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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.*;
import java.lang.reflect.Constructor;
import java.util.Collection;
import java.util.List;

import com.hfg.bio.DbXref;
import com.hfg.bio.HfgBioXML;
import com.hfg.bio.seq.format.SeqCitation;
import com.hfg.bio.seq.format.feature.FeatureKey;
import com.hfg.bio.seq.format.feature.SeqFeature;
import com.hfg.util.StringUtil;
import com.hfg.xml.XMLNode;


//------------------------------------------------------------------------------
/**
 Interface for a biological Protein, 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 interface BioSequence extends Cloneable
{

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

   //--------------------------------------------------------------------------
   public BioSequence clone();

   //--------------------------------------------------------------------------
   /**
    Sets the id or name for the sequence.
    Returns 'this' which can be useful for method chaining.
    @param inValue the id to use for this sequence
    @return this BioSequence to enable method chaining
    */
   public BioSequence setID(String inValue);

   //--------------------------------------------------------------------------
   public String getID();

   //--------------------------------------------------------------------------
   public BioSequenceType getType();

   //--------------------------------------------------------------------------
   public BioSequence setDescription(CharSequence inValue);

   //--------------------------------------------------------------------------
   public String getDescription();

   //--------------------------------------------------------------------------
   public BioSequence setSequence(CharSequence inValue);

   //--------------------------------------------------------------------------
   public BioSequence setSequence(Reader inReader);

   //--------------------------------------------------------------------------
   public String getSequence();

   //--------------------------------------------------------------------------
   public String getSubSequence(SeqLocation inSeqLocation);

   //--------------------------------------------------------------------------
   public int length();

   //--------------------------------------------------------------------------
   /**
    Returns the residue character at the specified (1-based) sequence location.
    @param inIndex the 1-based sequence location at which to retrieve the residue
    @return the residue at the specified index
    */
   public char residueAt(int inIndex);

   //--------------------------------------------------------------------------
   public Reader getSequenceReader();

   //--------------------------------------------------------------------------
   public Reader getSubSequenceReader(SeqLocation inSeqLocation);

   //--------------------------------------------------------------------------
   public InputStream getSequenceStream();


   //--------------------------------------------------------------------------
   public byte[] getMD5Checksum();

   //--------------------------------------------------------------------------
   public byte[] getSHA1Checksum();


   //--------------------------------------------------------------------------
   public void setAttribute(String inName, Object inValue);

   //--------------------------------------------------------------------------
   public Object getAttribute(String inName);

   //--------------------------------------------------------------------------
   public boolean hasAttribute(String inName);

   //--------------------------------------------------------------------------
   public Collection getAttributeNames();

   //--------------------------------------------------------------------------
   public Object removeAttribute(String inName);



   //--------------------------------------------------------------------------
   public XMLNode toXMLNode();

   //--------------------------------------------------------------------------
   public static BioSequence instantiate(XMLNode inXMLNode)
   {
      String classname = inXMLNode.getAttributeValue(HfgBioXML.CLASS_ATT);
      if (! StringUtil.isSet(classname))
      {
         throw new RuntimeException("No " + HfgBioXML.CLASS_ATT + " specified on sequence's XML tag!");
      }

      BioSequence seq = null;

      try
      {
         Class clazz = Class.forName(classname);
         Constructor constructor = clazz.getConstructor(XMLNode.class);
         seq = (BioSequence) constructor.newInstance(inXMLNode);
      }
      catch (Exception e)
      {
         throw new RuntimeException("Error during sequence instantiation from its XML tag!", e);
      }

      return seq;
   }
}