package com.hfg.bio.seq.pattern;

import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;

import com.hfg.bio.seq.BioSequenceType;
import com.hfg.bio.seq.Protein;
import com.hfg.bio.seq.SeqLocation;

//------------------------------------------------------------------------------
/**
 Container for a protein pattern (motif).
 <p>
 From the <a href='http://prosite.expasy.org/prosuser.html#conv_pa'>PROSITE user manual</a>:
 </p>
 <p>
 The patterns are described using the following conventions:
 <ul>
   <li>The standard IUPAC one-letter codes for the amino acids are used.</li>
   <li>The symbol 'x' is used for a position where any amino acid is accepted.</li>
   <li>Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses '[ ]'.
       For example: [ALT] stands for Ala or Leu or Thr.</li>
   <li>Ambiguities are also indicated by listing between a pair of curly brackets '{ }' the amino acids that are not accepted
       at a given position. For example: {AM} stands for any amino acid except Ala and Met.</li>
   <li>Each element in a pattern is separated from its neighbor by a '-'.</li>
   <li>Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical
       range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.</li>
   <li>When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a '&lt;' symbol
       or respectively ends with a '&gt;' symbol. In some rare cases (e.g. PS00267 or PS00539), '&gt;' can also occur inside square
       brackets for the C-terminal element. 'F-[GSTV]-P-R-L-[G&gt;]' means that either 'F-[GSTV]-P-R-L-G' or 'F-[GSTV]-P-R-L&gt;' are considered.</li>
   <li>A period ends the pattern.</li>
 </ul>
 <div>
   Examples:
   <pre>
    PA   [AC]-x-V-x(4)-{ED}.
   </pre>
   This pattern is translated as: [Ala or Cys]-any-Val-any-any-any-any-{any but Glu or Asp}
   <pre>
    PA   &lt;A-x-[ST](2)-x(0,1)-V.
   </pre>
   This pattern, which must be in the N-terminal of the sequence ('&lt;'), is translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
 </div>
 @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
// jataylor@hairyfatguy.com
//------------------------------------------------------------------------------

public class ProteinPattern extends SeqPattern<Protein, ProteinPatternMatch>
{
   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################

   //--------------------------------------------------------------------------
   public ProteinPattern(String inPrositePattern)
   {
      super(inPrositePattern);
   }

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

   //--------------------------------------------------------------------------
   public BioSequenceType getBioSequenceType()
   {
      return BioSequenceType.PROTEIN;
   }

   //--------------------------------------------------------------------------
   public ProteinPattern setIgnoreGaps(boolean inValue)
   {
      return (ProteinPattern) super.setIgnoreGaps(inValue);
   }

   //--------------------------------------------------------------------------
   @Override
   public ProteinPattern setMaxMismatches(int inValue)
   {
      return (ProteinPattern) super.setMaxMismatches(inValue);
   }

   //--------------------------------------------------------------------------
   protected ProteinPatternMatch createMatch(String inSeq, SeqLocation inLocation)
   {
      return new ProteinPatternMatch(this, inSeq, inLocation);
   }

}