Package eu.isas.reporter.cli

Enum ReporterCLIParameters

java.lang.Object

java.lang.Enum<ReporterCLIParameters>

eu.isas.reporter.cli.ReporterCLIParameters

All Implemented Interfaces:

Serializable, Comparable<ReporterCLIParameters>, java.lang.constant.Constable

public enum ReporterCLIParameters
extends Enum<ReporterCLIParameters>

Command line option parameters for ReporterCLI.

Author:

Marc Vaudel, Harald Barsnes

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
CONFIG_FOLDER
CONTAMINANTS
ID
IGNORE_MC
IGNORE_NULL
IGNORE_PTMS
ION_TOL
ISOTOPES
METHOD
MIN_UNIQUE
MOST_ACCURATE
NORMALIZATION_PEPTIDE
NORMALIZATION_PROTEIN
NORMALIZATION_PSM
OUT
PERCENTILE
PREC_WINDOW_MZ_TOL
PREC_WINDOW_MZ_TOL_PPM
PREC_WINDOW_RT_TOL
REFERENCE
REPORTER_IONS_LOCATION
RESOLUTION
STABLE_PROTEINS
THREADS
VALIDATION_PEPTIDE
VALIDATION_PROTEIN
VALIDATION_PSM
ZIP

Field Summary

Fields

Modifier and Type	Field	Description
String	description	Explanation for the CLI parameter.
String	id	Short Id for the CLI parameter.
boolean	mandatory	Boolean indicating whether the parameter is mandatory.

Method Summary

Modifier and Type	Method	Description
static void	createOptionsCLI(org.apache.commons.cli.Options aOptions)	Creates the options for the command line interface based on the possible values.
static String	getOptionsAsString()	Returns the options as a string.
static ReporterCLIParameters	valueOf(String name)	Returns the enum constant of this type with the specified name.
static ReporterCLIParameters[]	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, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

ID

public static final ReporterCLIParameters ID

OUT

public static final ReporterCLIParameters OUT

ISOTOPES

public static final ReporterCLIParameters ISOTOPES

METHOD

public static final ReporterCLIParameters METHOD

REFERENCE

public static final ReporterCLIParameters REFERENCE

ION_TOL

public static final ReporterCLIParameters ION_TOL

MOST_ACCURATE

public static final ReporterCLIParameters MOST_ACCURATE

REPORTER_IONS_LOCATION

public static final ReporterCLIParameters REPORTER_IONS_LOCATION

PREC_WINDOW_MZ_TOL

public static final ReporterCLIParameters PREC_WINDOW_MZ_TOL

PREC_WINDOW_MZ_TOL_PPM

public static final ReporterCLIParameters PREC_WINDOW_MZ_TOL_PPM

PREC_WINDOW_RT_TOL

public static final ReporterCLIParameters PREC_WINDOW_RT_TOL

IGNORE_NULL

public static final ReporterCLIParameters IGNORE_NULL

IGNORE_MC

public static final ReporterCLIParameters IGNORE_MC

PERCENTILE

public static final ReporterCLIParameters PERCENTILE

RESOLUTION

public static final ReporterCLIParameters RESOLUTION

MIN_UNIQUE

public static final ReporterCLIParameters MIN_UNIQUE

IGNORE_PTMS

public static final ReporterCLIParameters IGNORE_PTMS

VALIDATION_PSM

public static final ReporterCLIParameters VALIDATION_PSM

VALIDATION_PEPTIDE

public static final ReporterCLIParameters VALIDATION_PEPTIDE

VALIDATION_PROTEIN

public static final ReporterCLIParameters VALIDATION_PROTEIN

NORMALIZATION_PSM

public static final ReporterCLIParameters NORMALIZATION_PSM

NORMALIZATION_PEPTIDE

public static final ReporterCLIParameters NORMALIZATION_PEPTIDE

NORMALIZATION_PROTEIN

public static final ReporterCLIParameters NORMALIZATION_PROTEIN

STABLE_PROTEINS

public static final ReporterCLIParameters STABLE_PROTEINS

CONTAMINANTS

public static final ReporterCLIParameters CONTAMINANTS

ZIP

public static final ReporterCLIParameters ZIP

THREADS

public static final ReporterCLIParameters THREADS

CONFIG_FOLDER

public static final ReporterCLIParameters CONFIG_FOLDER

Field Details

id

public String id

Short Id for the CLI parameter.

description

public String description

Explanation for the CLI parameter.

mandatory

public boolean mandatory

Boolean indicating whether the parameter is mandatory.

Method Details

values

public static ReporterCLIParameters[] values()

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

Returns:

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

valueOf

public static ReporterCLIParameters 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

createOptionsCLI

public static void createOptionsCLI(org.apache.commons.cli.Options aOptions)

Creates the options for the command line interface based on the possible values.

Parameters:

aOptions - the options object where the options will be added

getOptionsAsString

public static String getOptionsAsString()

Returns the options as a string.

Returns:

the options as a string