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com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.phylogeny;

import com.hfg.bio.seq.BioSequence;

//------------------------------------------------------------------------------
/**
 Distance matrix calculation method that is simply the fraction of mismatches.
  distance = mismatches / aligned_length
 
 If both sequences contain a gap at a given position, it is not counted towards
 the alignment length.

 @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 UncorrectedModel implements DistanceMatrixModel
{
   //---------------------------------------------------------------------------
   public UncorrectedModel()
   {
   }

   //---------------------------------------------------------------------------
   /**
    Returns the model name as required by the DistanceMatrixModel interface.
    */
   public String name()
   {
      return "Uncorrected";
   }

   //---------------------------------------------------------------------------
   /**
    Calculates the distance score for a pair of sequences.
    The sequences must be aligned to be the same length.
    If both sequences contain a gap at a given position, it is not counted towards
    the alignment length.
    */
   public float calculateDistance(BioSequence inSeq1, BioSequence inSeq2)
   {
      if (inSeq1.length() != inSeq2.length())
      {
         throw new RuntimeException("The length of seq1 [" + inSeq1.length() + "] and seq2 [" + inSeq2.length() + "] don't match!");
      }

      int mismatches = 0;
      int length = 0;

      String seq1 = inSeq1.getSequence().toUpperCase();
      String seq2 = inSeq2.getSequence().toUpperCase();

      // This way will avoid a NaN result from comparing two all-gapped sequences.

      float distance = 0.0f;
      if (! seq1.equals(seq2))
      {
         for (int i = 0; i < seq1.length(); i++)
         {
            char char1 = seq1.charAt(i);
            char char2 = seq2.charAt(i);
            if (char1 != char2) mismatches++;
            // If both seqs are gapped at this position, don't count it against length.
            if (!(char1 == '-' && char2 == '-')) length++;
         }

         distance = mismatches / (float) length;
      }

      return distance;
   }
}