picard.util

Enum IlluminaUtil.IlluminaAdapterPair

java.lang.Object

java.lang.Enum<IlluminaUtil.IlluminaAdapterPair>

picard.util.IlluminaUtil.IlluminaAdapterPair

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<IlluminaUtil.IlluminaAdapterPair>, AdapterPair

Enclosing class:

IlluminaUtil

public static enum IlluminaUtil.IlluminaAdapterPair
extends java.lang.Enum<IlluminaUtil.IlluminaAdapterPair>
implements AdapterPair

Describes adapters used on each pair of strands

Enum Constant Summary

Enum Constants

Enum Constant and Description
ALTERNATIVE_SINGLE_END
DUAL_INDEXED
FLUIDIGM
INDEXED
NEXTERA_V1
NEXTERA_V2
PAIRED_END The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc.
SINGLE_END
TRUSEQ_SMALLRNA

Method Summary

Modifier and Type	Method and Description
java.lang.String	get3PrimeAdapter()
byte[]	get3PrimeAdapterBytes()
byte[]	get3PrimeAdapterBytesInReadOrder()
java.lang.String	get3PrimeAdapterInReadOrder()
java.lang.String	get5PrimeAdapter()
byte[]	get5PrimeAdapterBytes()
byte[]	get5PrimeAdapterBytesInReadOrder()
java.lang.String	get5PrimeAdapterInReadOrder()
java.lang.String	getName()
static IlluminaUtil.IlluminaAdapterPair	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static IlluminaUtil.IlluminaAdapterPair[]	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

PAIRED_END

public static final IlluminaUtil.IlluminaAdapterPair PAIRED_END

The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc. All rights reserved. Derivative works created by Illumina customers are authorized for use with Illumina instruments and products only. All other uses are strictly prohibited.

INDEXED

public static final IlluminaUtil.IlluminaAdapterPair INDEXED

SINGLE_END

public static final IlluminaUtil.IlluminaAdapterPair SINGLE_END

NEXTERA_V1

public static final IlluminaUtil.IlluminaAdapterPair NEXTERA_V1

NEXTERA_V2

public static final IlluminaUtil.IlluminaAdapterPair NEXTERA_V2

DUAL_INDEXED

public static final IlluminaUtil.IlluminaAdapterPair DUAL_INDEXED

FLUIDIGM

public static final IlluminaUtil.IlluminaAdapterPair FLUIDIGM

TRUSEQ_SMALLRNA

public static final IlluminaUtil.IlluminaAdapterPair TRUSEQ_SMALLRNA

ALTERNATIVE_SINGLE_END

public static final IlluminaUtil.IlluminaAdapterPair ALTERNATIVE_SINGLE_END

Method Detail

values

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

Returns:

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

valueOf

public static IlluminaUtil.IlluminaAdapterPair 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

get3PrimeAdapter

public java.lang.String get3PrimeAdapter()

Specified by:

get3PrimeAdapter in interface AdapterPair

get5PrimeAdapter

public java.lang.String get5PrimeAdapter()

Specified by:

get5PrimeAdapter in interface AdapterPair

get3PrimeAdapterInReadOrder

public java.lang.String get3PrimeAdapterInReadOrder()

Specified by:

get3PrimeAdapterInReadOrder in interface AdapterPair

get5PrimeAdapterInReadOrder

public java.lang.String get5PrimeAdapterInReadOrder()

Specified by:

get5PrimeAdapterInReadOrder in interface AdapterPair

get3PrimeAdapterBytes

public byte[] get3PrimeAdapterBytes()

Specified by:

get3PrimeAdapterBytes in interface AdapterPair

get5PrimeAdapterBytes

public byte[] get5PrimeAdapterBytes()

Specified by:

get5PrimeAdapterBytes in interface AdapterPair

get3PrimeAdapterBytesInReadOrder

public byte[] get3PrimeAdapterBytesInReadOrder()

Specified by:

get3PrimeAdapterBytesInReadOrder in interface AdapterPair

get5PrimeAdapterBytesInReadOrder

public byte[] get5PrimeAdapterBytesInReadOrder()

Specified by:

get5PrimeAdapterBytesInReadOrder in interface AdapterPair

getName

public java.lang.String getName()

Specified by:

getName in interface AdapterPair