com.milaboratory.core.io.sequence.fastq

Enum QualityFormat

java.lang.Object

java.lang.Enum<QualityFormat>

com.milaboratory.core.io.sequence.fastq.QualityFormat

All Implemented Interfaces:

Serializable, Comparable<QualityFormat>

public enum QualityFormat
extends Enum<QualityFormat>

A base class to store various sequencing quality formats. See corresponding Wikipedia page for details: link.

Enum Constant Summary

Enum Constants

Enum Constant and Description
Phred33 Phred quality values encoded with 33 value offset.
Phred64 Phred quality values encoded with 64 value offset.

Method Summary

Methods

Modifier and Type	Method and Description
static QualityFormat	fromName(String name)
byte	getMaxValue()
byte	getMinValue()
String	getName()
byte	getOffset()
String	toString()
static QualityFormat	valueOf(String name) Returns the enum constant of this type with the specified name.
static QualityFormat[]	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, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

Phred33

public static final QualityFormat Phred33

Phred quality values encoded with 33 value offset.

Allowed quality score values range is 0-50.

Phred64

public static final QualityFormat Phred64

Phred quality values encoded with 64 value offset.

Allowed quality score values range is 0-41.

Method Detail

values

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

Returns:

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

valueOf

public static QualityFormat 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

getMinValue

public byte getMinValue()

getMaxValue

public byte getMaxValue()

getOffset

public byte getOffset()

fromName

public static QualityFormat fromName(String name)

getName

public String getName()

toString

public String toString()

Overrides:

toString in class Enum<QualityFormat>