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

import java.util.HashMap;
import java.util.Map;

import com.hfg.bio.seq.BioSequenceType;
import com.hfg.bio.seq.alignment.matrix.SubstitutionMatrix;
import com.hfg.exception.ProgrammingException;
import com.hfg.util.collection.SparseMatrix;


//------------------------------------------------------------------------------
/**
 Container for multiple sequence alignment settings.
 
 @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 class MSA_Settings implements Cloneable
{
   private SubstitutionMatrix mMatrix;
   private boolean            mCaseInsensitive = false;
   private int                mKMerSize = sDefaultKMerSize;

   private Map mGapPenaltyMap = new HashMap<>(2);
   private SparseMatrix mTerminalPenaltyMatrix = new SparseMatrix<>();

   private static int sDefaultKMerSize = 3;
   private static GapPenalties       sDefaultGapPenalties = new GapPenalties().setOpenPenalty(-5f).setExtensionPenalty(-2f);
   private static Map sDefaultMatrixMap = new HashMap<>(2);

   static
   {
      sDefaultMatrixMap.put(BioSequenceType.PROTEIN, SubstitutionMatrix.BLOSUM62);
      sDefaultMatrixMap.put(BioSequenceType.NUCLEIC_ACID, SubstitutionMatrix.NUCLEOTIDE);
   }


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

   //---------------------------------------------------------------------------
   public MSA_Settings()
   {
      init();
   }

   //---------------------------------------------------------------------------
   private void init()
   {
      setGapPenalties(sDefaultGapPenalties);
      setPenalizeTerminalGaps(true);
   }

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

   //---------------------------------------------------------------------------
   public MSA_Settings setKMerSize(int inValue)
   {
      mKMerSize = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public int getKMerSize()
   {
      return mKMerSize;
   }

   //---------------------------------------------------------------------------
   public MSA_Settings setSubstitutionMatrix(SubstitutionMatrix inValue)
   {
      mMatrix = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public SubstitutionMatrix getSubstitutionMatrix(BioSequenceType inSeqType)
   {
      if (null == mMatrix)
      {
         mMatrix = sDefaultMatrixMap.get(inSeqType != null ? inSeqType : BioSequenceType.NUCLEIC_ACID);
      }

      return mMatrix;
   }



   //---------------------------------------------------------------------------
   /**
    If specified as true, the scoring matrix's scoreCaseInsensitive() method is used.
    @param inValue whether or not scoring is case insensitive
    @return this settings object (for possible method chaining)
    */
   public MSA_Settings setScoreCaseInsensitive(boolean inValue)
   {
      mCaseInsensitive = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public boolean getScoreCaseInsensitive()
   {
      return mCaseInsensitive;
   }


   //---------------------------------------------------------------------------
   /**
    Sets the specified gap penalties for both the query and subject.
    @param inValue GapPenalties to apply
    @return this settings object (for possible method chaining)
    */
   public MSA_Settings setGapPenalties(GapPenalties inValue)
   {
      setGapPenalties(PairwiseSeqType.QUERY, inValue.clone());
      setGapPenalties(PairwiseSeqType.SUBJECT, inValue.clone());
      return this;
   }

   //---------------------------------------------------------------------------
   public MSA_Settings setGapPenalties(PairwiseSeqType inPairwiseSeqType, GapPenalties inValue)
   {
      mGapPenaltyMap.put(inPairwiseSeqType, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   public GapPenalties getGapPenalties(PairwiseSeqType inPairwiseSeqType)
   {
      return mGapPenaltyMap.get(inPairwiseSeqType);
   }

   //---------------------------------------------------------------------------
   public MSA_Settings setPenalizeTerminalGaps(boolean inValue)
   {
      setPenalizeTerminalGaps(PairwiseSeqType.QUERY, inValue);
      setPenalizeTerminalGaps(PairwiseSeqType.SUBJECT, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   public MSA_Settings setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, boolean inValue)
   {
      setPenalizeTerminalGaps(inPairwiseSeqType, PairwiseSeqTerminus.LEFT, inValue);
      setPenalizeTerminalGaps(inPairwiseSeqType, PairwiseSeqTerminus.RIGHT, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   public MSA_Settings setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus, boolean inValue)
   {
      mTerminalPenaltyMatrix.put(inPairwiseSeqType, inPairwiseSeqTerminus, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   public Boolean getPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus)
   {
      return mTerminalPenaltyMatrix.get(inPairwiseSeqType, inPairwiseSeqTerminus);
   }


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

      return cloneObj;
   }
}