Package jebl.evolution.align

Class 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 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)

      • 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