jebl.evolution.align
Class ProfileCharacter
java.lang.Object
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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
ProfileCharacter
public ProfileCharacter(int alphabetSize)
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/