IlluminaUtil.IlluminaAdapterPair (picard 2.8.1 API)

java.lang.Object
- java.lang.Enum<IlluminaUtil.IlluminaAdapterPair>
- - picard.util.IlluminaUtil.IlluminaAdapterPair

All Implemented Interfaces:

Serializable, Comparable<IlluminaUtil.IlluminaAdapterPair>, AdapterPair

Enclosing class:

IlluminaUtil
```
public static enum IlluminaUtil.IlluminaAdapterPair
extends 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

SINGLE_END

TRUSEQ_SMALLRNA

Enum Constants
Enum Constant and Description
`ALTERNATIVE_SINGLE_END`
`DUAL_INDEXED`
`FLUIDIGM`
`INDEXED`
`NEXTERA_V1`
`NEXTERA_V2`
`PAIRED_END`
`SINGLE_END`
`TRUSEQ_SMALLRNA`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`get3PrimeAdapter()`
`byte[]`	`get3PrimeAdapterBytes()`
`byte[]`	`get3PrimeAdapterBytesInReadOrder()`
`String`	`get3PrimeAdapterInReadOrder()`
`String`	`get5PrimeAdapter()`
`byte[]`	`get5PrimeAdapterBytes()`
`byte[]`	`get5PrimeAdapterBytesInReadOrder()`
`String`	`get5PrimeAdapterInReadOrder()`
`String`	`getName()`
`static IlluminaUtil.IlluminaAdapterPair`	`valueOf(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
```
  - 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(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
  - get3PrimeAdapter
```
public String get3PrimeAdapter()
```
    Specified by:
    
    get3PrimeAdapter in interface AdapterPair
  - get5PrimeAdapter
```
public String get5PrimeAdapter()
```
    Specified by:
    
    get5PrimeAdapter in interface AdapterPair
  - get3PrimeAdapterInReadOrder
```
public String get3PrimeAdapterInReadOrder()
```
    Specified by:
    
    get3PrimeAdapterInReadOrder in interface AdapterPair
  - get5PrimeAdapterInReadOrder
```
public 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 String getName()
```
    Specified by:
    
    getName in interface AdapterPair

Enum IlluminaUtil.IlluminaAdapterPair

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

PAIRED_END

INDEXED

SINGLE_END

NEXTERA_V1

NEXTERA_V2

DUAL_INDEXED

FLUIDIGM

TRUSEQ_SMALLRNA

ALTERNATIVE_SINGLE_END

Method Detail

values

valueOf

get3PrimeAdapter

get5PrimeAdapter

get3PrimeAdapterInReadOrder

get5PrimeAdapterInReadOrder

get3PrimeAdapterBytes

get5PrimeAdapterBytes

get3PrimeAdapterBytesInReadOrder

get5PrimeAdapterBytesInReadOrder

getName