com.hfg.bio.seq.pattern.ProteinPatternMatcher Maven / Gradle / Ivy

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

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

import com.hfg.bio.seq.Protein;
import com.hfg.util.collection.CollectionUtil;

//------------------------------------------------------------------------------
/**
 Examines a query sequence to find instances of the specified patterns.
 
 @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 ProteinPatternMatcher
{
   private List mPatterns;

   private boolean mIgnoreGaps = false;

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

   //--------------------------------------------------------------------------
   public ProteinPatternMatcher()
   {
   }

   //--------------------------------------------------------------------------
   public ProteinPatternMatcher(ProteinPattern inPattern)
   {
      addPattern(inPattern);
   }

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

   //--------------------------------------------------------------------------
   public ProteinPatternMatcher addPattern(ProteinPattern inValue)
   {
      if (null == mPatterns)
      {
         mPatterns = new ArrayList<>(25);
      }

      mPatterns.add(inValue);
      inValue.setIgnoreGaps(mIgnoreGaps);

      return this;
   }

   //--------------------------------------------------------------------------
   public ProteinPatternMatcher addPatterns(Collection inValues)
   {
      if (CollectionUtil.hasValues(inValues))
      {
         for (ProteinPattern pattern : inValues)
         {
            addPattern(pattern);
         }
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public ProteinPatternMatcher setIgnoreGaps(boolean inValue)
   {
      mIgnoreGaps = inValue;
      if (CollectionUtil.hasValues(mPatterns))
      {
         for (ProteinPattern pattern : mPatterns)
         {
            pattern.setIgnoreGaps(inValue);
         }
      }

      return this;
   }

   //--------------------------------------------------------------------------
   public List match(Protein inQuery)
   {
      List matches = new ArrayList<>(25);

      for (ProteinPattern proteinPattern : mPatterns)
      {
         List chains = new ArrayList<>(5);
         if (CollectionUtil.hasValues(inQuery.getChains()))
         {
            chains.addAll(inQuery.getChains());
         }
         else
         {
            chains.add(inQuery);
         }

         for (Protein chain : chains)
         {
            SeqPatternMatcher m = proteinPattern.matcher(chain);
            List patternMatches = m.findAll();
            if (CollectionUtil.hasValues(patternMatches))
            {
               matches.addAll(patternMatches);
            }
         }
      }

      return matches;
   }
}