Package org.biojava.nbio.phylo

Class Comparison

java.lang.Object
org.biojava.nbio.phylo.Comparison
public class Comparison extends Object
This class provides static methods for the calculation of the percentage of identity between two aligned sequences.

Since 4.1.1 the methods for distance inference in forester are also used in BioJava, so this implementation of percentage of identity is not needed anymore. However, the code is maintained as the own BioJava implementation.

Author:
Scooter Willis

  • Constructor Details

    • Comparison

      public Comparison()

  • Method Details

    • PID

      public static final float PID(String seq1, String seq2)
      this is a gapped PID calculation
      Parameters:
      s1 - SequenceI
      s2 - SequenceI
      Returns:
      float

    • PID

      public static final float PID(String seq1, String seq2, int start, int end)

    • isGap

      public static final boolean isGap(char c)
      Method that determines if a character means a gap in the alignment.
      Parameters:
      c - gap character is one of the symbols in {' ','-','.'}
      Returns:
      true if it is a gap, false otherwise