Class ProfileCharacter

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

public class ProfileCharacter extends 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 Details

    • ProfileCharacter

      public ProfileCharacter(int alphabetSize)
  • Method Details

    • 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 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