picard.illumina.parser

Enum IlluminaMetricsCode

java.lang.Object

java.lang.Enum<IlluminaMetricsCode>

picard.illumina.parser.IlluminaMetricsCode

All Implemented Interfaces:

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

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

Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g. phasing values are computed from a base of 200).

Author:

jgentry

Enum Constant Summary

Enum Constants

Enum Constant and Description
CLUSTER_ID
DENSITY_ID
PHASING_BASE
PREPHASING_BASE

Method Summary

Modifier and Type	Method and Description
int	getMetricsCode()
static int	getPhasingCode(int readDescriptorIndex, IlluminaMetricsCode phasingType) Phasing codes are between 200 and 299 (inclusive).
static boolean	isPhasing(IlluminaMetricsCode metricsCode)
static IlluminaMetricsCode	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static IlluminaMetricsCode[]	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

DENSITY_ID

public static final IlluminaMetricsCode DENSITY_ID

CLUSTER_ID

public static final IlluminaMetricsCode CLUSTER_ID

PHASING_BASE

public static final IlluminaMetricsCode PHASING_BASE

PREPHASING_BASE

public static final IlluminaMetricsCode PREPHASING_BASE

Method Detail

values

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

Returns:

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

valueOf

public static IlluminaMetricsCode 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

getPhasingCode

public static int getPhasingCode(int readDescriptorIndex,
                                 IlluminaMetricsCode phasingType)

Phasing codes are between 200 and 299 (inclusive). Phasing codes are defined as being (200 + ((N - 1) * 2)) for (a 0-based) read descriptor N (i.e., 200, 202, 204, etc.) Prephasing codes are defined as being (201 + ((N - 1) * 2)) for read descriptor N (i.e., 201, 203, 205, etc.). So for a 101T8B101T read structure, there will be phasing codes of 200, 202 and 204 and prephasing codes of 201, 203, 205.

isPhasing

public static boolean isPhasing(IlluminaMetricsCode metricsCode)

getMetricsCode

public int getMetricsCode()