com.hfg.bio.seq.pattern.PrositePatternPosition 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 com.hfg.math.Range;
import com.hfg.util.StringBuilderPlus;

//------------------------------------------------------------------------------
/**
 Prosite pattern position.
 
 @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 PrositePatternPosition
{
   private PrositePatternPositionType mType;
   private String         mResidues;
   private Range mCountRange;
   private boolean        mLazyMatchMode;
   private boolean        mMismatchNotAllowed;

   //###########################################################################
   // PACKAGE METHODS
   //###########################################################################

   //------------------------------------------------------------------------
   @Override
   public String toString()
   {
      StringBuilderPlus buffer = new StringBuilderPlus();

      if (getType().equals(PrositePatternPositionType.NOT))
      {
         buffer.append("^");
      }
      else if (getType().equals(PrositePatternPositionType.ONE_OF))
      {
         buffer.append("[");
      }

      String residues = getResidues();
      buffer.append(residues != null ? residues : "x");

      if (getType().equals(PrositePatternPositionType.ONE_OF))
      {
         buffer.append("]");
      }

      Range countRange = getCountRange();
      if (countRange != null)
      {
         buffer.append("(")
               .append(countRange.getStart())
               .delimitedAppend(countRange.length() > 1 ? countRange.getEnd() : "")
               .append(")");
      }
      
      return buffer.toString();
   }

   //------------------------------------------------------------------------
   void setType(PrositePatternPositionType inValue)
   {
      mType = inValue;
   }

   //------------------------------------------------------------------------
   PrositePatternPositionType getType()
   {
      return mType;
   }

   //------------------------------------------------------------------------
   void setResidues(String inValue)
   {
      mResidues = inValue;
   }

   //------------------------------------------------------------------------
   String getResidues()
   {
      return mResidues;
   }

   //------------------------------------------------------------------------
   boolean matchesResidue(char inTargetResidue)
   {
      boolean result = false;
      switch (mType)
      {
         case IS_ANY:
            result = true;
            break;
         case IS:
         case ONE_OF:
            result = mResidues.contains(inTargetResidue + "");
            break;
         case NOT:
            result = ! mResidues.contains(inTargetResidue + "");
            break;
      }

      return result;
   }

   //------------------------------------------------------------------------
   void setCountRange(Range inValue)
   {
      mCountRange = inValue;
   }

   //------------------------------------------------------------------------
   boolean hasCountRange()
   {
      return mCountRange != null;
   }

   //------------------------------------------------------------------------
   Range getCountRange()
   {
      return mCountRange;
   }


   //------------------------------------------------------------------------
   void setUseLazyMatchMode(boolean inValue)
   {
      mLazyMatchMode = inValue;
   }

   //------------------------------------------------------------------------
   boolean useLazyMatchMode()
   {
      return mLazyMatchMode;
   }


   //------------------------------------------------------------------------
   void setMismatchNotAllowed(boolean inValue)
   {
      mMismatchNotAllowed = inValue;
   }

   //------------------------------------------------------------------------
   boolean mismatchNotAllowed()
   {
      return mMismatchNotAllowed;
   }

}