jebl.evolution.align
Class ProfileCharacter

java.lang.Object
  jebl.evolution.align.ProfileCharacter

public class ProfileCharacter
extends Object

Author:

Matt Kearse

Field Summary

char[]	characters
int[]	count
int	numberOfUniqueCharacters
int	totalCharacters

Constructor Summary

ProfileCharacter(int alphabetSize)

Method Summary

void	addCharacter(char character, int increment)
void	addGaps(int count)
void	addProfileCharacter(ProfileCharacter character)
void	clear()
float	gapFraction()
boolean	isAllGaps()
int	print()
void	removeCharacter(char character, int increment)
void	removeProfileCharacter(ProfileCharacter character)
static float	score(ProfileCharacter character1, ProfileCharacter character2, Scores scores)
static float	scoreSelf(ProfileCharacter character, Scores scores)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

characters

public char[] characters

count

public int[] count

numberOfUniqueCharacters

public int numberOfUniqueCharacters

totalCharacters

public int totalCharacters

Constructor Detail

ProfileCharacter

public ProfileCharacter(int alphabetSize)

Method Detail

addCharacter

public void addCharacter(char character,
                         int increment)

removeCharacter

public void removeCharacter(char character,
                            int increment)

addProfileCharacter

public void addProfileCharacter(ProfileCharacter character)

removeProfileCharacter

public void removeProfileCharacter(ProfileCharacter character)

addGaps

public void addGaps(int count)

score

public static float score(ProfileCharacter character1,
                          ProfileCharacter character2,
                          Scores scores)

scoreSelf

public static float scoreSelf(ProfileCharacter character,
                              Scores scores)

print

public int print()

toString

public String toString()

Overrides:

toString in class Object

isAllGaps

public boolean isAllGaps()

clear

public void clear()

gapFraction

public float gapFraction()

Returns:

the fraction of characters that are gap Characters in this profile