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 Summary

Constructors

Constructor	Description
Comparison()

Method Summary

Modifier and Type	Method	Description
static boolean	isGap(char c)	Method that determines if a character means a gap in the alignment.
static float	PID(String seq1, String seq2)	this is a gapped PID calculation
static float	PID(String seq1, String seq2, int start, int end)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Comparison

public Comparison()

Method Detail

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