jebl.evolution.align
Class ProfileCharacter

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

public class ProfileCharacter
extends java.lang.Object

Version:
$Id: ProfileCharacter.java 1025 2009-10-23 01:29:48Z matt_kearse $ Represents a single residue in a multiple alignment profile It can represent character frequencies inside an alignment column as a fraction of the total number of characters in that column.
Author:
Matt Kearse

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()
           
static ProfileCharacter getImmutableProfileCharacter(char character)
          An immutable ProfileCharacter that uses less memory than a mutable profile character.
 boolean isAllGaps()
           
 int print()
           
 void removeProfileCharacter(ProfileCharacter character)
           
static float score(ProfileCharacter character1, ProfileCharacter character2, Scores scores)
           
static float scoreSelf(ProfileCharacter character, Scores scores)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ProfileCharacter

public ProfileCharacter(int alphabetSize)
Method Detail

getImmutableProfileCharacter

public static ProfileCharacter getImmutableProfileCharacter(char character)
An immutable ProfileCharacter that uses less memory than a mutable profile character. The same immtuable ProfileCharacter may also be returned from other calls to this method.

Parameters:
character - the single character to wrap in a profile.
Returns:
an immutable ProfileCharacter

addCharacter

public void addCharacter(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 java.lang.String toString()
Overrides:
toString in class java.lang.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


http://code.google.com/p/jebl2/