org.utgenome.gwt.utgb.client.bio
Enum IUPAC

java.lang.Object
  java.lang.Enum<IUPAC>
      org.utgenome.gwt.utgb.client.bio.IUPAC

All Implemented Interfaces:

Serializable, Comparable<IUPAC>

public enum IUPAC
extends Enum<IUPAC>

IUPAC: allele variation notation

Author:

leo

Enum Constant Summary

A

B

C

D

G

H

K

M

N

None

R

S

T

V

W

Y

Field Summary

int	bitFlag
String	variation

Method Summary

IUPAC	complement()
static IUPAC	decode(byte code)
static IUPAC	encode(char base)
static IUPAC	find(String iupacCode)
String	toGenoType() Convert this IUPAC code the concatenation of allele bases (e.g., AC, AT, CGT, etc.)
static IUPAC	toIUPAC(String genoType) Translate a genotype to the corresponding IUPAC code
static IUPAC	valueOf(String name) Returns the enum constant of this type with the specified name.
static IUPAC[]	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

None

public static final IUPAC None

A

public static final IUPAC A

C

public static final IUPAC C

G

public static final IUPAC G

T

public static final IUPAC T

M

public static final IUPAC M

R

public static final IUPAC R

W

public static final IUPAC W

S

public static final IUPAC S

Y

public static final IUPAC Y

K

public static final IUPAC K

V

public static final IUPAC V

H

public static final IUPAC H

D

public static final IUPAC D

B

public static final IUPAC B

N

public static final IUPAC N

Field Detail

variation

public final String variation

bitFlag

public final int bitFlag

Method Detail

values

public static IUPAC[] 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 (IUPAC c : IUPAC.values())
    System.out.println(c);

Returns:

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

valueOf

public static IUPAC valueOf(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:

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

NullPointerException - if the argument is null

complement

public IUPAC complement()

toGenoType

public String toGenoType()

Convert this IUPAC code the concatenation of allele bases (e.g., AC, AT, CGT, etc.)

Returns:

toIUPAC

public static IUPAC toIUPAC(String genoType)

Translate a genotype to the corresponding IUPAC code

Parameters:

genoType - concatenation of ACGT characters

Returns:

find

public static IUPAC find(String iupacCode)

encode

public static IUPAC encode(char base)

decode

public static IUPAC decode(byte code)