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

import com.hfg.bio.HfgBioXML;
import com.hfg.bio.seq.BioSequence;
import com.hfg.bio.seq.SeqLocation;
import com.hfg.exception.ProgrammingException;
import com.hfg.util.StringUtil;
import com.hfg.xml.XMLNode;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Base class for the aligned sequences that compose a pairwise sequence alignment.
 
 @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 abstract class AlignedSeq implements Cloneable
{
   private BioSequence mSeq;
   private String      mAlignedSeq;
   private SeqLocation mLocation;

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

   //---------------------------------------------------------------------------
   public AlignedSeq(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)
   {
      init(inSeq, inAlignedSeq, inStart);
   }

   //--------------------------------------------------------------------------
   public AlignedSeq(XMLNode inXMLNode)
   {
      int start = Integer.parseInt(inXMLNode.getAttributeValue(HfgBioXML.START_ATT));

      XMLNode seqTag = inXMLNode.getOptionalSubtagByName(HfgBioXML.QUERY);
      if (null == seqTag)
      {
         seqTag = inXMLNode.getOptionalSubtagByName(HfgBioXML.SUBJECT);
      }

      BioSequence seq = (seqTag != null ? BioSequence.instantiate((XMLNode) seqTag.getSubtags().get(0)) : null);

      init(seq, inXMLNode.getUnescapedContent(), start);
   }

   //---------------------------------------------------------------------------
   private void init(BioSequence inSeq, CharSequence inAlignedSeq, int inStart)
   {
      mSeq        = inSeq;
      mAlignedSeq = inAlignedSeq.toString();
      mLocation   = new SeqLocation().setStart(inStart);

      mLocation.setEnd(mAlignedSeq.length() - StringUtil.getCharCount(mAlignedSeq, '-') + mLocation.getStart() - 1);
   }

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

   //---------------------------------------------------------------------------
   @Override
   public String toString()
   {
      StringBuilder buffer = new StringBuilder();
      if (mLocation != null)
      {
         buffer.append(mLocation);
      }

      return buffer.toString();
   }

   //--------------------------------------------------------------------------
   public XMLNode toXMLNode()
   {
      XMLTag tag = new XMLTag(this instanceof AlignedQuery ? HfgBioXML.ALIGNED_QUERY : HfgBioXML.ALIGNED_SUBJECT);

      tag.setAttribute(HfgBioXML.START_ATT, mLocation.getStart());
      tag.setContent(mAlignedSeq);

      if (mSeq != null)
      {
         XMLTag seqTag = new XMLTag(this instanceof AlignedQuery ? HfgBioXML.QUERY : HfgBioXML.SUBJECT);
         seqTag.addSubtag(mSeq.toXMLNode());

         tag.addSubtag(seqTag);
      }

      return tag;
   }

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

      if (mSeq != null)
      {
         cloneObj.mSeq = mSeq.clone();

      }

      if (mLocation != null)
      {
         cloneObj.mLocation = mLocation.clone();

      }

      return cloneObj;
   }

   //---------------------------------------------------------------------------
   public BioSequence getSeq()
   {
      return mSeq;
   }

   //---------------------------------------------------------------------------
   public AlignedSeq setAlignedSeq(CharSequence inValue)
   {
      mAlignedSeq = inValue.toString();
      return this;
   }

   //---------------------------------------------------------------------------
   public String getAlignedSeq()
   {
      return mAlignedSeq;
   }

   //---------------------------------------------------------------------------
   public SeqLocation getSeqLocation()
   {
      return mLocation;
   }

   //---------------------------------------------------------------------------
   public int getIndexedPosition(int inLinearPosition)
   {
      int indexedPosition = 0;
      int linearPosition = 0;

      int residueCount = 0;
      int index = 0;
      for (char residue : mAlignedSeq.toCharArray())
      {
         if (residue != '-')
         {
            residueCount++;
         }

         linearPosition = mLocation.getStart() + residueCount - 1 + (residue != '-' ? 0 : 1);
         if (linearPosition == inLinearPosition)
         {
            indexedPosition = index;
            break;
         }

         index++;
      }

      return indexedPosition;
   }

   //---------------------------------------------------------------------------
   public int getLinearPosition(int inIndexedPosition)
   {
      int linearPosition = 0;

      int residueCount = 0;
      int index = 0;
      for (char residue : mAlignedSeq.toCharArray())
      {
         if (residue != '-')
         {
            residueCount++;
         }

         if (index == inIndexedPosition)
         {
            linearPosition = mLocation.getStart() + residueCount - 1 + (residue != '-' ? 0 : 1);
            break;
         }

         index++;
      }

      return linearPosition;
   }

   //---------------------------------------------------------------------------
   public int getNTerminalGapLength()
   {
      int gapLength = 0;
      for (int i = 0; i < mAlignedSeq.length(); i++)
      {
         if ('-' == mAlignedSeq.charAt(i))
         {
            gapLength++;
         }
         else
         {
            break;
         }
      }

      return gapLength;
   }

   //---------------------------------------------------------------------------
   public int getCTerminalGapLength()
   {
      int gapLength = 0;
      for (int i = mAlignedSeq.length() - 1; i > 0; i--)
      {
         if ('-' == mAlignedSeq.charAt(i))
         {
            gapLength++;
         }
         else
         {
            break;
         }
      }

      return gapLength;
   }
}