = StreamUtil.inputStreamToString(getReverseSequenceStream());
      }
      catch (IOException e)
      {
         throw new RuntimeException(e);
      }

      return outRevCompSeq;
   }

   //--------------------------------------------------------------------------
   public String getReverseComplementSequence()
   {
      String outRevCompSeq = null;

      try
      {
         outRevCompSeq = StreamUtil.inputStreamToString(getReverseComplementSequenceStream());
      }
      catch (IOException e)
      {
         throw new RuntimeException(e);
      }

      return outRevCompSeq;
   }

   //--------------------------------------------------------------------------
   public Reader getComplementSequenceReader()
   {
      InputStream seqStream = getComplementSequenceStream();
      return (null == seqStream ? null : new InputStreamReader(seqStream));
   }

   //--------------------------------------------------------------------------
   protected Reader getReverseSequenceReader()
   {
      InputStream seqStream = getReverseSequenceStream();
      return (null == seqStream ? null : new InputStreamReader(seqStream));
   }

   //--------------------------------------------------------------------------
   public Reader getReverseComplementSequenceReader()
   {
      InputStream seqStream = getReverseComplementSequenceStream();
      return (null == seqStream ? null : new InputStreamReader(seqStream));
   }

   //--------------------------------------------------------------------------
   public InputStream getComplementSequenceStream()
   {
      InputStream seqStream = getSequenceStream();
      return (null == seqStream ? null : new NucleicAcidComplementFilterInputStream(seqStream));
   }

   //--------------------------------------------------------------------------
   @Override
   public InputStream getReverseSequenceStream()
   {
      return super.getReverseSequenceStream();
   }

   //--------------------------------------------------------------------------
   public InputStream getReverseComplementSequenceStream()
   {
      InputStream seqStream = getReverseSequenceStream();
      return (null == seqStream ? null : new NucleicAcidComplementFilterInputStream(seqStream));
   }

   //--------------------------------------------------------------------------
   public NucleicAcid setSeqQualityScores(SeqQualityScores inValue)
   {
      mQualityScores = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public SeqQualityScores getSeqQualityScores()
   {
      return mQualityScores;
   }

}