info.bioinfweb.commons.bio

Enum CharacterSymbolMeaning

java.lang.Object

java.lang.Enum<CharacterSymbolMeaning>

info.bioinfweb.commons.bio.CharacterSymbolMeaning

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<CharacterSymbolMeaning>

public enum CharacterSymbolMeaning
extends java.lang.Enum<CharacterSymbolMeaning>

Enumerates defined meanings of single character states in sequence alignments.

Since:

1.2.0

Author:

Ben Stöver

Enum Constant Summary

Enum Constants

Enum Constant and Description
CHARACTER_STATE Indicates that a token is a representation of a character state (e.g.
GAP Indicates that the string representation of a token is the gap character or token (e.g.
MATCH Indicates that the string representation of a token is the match character or token (e.g.
MISSING Indicates that the string representation of a token is the missing data character or token (e.g.
OTHER Indicates that a token has some other meaning which is not enumerated by this class.

Method Summary

Modifier and Type	Method and Description
java.lang.Character	getDefaultSymbol() Returns the symbol usually used to represent this meaning.
static CharacterSymbolMeaning	meaningByDefaultSymbol(char c) Returns the according meaning, if the specified character is one of , or .
static CharacterSymbolMeaning	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static CharacterSymbolMeaning[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

GAP

public static final CharacterSymbolMeaning GAP

Indicates that the string representation of a token is the gap character or token (e.g. '-').

MISSING

public static final CharacterSymbolMeaning MISSING

Indicates that the string representation of a token is the missing data character or token (e.g. '?').

MATCH

public static final CharacterSymbolMeaning MATCH

Indicates that the string representation of a token is the match character or token (e.g. '.').

CHARACTER_STATE

public static final CharacterSymbolMeaning CHARACTER_STATE

Indicates that a token is a representation of a character state (e.g. a nucleotide, an amino acid, an ambiguity code, ...).

OTHER

public static final CharacterSymbolMeaning OTHER

Indicates that a token has some other meaning which is not enumerated by this class.

Method Detail

values

public static CharacterSymbolMeaning[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (CharacterSymbolMeaning c : CharacterSymbolMeaning.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static CharacterSymbolMeaning valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

getDefaultSymbol

public java.lang.Character getDefaultSymbol()

Returns the symbol usually used to represent this meaning.

Returns:

the default symbol or null if the current state is not GAP, MISSING or MATCH

meaningByDefaultSymbol

public static CharacterSymbolMeaning meaningByDefaultSymbol(char c)

Returns the according meaning, if the specified character is one of , or .

Parameters:

c - the character to be converted

Returns:

the according meaning or null if the meaning could not be determined from the character