public class Comparison
extends java.lang.Object
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.
Constructor | Description |
---|---|
Comparison() |
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(java.lang.String seq1,
java.lang.String seq2) |
this is a gapped PID calculation
|
static float |
PID(java.lang.String seq1,
java.lang.String seq2,
int start,
int end) |
public static final float PID(java.lang.String seq1, java.lang.String seq2)
s1
- SequenceIs2
- SequenceIpublic static final float PID(java.lang.String seq1, java.lang.String seq2, int start, int end)
public static final boolean isGap(char c)
c
- gap character is one of the symbols in {' ','-','.'}