Package jebl.evolution.align

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